Virology Journal

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Online ISSN: 1743-422X
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Recently, The Lancet published a study on the effectiveness of COVID-19 vaccines and the waning of immunity with time. The study showed that immune function among vaccinated individuals 8 months after the administration of two doses of COVID-19 vaccine was lower than that among the unvaccinated individuals. According to European Medicines Agency recommendations, frequent COVID-19 booster shots could adversely affect the immune response and may not be feasible. The decrease in immunity can be caused by several factors such as N1-methylpseudouridine, the spike protein, lipid nanoparticles, antibody-dependent enhancement, and the original antigenic stimulus. These clinical alterations may explain the association reported between COVID-19 vaccination and shingles. As a safety measure, further booster vaccinations should be discontinued. In addition, the date of vaccination should be recorded in the medical record of patients. Several practical measures to prevent a decrease in immunity have been reported. These include limiting the use of non-steroidal anti-inflammatory drugs, including acetaminophen to maintain deep body temperature, appropriate use of antibiotics, smoking cessation, stress control, and limiting the use of lipid emulsions, including propofol, which may cause perioperative immunosuppression. In conclusion, COVID-19 vaccination is a major risk factor for infections in critically ill patients.
 
Increased number of circulating peripheral blood CD56 bright NK cells counts in HPV16(+) CIN II-III. A(a) Representative flow cytometry dot plots (SSC-A vs FSC-A). A(b) gated from A(a) and stained to obtain NK cells using CD3 − CD56 + as a marker. A(c) A representative dot plot in which two NK cell subsets were gated based on CD56 and CD16 expression: CD56 dim and CD56 bright NK cells. B(a-c) The percentage of NK cells and its subsets was analyzed from HPV16(+) women with different CIN grades or HPV(−) women using violin plots, in which each dot represents a donor. B(d-f ) the absolute count of NK cells and their subsets was analyzed from HPV16(+) women with different CIN grades or HPV(−) women using violin plots, in which each dot represents a donor. The Kruskal-Wallis test was used to determine statistical significance
Circulating CD56 bright NK cells from HPV16(+) subjects with CIN showed a reduced ability to secrete IFN-γ. A Statistical graph displays percentage of IFN-γ created by CD56 dim and CD56 bright NK cells in the HPV16(+) women with different CIN grades and HPV(−) women. B Statistical graph displays percentage of TNF-α created by CD56 dim and CD56 bright NK cells in the HPV16(+) women with different CIN grades and HPV(−) women. C Representative dot plots of IFN-γ and TNF-α created by CD56 bright NK cells in the HPV(−) CIN 0 group and HPV16(+) CIN II-III groups
Increased expression of TIGIT and KLRG1 expression on CD56 bright NK cells in HPV16(+)-related CIN. a-l The percentage and MFI of inhibitory receptors TIGIT, NKG2A, CD300a, KLRG1, LAIR1, and Siglec-7 on NK cells were analyzed from HPV16(+) women with different CIN grades or HPV(−) women.. The Kruskal-Wallis test was used to test for statistical significance
Increased expression of PVR, N-Cadherin and E-Cadherin in HPV16(+) CIN. A(a-c) Representative immunohistochemical sections of PVR, E-Cadherin and N-Cadherin expression in cervical tissues with HPV(−) CIN 0 and HPV16(+) CIN. B(a, b) Summary of the Allred scores in each group. Error bars indicate SD, original magnification: × 200
Background The onset and progression of cervical intraepithelial neoplasia (CIN) are closely associated with the persistent infection of high-risk HPV (especially type16), which is mainly caused by immune escape. Natural killer (NK) cells play an important role against virally infected cells and tumor cells through a fine balance of signals from multiple surface receptors. Overexpression of non-MHC-I specific inhibitory receptors TIGIT, KLRG1, Siglec-7, LAIR-1, and CD300a on NK cells correlates with cellular exhaustion and immune evasion, but these receptors have not been investigated in CIN. The aim of the present study was to examine the potential role of NK cell non-MHC-I specific inhibitory receptors expression in immune escape from HPV16(+)CIN patients. Methods The subset distribution, IFN-γ and TNF-α expression levels and immunophenotype of TIGIT, KLRG1, Siglec-7, LAIR-1, and CD300a of NK cells were investigated in peripheral blood mononuclear cell samples by flow cytometry from 82 women who were HPV16(+) with CIN grades 0, I, II–III or HPV(−) CIN 0. Immunohistochemistry was applied to detect the expression of ligands for NK receptors in the cervical tissues. HPV types were identified by PCR assays. Results The HPV16(+) subjects with high-grade lesions had an increased number of circulating peripheral blood CD56 bright NK cells with reduced functionality and IFN-γ secretion. The expression levels of the inhibitory molecules TIGIT and KLRG1 on CD56 bright NK cells increased in parallel with increasing CIN grade. In addition, TIGIT and KLRG1 related ligands, Poliovirus receptor (PVR), N-Cadherin and E-Cadherin expression level was also elevated with increasing CIN grade. Conclusions Our results suggest that up-regulation of the inhibitory TIGIT, KLRG1 and their ligands may negatively regulate cervical CD56 bright NK-mediated immunity to HPV16 and contribute to the progression of CIN. These results may facilitate the development of early-warning immune predictors and therapeutic strategies for HPV16(+) CIN based on the TIGIT and KLRG1 inhibitory pathways of NK cells.
 
Background Early and accurate identification of infection viruses among children can benefit the personalized medical treatment and management, and reduce the future occurrence of serious symptoms. Thus, it is critical to develop a high-throughput multiplex real-time RT-PCR method to improve the accuracy and efficiency in routine clinical lab tests. Methods We developed a real time RT-PCR combined with melting curve analysis (RRCMC) method for simultaneous detection of rotavirus A, B, C, norovirus GI and GII, adenovirus, astrovirus and sapovirus. Results Stool samples were collected from 160 children with acute diarrhea and tested by RRCMC assay. A total of 71 patients were tested positive with norovirus, adenovirus or rotavirus. The RRCMC assay has high specificity. There is no internal cross-reaction among the 8 diarrhea viruses and no cross-reaction of other commonly intestinal pathogens and human genome. The limit detection was ranged from 1 × 10 ² to 1 × 10 ⁵ nucleic acid copies/ml for each diarrhea virus. Conclusion The RRCMC method is a suitable rapid clinical test for infectious viruses, with the advantages of high-throughput, low cost, high sensitivity and specificity.
 
Expression of TRIM28 in 330 whole blood samples from 3 groups: Mild and Severe COVID-19 patients and 160 uninfected individuals as control group. Ctrl: control group Mild: infected patients with mild symptoms. Severe: infected patients with severe disease. A horizontal line shows the median values with SEM error bars. Median values and interquartile range (IQR) for TRIM28 Ctrl: median 0.00, IQR − 3.12, 9.85; Mild: median − 5.47, IQR − 15.61, 2.59; Severe: median: -7.64, IQR − 18.79, -0.3. Statistical analysis: the Mann-Whitney test was used to compare the transcriptional levels of each group of patients with control group
ROC curve with the TRIM28 gene expression for prediction the severity of COVID-19 infection
  • Rezvan TavakoliRezvan Tavakoli
  • Pooneh RahimiPooneh Rahimi
  • Mojtaba Hamidi-FardMojtaba Hamidi-Fard
  • [...]
  • Abolfazl FatehAbolfazl Fateh
Background Tripartite motif-containing 28 (TRIM28) is an impressive regulator of the epigenetic control of the antiviral immune response. This study evaluated if the differential expression of TRIM28 correlates with the severity of coronavirus disease 2019 (COVID-19) infection. Methods A total of 330 COVID-19 patients, including 188 mild and 142 severe infections, and 160 healthy controls were enrolled in this study. Quantitative real-time polymerase chain reaction (qPCR) was used to determine the expression levels of TRIM28 in the studied patients. Results TRIM28 mRNA levels were significantly lower in both groups of patients versus the control group and in the severe group indicated further reduction in comparison to mild infection. The multivariate logistic regression analysis showed the mean age, lower levels of low-density lipoprotein (LDL), high-density lipoprotein (HDL), cholesterol, lower 25-hydroxyvitamin D, and PCR cycle threshold (Ct) value and higher levels of erythrocyte sedimentation rate (ESR) and differential expression of TRIM28 were linked to the severity of COVID-19 infection. Conclusion The results of this study proved that the downregulation of TRIM28 might be associated with the severity of COVID-19 infection. Further studies are required to determine the association between the COVID-19 infection severity and TRIM family proteins.
 
The scatter charts present country specific CMV prevalence (mean) plotted against estimated age-standardized (world) annual incidence rates (per 100,000) of microscopically verified cases of B-cell types of cancer in 74 countries (blue circles) [35, 36, 69]. A) B-cell malignancies (all types) (Spearman ρ = -0.625, p < 0.001), B) Hodgkin’s disease (Spearman ρ = -0.618, p < 0.001), C) non-Hodgkin lymphomas (Spearman ρ =  = -0.617, p < 0.001), and D) multiple myeloma (Spearman ρ = -0.633, p < 0.001) in 2020. The inverse relationship between viral pervasiveness and the annual incidence rate of hematologic malignancies is highly significant for all (A) and each individual B-cell cancer type (C-D)
(continued)
Statistical information on patient and control groups prior and after matching for age and gender
Country-specific CMV seroprevalence in patient cohorts compared to matched blood/organ donors and healthy general populations
Background Although cytomegalovirus (CMV) is not considered tumorigenic, there is evidence for its oncomodulatory effects and association with hematological neoplasms. Conversely, a number of experimental and clinical studies suggest its putative anti-tumour effect. We investigated the potential connection between chronic CMV infection in patients with B-lymphocyte (B-cell) malignancies in a retrospective single-center study and extracted relevant data on CMV prevalences and the incidences of B-cell cancers the world over. Methods In the clinical single-center study, prevalence of chronic CMV infection was compared between patients with B-cell leukemia/lymphoma and the healthy controls. Also, global data on CMV seroprevalences and the corresponding country-specific incidences of B- lineage neoplasms worldwide were investigated for potential correlations. Results Significantly higher CMV seropositivity was observed in control subjects than in patients with B-cell malignancies ( p = 0.035). Moreover, an unexpected seroepidemiological evidence of highly significant inverse relationship between country-specific CMV prevalence and the annual incidence of B-cell neoplasms was noted across the populations worldwide (ρ = −0.625, p < 0.001). Conclusions We try to draw attention to an unreported interplay between CMV infection and B-cell lymphomagenesis in adults. A large-scale survey across > 70 countries disclosed a link between CMV and B-cell neoplasms. Our evidence hints at an antagonistic effect of chronic CMV infection against B-lymphoproliferation.
 
A Chest computed tomography image obtained 5 days after admission. B Cerebral computed tomography image obtained 5 days after admission
Cytopathic effect (CPE) in SK-N-SH cells 48 h post-inoculation. A Control inoculated with DMEM. B Inoculated with isolated HAdV 7
Phylogenetic analysis of HAdV 7. The strain identified in our study (red circle) and other available sequences of HAdV 7 in GenBank were analyzed. A phylogenetic tree was constructed using the neighbor-joining method (Kimura’s two-parameter) with 1000 bootstrap values
A Genome sequence analysis of the penton base genes revealed 3 specific amino acid missense mutations. The penton base homology model of the reference strain (B) and our isolated strain (C)
Adenoviruses are highly prevalent pathogens responsible for a wide range of clinical diseases, including respiratory tract infection, acute gastroenteritis, and conjunctivitis. However, adenovirus infection is rarely associated with central nervous system involvement. Here, we report a fatal viral sepsis and encephalitis in a child caused by a human adenovirus type 7 infection. We detected human adenovirus type 7 in the patient’s nasopharyngeal swab, blood, and cerebrospinal fluid. Our findings indicate clinicians should be aware of the possible central nervous system involvement in adenovirus infection.
 
Background JC polyomavirus (JCPyV) is known to induce solid tumors such as astrocytomas, glioblastomas, and neuroblastomas in experimental animals, and recent studies have shown that the virus may be correlated with carcinogenesis. This study aimed to evaluate the impact of JCPyV on the progression of papillary thyroid cancer (PTC). Methods A total of 1057 samples, including 645 paraffin-embedded PTC biopsy samples (PEBS) and 412 fresh biopsy samples (FBS), and 1057 adjacent non-cancerous samples were evaluated for the presence of JCPyV DNA and RNA. Results We observed that 10.8% (114/1057) samples, including 17.5% (72/412) FBS and 6.5% (42/645) PEBS were positive for the JCPyV DNA. Among the JCPyV-positive samples, the mean JCPyV copy number was lower in patients with PEBS (0.3 × 10–4 ± 0.1 × 10–4 copies/cell) compared to FBS (1.8 × 10–1 ± 0.4 × 10–1 copies/cell) and non-PTC normal samples (0.2 × 10–5 ± 0.01 × 10–5 copies/cell), with a statistically significant difference (P < 0.001). The LT-Ag RNA expression was lower in PEBS than in FBS, while no VP1 gene transcript expression was found. Conclusions Although our results confirmed the presence of JCPyV in some Iranian patients with PTC, more research is needed to verify these results.
 
The coronavirus pandemic is a worldwide hazard that poses a threat to millions of individuals throughout the world. This pandemic is caused by the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which was initially identified in Wuhan, China's Hubei provincial capital, and has since spread throughout the world. According to the World Health Organization's Weekly Epidemiological Update, there were more than 250 million documented cases of coronavirus infections globally, with five million fatalities. Early detection of coronavirus does not only reduce the spread of the virus, but it also increases the chance of curing the infection. Spectroscopic techniques have been widely used in the early detection and diagnosis of COVID-19 using Raman, Infrared, mass spectrometry and fluorescence spectroscopy. In this review, the reported spectroscopic methods for COVID-19 detection were discussed with emphasis on the practical aspects, limitations and applications.
 
Aβ1–42 generation and aggregation were responsive for EV-A71 infection in SH-SY5Y cells. a Production of Aβ1–42 from the supernatant was quantified with an ELISA kit. SH-SY5Y cells were subjected to EV-A71 infection (MOI = 1) and collected at 6 or 12 h post-EV-A71 infection. b Production of intracellular Aβ1–42 was quantified by IFA assay. SH-SY5Y cells were subjected to EV-A71 infection at MOIs of 0.01, 0.1, and 1 for 8 h, respectively. IFA of Aβ1–42 protein was performed with an Alexa Fluor 488-conjugated antibody (green), and the nucleus was dyed with DAPI (blue). c Aβ1–42 high-molecular-weight oligomer accumulation in response to EV-A71 (MOI = 1) at 6 and 12 h after infection was detected by Western blot with anti-Aβ1–42 antibody (~ 70 kDa)
Cytotoxicity and anti-EV-A71 activity of Aβ1–42 in vitro. a Cytotoxicity of Aβ1–42 to multiple cell lines were determined by CCK assay at 48 h post-peptide treatment. b and c SH-SY5Y cells were infected with EV-A71 (MOI = 1) and followed by treatment with Aβ1–42 peptides or RBV (20 µg/mL) for 24 h. The concentrations of EV-A71 VP1 RNA and protein were assayed by qRT-PCR and WB, respectively. d Aβ1–42 peptides or RBV were added to EV-A71-infected Vero (MOI = 0.1) and RD cells (MOI = 0.01) for 24 h. The content of EV-A71 VP1 protein was analyzed by WB. Software “Gel-Pro analyzer” was used to analysis of the optical density ratio of the bands
Aβ1–42 targeted the attachment and post-attachment phases of EV-A71 infection. a Time-of-addition experiment. SH-SY5Y cells were subjected to EV-A71 infection (MOI = 10) at 0 h time point. At 1 h point, cells were cleaned in PBS buffer and collected at 8 hpi. EV-A71 VP1 was determined by WB assay. The grey column indicates the period in which 30 µg/mL Aβ1–42 peptides were present. b EV-A71 virus (MOI = 2.5) was added to precooled cell plates simultaneously with Aβ1–42 (30 µg/mL) or pirodavir (40 µM) at 4 °C for 1 h. The amounts of cell-bound EV-A71 particles were measured by qRT-PCR. c Precooled cells that adhered to EV-A71 were incubated with Aβ1–42 (30 µg/mL) or NH4Cl (40 µM) at 37 °C for 60 min. The content of vp1 RNA was identified by qRT-PCR
Aβ1–42 induced EV-A71 aggregation and directly bound to VP1. a Purified EV-A71 virus was incubated with Aβ1–42 (20 µg/mL) at 4 °C for 60 min, and EV-A71 aggregation was analyzed by TEM. b SH-SY5Y or Vero cells were subjected to EV-A71 infection (MOI = 2.5) for 8 h, and the co-localization between Aβ1–42 (detected with a 488-conjugated antibody against Aβ1–42, green) and EV-A71 VP1 (Alexafluor594-conjugated antibody against VP1, red) was identified by confocal assay. Images were captured at 100 × magnification with a PE UltraVIEW VOX. c Aβ1–42 (20 µg/mL) was mixed with activated protein A/G magnetic beads overnight at 4 °C. Subsequently, the mixture was cultivated with purified EV-A71 virus (MOI = 1) at 4 °C for h. After cleaning the beads to remove nonbound viruses, the magnetic beads were subjected to precipitation with a magnet holder and assayed by Western blot with VP1 antibody. d Pre-virus attachment inhibition assay of Aβ1–42 showed comparable inhibition capacity against EV-A71 infections. Virus (MOI = 2.5) with or without Aβ1–42 medium incubated at 4 °C for 1 h, followed by infecting precooled cells at 4 °C for another 1 h. The quantity of cell-bound EV-A71 virus was identified by qRT-PCR. Experiments were independently repeated three times
Aβ1–42 is directly bonded to SCARB2. a SH-SY5Y, Vero, and RD cells were pretreated with Aβ1–42 (20 µg/mL) or pirodavir (40 µM) at 4 °C for 60 min, followed by EV-A71 infection (MOI = 2.5) at 4 °C for another 1 h. The overall RNA was harvested, and EV-A71 VP1 RNA variation was evaluated by qRT-PCR. b SH-SY5Y cells were subjected to CVA16 or CVB3 infection (MOI = 1) and afterward subjected to Aβ1–42 peptide or RBV treatment (20 µg/mL) for 24 h. The virus VP1 RNA level was analyzed by qRT-PCR. c Vero cells were subjected to SCARB2-myc or pcDNA 3.1 + plasmid transfection for 24 h and lysed with protein lysate containing phosphatase and protease inhibitor. Subsequently, the lysis buffer supernatant was mixed with Aβ1–42 immobilized magnetic beads at 4 °C for 2 h. The bound beads were suspended with a 1 × sample loading buffer and boiled for 10 min. The binding of SCARB2 was detected by WB assay with anti-SCARB2 antibody
Background β-Amyloid (Aβ) protein is a pivotal pathogenetic factor in Alzheimer’s disease (AD). However, increasing evidence suggests that the brain has to continuously produce excessive Aβ to efficaciously prevent pathogenic micro-organism infections, which induces and accelerates the disease process of AD. Meanwhile, Aβ exhibits activity against herpes simplex virus type 1 (HSV-1) and influenza A virus (IAV) replication, but not against other neurotropic viruses. Enterovirus A71 (EV-A71) is the most important neurotropic enterovirus in the post-polio era. Given the limitation of existing research on the relationship between Aβ and other virus infections, this study aimed to investigate the potent activity of Aβ on EV-A71 infection and extended the potential function of Aβ in other unenveloped viruses may be linked to Alzheimer's disease or infectious neurological diseases. Methods Aβ peptides 1–42 are a major pathological factor of senile plaques in Alzheimer’s disease (AD). Thus, we utilized Aβ1–42 as a test subject to perform our study. The production of monomer Aβ1–42 and their high-molecular oligomer accumulations in neural cells were detected by immunofluorescence assay, ELISA, or Western blot assay. The inhibitory activity of Aβ1–42 peptides against EV-A71 in vitro was detected by Western blot analysis or qRT-PCR. The mechanism of Aβ1–42 against EV-A71 replication was analyzed by time-of-addition assay, attachment inhibition assay, pre-attachment inhibition analysis, viral-penetration inhibition assay, TEM analysis of virus agglutination, and pull-down assay. Results We found that EV-A71 infection induced Aβ production and accumulation in SH-SY5Y cells. We also revealed for the first time that Aβ1–42 efficiently inhibited the RNA level of EV-A71 VP1, and the protein levels of VP1, VP2, and nonstructural protein 3AB in SH-SY5Y, Vero, and human rhabdomyosarcoma (RD) cells. Mechanistically, we demonstrated that Aβ1–42 primarily targeted the early stage of EV-A71 entry to inhibit virus replication by binding virus capsid protein VP1 or scavenger receptor class B member 2. Moreover, Aβ1–42 formed non-enveloped EV-A71 particle aggregates within a certain period and bound to the capsid protein VP1, which partially caused Aβ1–42 to prevent viruses from infecting cells. Conclusions Our findings unveiled that Aβ1–42 effectively inhibited nonenveloped EV-A71 by targeting the early phase of an EV-A71 life cycle, thereby extending the potential function of Aβ in other non-envelope viruses linked to infectious neurological diseases.
 
Background Integrating CRISPR-Cas12a sensors with isothermal signal amplification can be exploited to develop low-cost, disposable, and ultrasensitive assays for the diagnostics of human pathogens. Methods RT-RAA-Cas12a-mediated real-time or end-point fluorescent and lateral flow strip (LFS) assays for direct detection of norovirus (NOV) genotype GII.4 or GII.17 were explored. Results The results showed that our RT-RAA-Cas12a-mediated fluorescent and LFS assay could detect NOV GII.4 or GII.17 by targeting the viral protein 1 gene. Our RT-RAA-Cas12a-mediated fluorescent and LFS assay can specifically detect NOV GII.4 or GII.17 with no cross-reactivity for other related viruses. The low limit of detection could reach 0.1 copies/μL within approximately 30–40 min, and the results were visualized using an ultraviolet light illuminator or on a LFS without complex equipment. In addition, our RT-RAA-Cas12a-mediated fluorescent and LFS assay provided a visual and faster alternative to real-time RT-PCR assay, with 95.7% and 94.3% positive predictive agreement and 100% negative predictive agreement. Conclusions Together, our RT-RAA-Cas12a-mediated approach would have a great potential for point-of-care diagnostics of NOV GII.4 and/or GII.17 in resource-limited settings.
 
Background Viruses negatively impact soybean production by causing diseases that affect yield and seed quality. Newly emerging or re-emerging viruses can also threaten soybean production because current control measures may not be effective against them. Furthermore, detection and characterization of new plant viruses requires major efforts when no sequence or antibody-based resources are available. Methods In this study, soybean fields were scouted for virus-like disease symptoms during the 2016–2019 growing seasons. Total RNA was extracted from symptomatic soybean parts, cDNA libraries were prepared, and RNA sequencing was performed using high-throughput sequencing (HTS). A custom bioinformatic workflow was used to identify and assemble known and unknown virus genomes. Results Several viruses were identified in single or mixed infections. Full- or nearly full-length genomes were generated for tobacco streak virus (TSV), alfalfa mosaic virus (AMV), tobacco ringspot virus (TRSV), soybean dwarf virus (SbDV), bean pod mottle virus (BPMV), soybean vein necrosis virus (SVNV), clover yellow vein virus (ClYVV), and a novel virus named soybean ilarvirus 1 (SIlV1). Two distinct ClYVV isolates were recovered, and their biological properties were investigated in Nicotiana benthamiana , broad bean, and soybean. In addition to infections by individual viruses, we also found that mixed viral infections in various combinations were quite common. Conclusions Taken together, the results of this study showed that HTS-based technology is a valuable diagnostic tool for the identification of several viruses in field-grown soybean and can provide rapid information about expected viruses as well as viruses that were previously not detected in soybean.
 
Correlation between serum glucose, uric acid, CD4⁺T and CD8⁺T cells count in Omicron variant infected patients
Risk factors for SARS-CoV2 clearance on day 14
Background Omicron variant (B.1.1.529) is a dominant variant worldwide. However, the risk factors for Omicron variant clearance are yet unknown. The present study aimed to investigate the risk factors for early viral clearance of Omicron variant in patients with a history of inactivated vaccine injection. Methods Demographic, clinical, and epidemiological data from 187 patients were collected retrospectively during the Omicron variant wave. Results 73/187 and 114/187 patients were administered two and three doses of vaccine, respectively. The median duration of SARS-CoV-2 RNA positivity was 9 days, and the difference between patients with two and three vaccine injections was insignificant (P = 0.722). Fever was the most common symptom (125/187), and most patients (98.4%) had a fever for < 7 days. The RNA was undetectable in 65/187 patients on day 7. Univariable logistic analysis showed that baseline glucose, uric acid, lymphocytes count, platelet count, and CD4 ⁺ T lymphocyte count were associated with SARS-CoV-2 RNA-positivity on day 7. Multivariable analysis showed that glucose ≥ 6.1 mmol/L and CD4 ⁺ T lymphocytes count were independent risk factors for RNA positivity on day 7. 163/187 patients had an undetectable RNA test on day 14, and uric acid was the only independent risk factor for RNA positivity. Moreover, baseline glucose was negatively correlated with uric acid and CD4 ⁺ and CD8 ⁺ T cell count, while uric acid was positively correlated with CD4 ⁺ and CD8 ⁺ T cell count. Conclusions Omicron variant clearance was delayed in breakthrough cases with elevated fasting blood glucose, irrespective of the doses of inactivated vaccine.
 
The comparison of miRNAs expression level between latent and active CMV infected groups of patients. A Except for miR-US-25-1-3p and miR-UL148D, the expression pattern for all tested miRs were the same and demonstrate increase in expression in the active CMV infected group. Comparison of the expression level of all tested miRNAs in latent CMV infected group (B); and Comparison of the expression level of all tested miRNAs in active CMV infected group (C); the content of viral miRNAs during activation and inactivation phase of virus life differs completely. p < 0.05*, p < 0.01**, p < 0.001***
Comparing the correlation between viral precursor miRNAs gene expression in latent CMV infected group, miRNAs that has one precursor arise from the same origin but some of them has different expression rate during inactivation of CMV
Comparing the correlation between viral precursor miRNAs gene expression in active CMV infected group, miRNAs that has one precursor arise from the same origin but some of them has different expression rate during activation of CMV
The ROC curve analyses of CMV miRNAs between latent and active CMV infected groups
Background Human cytomegalovirus (CMV) can establish a latent infection with periodic or sporadic reactivation after the first infection happens. Primary and recurrent infection, results in different problems in patients with impaired or immature immune systems, such as kidney transplant recipients (KTRs). MicroRNAs (miRNAs, miRs) are important regulatory molecules in the outcome of CMV-infected KTRs. Therefore, in this study the expression level of CMV miRNAs were evaluated in active vs. latent CMV infected KTRs. Methods Expression of viral miRNAs were studied in 61 KTRs which were divided into 30 active CMV and 31 latent CMV infected individuals. In order to study the expression level of selected miRNAs, SYBR Green Real-time PCR technique was exploited. Also, mature miRNAs expression level that were produced from one precursor, studied both in active and latent situations. Results Among studied miRNAs’ expression level, CMV miR-UL112-3p/5p, -UL22A-3p/5p, -US25-1-5p, -US25-2-3p/5p, -UL36-3p/5p and -UL70-3p showed significant increase in active CMV infected KTRs in comparison to latent ones. The ROC curve analysis results for miR-UL112-3p, -UL22A-3p, -US25-2-3p, -UL36-3p and -UL70-3p showed significant difference between two studied patient groups. Conclusion This study revealed an extremely high expression level in CMV miR-UL112-3p/5p, -UL22A-3p/5p, -US25-1-5p, -US25-2-3p/5p, -UL36-3p/5p and -UL70-3p in active CMV infected KTRs in comparison to latent ones. Further studies might help in finding the capability of miRNAs to differentiate active from latent stage of CMV infection in KTRs.
 
Background The evaluation of human papillomavirus (HPV) prevalence rate dynamics and genotype distribution could support the adoption of more targeted prevention and treatment of cervical cancer. We aimed to assess the infection status and genotype characteristics of HPV among gynecological outpatients in Shanghai, China. Methods Clinical specimens were collected from patients attending gynaecological department of the Putuo Hospital, Shanghai University of Traditional Chinese Medicine, between January 2015 and December 2019. The cervicovaginal infection of 17 high-risk genotypes and 10 low-risk genotypes were analyzed by Luminex-based multiple assays. Results The overall HPV infection rate was 18.81% (95% CI 18.31–19.30%) in Shanghai city, with high-risk, low-risk and mixed high- and low-risk HPV prevalence being 11.65% (95% CI 11.24–12.06%), 4.19% (95% CI 3.94–4.44%) and 2.96% (95% CI 2.74–3.17%), respectively. The five most prevalent high-risk genotypes were HPV-52 (2.95%), HPV-16 (2.34%), HPV-58 (2.07%), HPV-53 (1.67%) and HPV-39 (1.36%). The most common low-risk genotype was HPV-61 (1.52%), followed by HPV-6 (1.29%) and HPV-81 (1.19%). Moreover, the coverage of HPV genotype by nonavalent vaccine was 10.42%, and non-vaccine-covered high-risk genotype was 7.70%. The 15–24 years age group demonstrated the highest HPV prevalence (43.14%), and significant differences were observed among different age groups ( P < 0.001). Conclusions This study revealed the HPV prevalence and genotype distribution among women in Shanghai city, which could serve as guidance for HPV vaccination and preventative strategies against cervical cancer in this area.
 
Diagram flow chart
Cumulative incidence for agitation-free days in Covid-19 and influenza patients
Background: A growing body of evidence reports that agitation and encephalopathy are frequent in critically ill Covid-19 patients. We aimed to assess agitation's incidence and risk factors in critically ill ARDS patients with Covid-19. For that purpose, we compared SARS-CoV-2 acute respiratory distress syndrome (ARDS) patients with a population of influenza ARDS patients, given that the influenza virus is also known for its neurotropism and ability to induce encephalopathy. Methods: We included all the patients with laboratory-confirmed Covid-19 infection and ARDS admitted to our medical intensive care unit (ICU) between March 10th, 2020 and April 16th, 2021, and all the patients with laboratory-confirmed influenza infection and ARDS admitted to our ICU between April 10th, 2006 and February 8th, 2020. Clinical and biological data were prospectively collected and retrospectively analyzed. We also recorded previously known factors associated with agitation (ICU length of stay, length of invasive ventilation, SOFA score and SAPS II at admission, sedative and opioids consumption, time to defecation). Agitation was defined as a day with Richmond Agitation Sedation Scale greater than 0 after exclusion of other causes of delirium and pain. We compared the prevalence of agitation among Covid-19 patients during their ICU stay and in those with influenza patients. Results: We included 241 patients (median age 62 years [53-70], 158 males (65.5%)), including 146 patients with Covid-19 and 95 patients with Influenza. One hundred eleven (46.1%) patients had agitation during their ICU stay. Patients with Covid-19 had significantly more agitation than patients with influenza (respectively 80 patients (54.8%) and 31 patients (32.6%), p < 0.01). After matching with a propensity score, Covid-19 patients remained more agitated than influenza patients (49 (51.6% vs 32 (33.7%), p = 0.006). Agitation remained independently associated with mortality after adjustment for other factors (HR = 1.85, 95% CI 1.37-2.49, p < 0.001). Conclusion: Agitation in ARDS Covid-19 patients was more frequent than in ARDS influenza patients and was not associated with common risk factors, such as severity of illness or sedation. Systemic hyperinflammation might be responsible for these neurological manifestations, but there is no specific management to our knowledge.
 
The literature search on COVID-19 in children before and during the Delta and Omicron variants era
Prevalence of positive COVID-19 infants in different regions of the World Health Organization (WHO): AMR colored in red, EMR colored in yellow, ER colored in purple, AR colored in blue, SEAR colored in green and WPR colored in blue light
Prevalence of hospital admission of COVID-19 infants before and after the emergence of omicron variant
Background COVID-19, the coronavirus disease that emerged in December 2019, caused drastic damage worldwide. At the beginning of the pandemic, available data suggested that the infection occurs more frequently in adults than in infants. In this review, we aim to provide an overview of SARS-CoV-2 infection in children before and after B.1.617.2 Delta and B.1.1.529 Omicron variants emergence in terms of prevalence, transmission dynamics, clinical manifestations, complications and risk factors. Methods Our method is based on the literature search on PubMed, Science Direct and Google Scholar. From January 2020 to July 2022, a total of 229 references, relevant for the purpose of this review, were considered. Results The incidence of SARS-CoV-2 infection in infants was underestimated. Up to the first half of May, most of the infected children presented asymptomatic or mild manifestations. The prevalence of COVID-19 varied from country to another: the highest was reported in the United States (22.5%). COVID-19 can progress and become more severe, especially with the presence of underlying health conditions. It can also progress into Kawasaki or Multisystem Inflammatory Syndrome (MIS) manifestations, as a consequence of exacerbating immune response. With the emergence of the B.1.617.2 Delta and B.1.1.529 Omicron variants, it seems that these variants affect a large proportion of the younger population with the appearance of clinical manifestations similar to those presented by adults with important hospitalization rates. Conclusion The pediatric population constitutes a vulnerable group that requires particular attention, especially with the emergence of more virulent variants. The increase of symptomatic SARS-CoV-2 infection and hospitalization rate among children highlights the need to extend vaccination to the pediatric population.
 
Bispecific antibody design, purification and SDS-PAGE analysis. A Left panel: Schematic of iMab-N6 engineered using knob-in-a-hole mutations in the CH3 region of N6 and CrossMAbCH1_CL mutations in iMab. These mutations promote preferential assembly of iMab-N6 by limiting the formation of by-products. A Right panel: To show that these mutations do not affect the function of the antibody, iMab monoclonal antibody was engineered with knob-in-a-hole and CrossMAbCH1_CL mutations. B Chromatograms of size exclusion chromatography (SEC) purified antibodies with elution fractions corresponding to the correctly assembled antibody confirmation represented by the shaded rectangles. C Antibodies were resolved on a gradient SDS-PAGE post SEC under reduced and non-reduced conditions
Binding characterisation of purified antibodies by ELISA. A Left panel: HIV-1 Env targeting moieties (N6 and iMab-N6) were tested against gp140FVCGCN4 with iMab being used as a negative control. A Right panel: iMab-N6 was used at double the concentration of N6 to try and correct for the difference in binding affinity seen in A Left panel. B CD4 binding moieties (iMab and iMab-N6) were tested against 4dCD4 with N6 serving as an appropriate negative control
Comparison of antibody breadth and potency against a panel of 21 HIV-1 pseudoviruses. A IC50 heat map of the parental monoclonal antibodies alone, iMab and N6; antibody combination iMab + N6; and the bibNAb iMab-N6. The numbers in brackets next to iMab + N6 represent the fold difference in potency (red = enhancement, black = reduction) of iMab-N6 over iMab + N6. The numbers in brackets next to iMab-N6 represent the fold difference in potency (green = no enhancement) of iMab-N6 over parental N6 and iMab antibodies, respectively. Individual cells are colour-coded according to IC50 potency (number), with lower numbers and darker red representing greater potency. ND not done. B Scatter plot depicting IC50 values of dual sensitive HIV-1 pseudoviruses for each antibody with the median and IQR shown. Comparisons were done using non-parametric t-test (Wilcoxon matched-pairs signed rank test) with *p < 0.0167 and ***p < 0.001
Predicting the clinical utility of iMab-N6. A–F Scatter plots depicting IC80 values with median and IQR shown (A, C and E), and Breadth-Potency curves (B, D, and F) of each antibody against the full panel (n = 21) (A and B), dual sensitive viruses (n = 18) (C and D) and the expanded CATNAP virus panel (n = 97) (E and F). A–F Dotted lines represent the IC80 = 1 µg/ml threshold. A and C Statistical analysis were done using non-parametric t-test (Wilcoxon matched-pairs signed rank test) with *p < 0.0167, **p < 0.005 and ***p < 0.001. A–D bibNAb iMab-N6 exhibited median IC80 6–6.5× lower than 1 µg/ml AMP trial threshold and showed good neutralisation coverage of 90–94% at IC80 < 1 µg/ml. E and F N6 and iMab data was sourced from the CATNAP data base and used to generate iMab + N6, Bliss-Hill prediction data
The recently published AMP trial (HVTN 703/HPTN 081 and HVTN704/HPTN 085) results have validated broad neutralising antibodies (bNAbs) as potential anti-HIV-1 agents. However, single bNAb preparations are unlikely to cope with the onslaught of existing and de novo resistance mutations, thus necessitating the use of bNAb combinations to achieve clinically relevant results. Specifically engineered antibodies incorporating two bNAbs into a single antibody structure have been developed. These bispecific antibodies (bibNAbs) retain the benefits of bNAb combinations, whilst several conformations exhibit improved neutralisation potency over the parental bNAbs. Here we report on the engineering of a bibNAb comprising of an HIV-1 spike targeting bNAb N6 and a host CD4 targeting antibody ibalizumab (iMab). Antibodies were expressed in HEK293T cells and purified by protein-A affinity chromatography followed by size exclusion chromatography to achieve homogenous, monomeric, bibNAb preparations. Antibody purity was confirmed by SDS-PAGE whilst epitope specificity and binding were confirmed by ELISA. Finally, antibody breadth and potency data were generated by HIV-1 neutralisation assay (n = 21, inclusive of the global panel). iMab-N6 exhibited better neutralisation breadth (100% coverage) in comparison to its parental bNAbs iMab (90%) and N6 (95%). This is encouraging as exceptional neutralisation breadth is necessary for HIV-1 treatment or prevention. Unfortunately, iMab-N6 did not exhibit any enhancement in potency over the most potent parental antibody, iMab ( p = 0.1674, median IC 50 of 0.0475 µg/ml, and 0.0665 µg/ml respectively) or the parental combination, iMab + N6 ( p = 0.1964, median IC 50 : combination 0.0457 µg/ml). This result may point to a lack of dual engagement of the bibNAb Fab moieties necessary for potency enhancement. Against the previously reported bibNAbs; iMab-CAP256, 10E08-iMab, and PG9-iMab; iMab-N6 was the lowest performing bibNAb. The re-engineering of iMab-N6 to enhance its potency, while retaining breadth, is a worthwhile endeavour due to its clinical potential.
 
Monthly A and seasonal B distributions of the identified HPIV by serotype. HPIV Human parainfluenza virus
Background The development of the polymerase chain reaction (PCR) test promoted the evaluation of the epidemiological and clinical characteristics of human parainfluenza virus (HPIV) type 4, which has been rarely studied using conventional diagnostic methods. This study aimed to determine the seasonal epidemiological and clinical characteristics of all four HPIV serotypes (HPIV-1, HPIV-2, HPIV-3, and HPIV-4) during the era of PCR testing. Methods The medical records of hospitalized pediatric patients diagnosed with HPIV infections by a multiplex PCR test between 2015 and 2021 were retrospectively reviewed to determine the seasonal distributions of each HPIV serotype. For patients with a single HPIV infection, the clinical characteristics of each HPIV serotype were evaluated and compared with one another. Results Among the 514 cases of HPIV infection, HPIV-1, HPIV-2, HPIV-3, and HPIV-4 were identified in 27.2%, 11.9%, 42.6%, and 18.3% of cases, respectively. HPIV-3 was most prevalent in spring, and the other three serotypes were most prevalent in autumn. For patients with a single HPIV infection, those infected by HPIV-1 and HPIV-3 were younger than those infected by HPIV-2 and HPIV-4 ( P < 0.001). Croup and lower respiratory tract infection (LRI) were most frequently diagnosed in patients infected by HPIV-1 ( P < 0.001) and HPIV-4 ( P = 0.002), respectively. During 2020–2021, HPIV-3 was most prevalent in autumn and caused fewer LRIs ( P = 0.009) and more seizures ( P < 0.001) than during 2015–2019. Conclusions Each HPIV serotype exhibited a distinct seasonal predominance, and some differences in the clinical characteristics of the HPIV serotypes were observed. HPIV-4 acted as an important cause of LRI. Considering the recent changes in the epidemiological and clinical characteristics of HPIV-3, more time-series analyses should be conducted.
 
The radiographs in this case. A At 19th day of illness onset, lung CT indicated consolidation in the right lung. B At 24th day of illness onset, lung CT indicated aggravated consolidation in the lower lobe of bilateral lung adjacent to the pleura, mainly in the right lung. C At 5th day of illness onset, brain MRI (T2 weighted image) was normal. D At 24th day of illness onset, enhanced brain MRI was normal. E At 24th day of illness onset, spine MRI (T2 weighted image) was normal
Background The presentation of Guillain–Barré syndrome (GBS) caused by Japanese encephalitis virus (JEV) is uncommon, although clusters of GBS cases were observed in China in 2018. The underlying mechanism is unclear, particularly in individuals vaccinated against Japanese encephalitis in childhood. Case presentation We report a patient with acute flaccid paralysis involving four extremities and respiratory muscles, while magnetic resonance imaging of the brain and spine were standard. Electrophysiological examination displayed slowed motor nerve conduction speed and reduced evoked velocity amplitude. GBS was finally considered which was related to JEV infection verified by positive anti-JEV immunoglobulin M antibody and positive immunoglobulin G antibody in the serum. Unfortunately, the patient refused intravenous immunoglobulin and declined the use of mechanical ventilation again. He voluntarily withdrew from the hospital and died on the 36th day after the onset of illness. We also performed a review of previously reported related cases and discussed the underlying mechanism. Conclusion JEV infection-associated GBS is unusual. We should pay attention to the atypical manifestations of JEV infection and explore possible pathogenesis in particular individuals.
 
Flowchart of the approach used in the current study
Pearson’s linear correlation between the ORF1ab and N genes. A positive linear correlation was observed between the cycle threshold (Ct) value of ORF1ab and N genes in both A Ag-RDT(−) group (slope = 1.15 + 0.05, R2 = 0.91) and B Ag-RDT(+) group (slope = 1.12 + 0.05, R2 = 0.94)
The comparison of ORF1ab and N genes expression between the Ag-RDT(−) and Ag-RDT(+) group. The Ag-RDT(−) group demonstrated significantly lower cycle threshold (Ct) values of ORF1ab and N genes than that of the Ag-RDT(+) group (both p < 0.0001)
Background Rapid and accurate detection of SARS-CoV-2 infection is the cornerstone of prompt patient care. However, the reliability of the antigen rapid diagnostic test (Ag-RDT) in the diagnosis of SARS-CoV-2 infection remains inconclusive. Methods We conducted a field evaluation of Ag-RDT performance during the Shanghai Coronavirus disease 2019 (COVID-19) quarantine and screened 7225 individuals visiting our Emergency Department. 83 asymptomatic SARS-CoV-2 (+) individuals were enrolled in the current study. Simultaneously, Ag-RDT was performed to evaluate its testing performance. Results For the Ag-RDT(−) cases, the average cycle threshold (Ct) values of the N gene were 27.26 ± 4.59, which were significantly higher than the Ct value (21.9 ± 4.73) of the Ag-RDT(+) individuals ( p < 0.0001). The overall sensitivity of Ag-RDT versus that of RT-PCR was 43.37%. The Ag-RDT(+) individuals regarding the N gene’s Ct value were 16 cases in the < 20 range, 12 in 20–25, 5 in 25–30, and 3 in 30–35. The corresponding sensitivity was 84.21%, 52.17%, 21.74% and 16.67%, respectively. Meanwhile, sampling had a straight specificity of 100% regardless of the Ct value. Conclusions The Ag-RDT were extremely sensitive in asymptomatic COVID-19 individuals with a Ct value < 20.
 
Background Rodents are important virus reservoirs and natural hosts for multiple viruses. They are one of the wild animals that are extremely threatening to the spread of human viruses. Therefore, research on rodents carrying viruses and identifying new viruses that rodents carry is of great significance for preventing and controlling viral diseases. Methods In this study, fecal samples from six species of forest rodents in Northeast China were sequenced using metagenomics, and an abundance of virome information was acquired. Selection of important zoonotic in individual rodents for further sequence and evolutionary analysis. Results Among the top 10 most abundant viral families, RNA virus include Orthomyxoviridae, Picornaviridae, Bunyaviridae and Arenaviridae, DNA virus include Herpesviridae, Insect virus include Nodaviridae and Baculoviridae, Plant virus Tombusviridae and Phage (Myoriviridae). Except for Myoviridae, there was no significant difference in the abundance of virus families in the feces of each rodent species. In addition, a new strain of astrovirus was discovered, with an ORF and genome arrangement comparable to other rodent astroviruses.The newly identified astrovirus had the highest similarity with the rodent astrovirus isolate, CHN/100. Conclusions The data obtained in this study provided an overview of the viral community present in these rodent fecal samples, revealing some rodent-associated viruses closely related to known human or animal pathogens. Strengthening our understanding of unclassified viruses harbored by rodents present in the natural environment could provide scientific guidance for preventing and controlling new viral outbreaks that can spread via rodents.
 
Background The purpose of this study was to evaluate the distributions of vaginal microbiome dysbiosis and human papillomavirus (HPV) subtypes in infertile women and explore the correlations of HPV infection and vaginal microbiome dysbiosis with infertility. Methods In total, 1464 women aged 18–50 years were included in this study; 649 participants were included in the infertility group, and 815 participants were included in the normal group. The participants were tested for HPV, and their vaginal microecology was examined. The χ ² test and Spearman regression were used for statistical analysis, and binary logistic regression was performed to identify the risk factors for infertility. Results The patients in the infertility group were younger than those in the normal group, and the proportions of bacterial vaginosis and vaginal imbalance in the infertility group were significantly higher than those in the normal group. The incidence proportions of high-risk HPV types in the infertility group were significantly higher than those in the normal group, and the proportions of high-risk subtytes HPV16, HPV39, HV52, HPV56, and HPV68 were significantly higher in the infertility group than in the normal group. However, there were no significant differences in the incidences of low-risk HPV types. The incidence proportions of vaginal flora imbalance and HPV infection in the infertility group were significantly higher than those in the normal group. HPV16, HPV33, HPV51, HPV52and HPV58 infections were independent risk factors for infertility. Conclusions Vaginal microecological imbalance and HPV infection are directly related to infertility, and precautions should be taken.
 
Analysis of N-linked glycosylation in CedV F protein. a Schematic of localization of potential N-glycans. N-glycosylation mutants are named g1–g6. Black triangles indicate potential N-glycosylation sites within the F1 and F2 subunits. TM: transmembrane domain; CD: cytoplasmic domain; b PNGase F digest of CedV F protein. MDCK cells expressing CedV F protein were metabolically labeled for 15 min (pulse) and then incubated for 2 h in serum-free nonradioactive medium (chase). After immunoprecipitation of F proteins from cell lysates, samples were suspended in sample buffer and then treated with N-glycosidase F (PNGase F) according to the instructions of the manufacturer, or left untreated. After separation on a 12% SDS-gel under reducing conditions, samples were analyzed by autoradiography; c Proteolytic processing of CedV F and F mutants. MDCK cells expressing F proteins are metabolically labeled as described above. After immunoprecipitation of F proteins from cell lysates and separation on a 12% SDS-gel under reducing conditions, samples were analyzed by autoradiography. Molecular masses of marker proteins are indicated. n = 2. Stars indicate the F2 subunit
Analysis of amino acid substitutions at N-glycan consensus sequence 413–415 (g4) for expression. a Cells were transfected with either the wt F, g4, g4AST or the g4NSA gene. At 24 h p.t., cells were metabolically labeled for 15 min (pulse) and then incubated for 2 h in serum-free nonradioactive medium (chase). After immunoprecipitation of F proteins from cell lysates and separation on a 12% SDS-gel under reducing conditions, samples were analyzed by autoradiography. wt: wild-type; b Cell surface expression of CedV F proteins. Cells were transfected with either wt F, g4, g4AST or the g4NSA gene. At 24 h p.t., MDCK-2 cells expressing F proteins were surface-labeled with biotin on ice. After cell lysis, biotinylated proteins were immunoprecipitated using NeutrAvidin beads and subjected to SDS-PAGE under non-reducing conditions. Precipitated F proteins were visualized using an antibody against the HA-tag (H6908), HRP-labeled secondary antibodies and chemiluminescence. Representative blots are shown from four independent experiments. c Intracellular localization of wt and mutant CedV F proteins in MDCK-2 cells. F proteins are stained with anti-HA-tag specific primary antibodies and AlexaFluor488-conjugated secondary antibodies. The endoplasmic reticulum (ER) was visualized using a pDS Red2-ER plasmid-derived red fluorescent labeling. Representative images from two independent experiments are displayed. Inserts show magnifications of indicated areas. Magnification, × 63
Cell surface expression of CedV F proteins. At 24 h p.t., MDCK-2 cells expressing F proteins were surface-labeled with biotin on ice. After cell lysis, biotinylated proteins were immunoprecipitated using NeutrAvidin beads and subjected to SDS-PAGE under a non-reducing and b reducing conditions (n = 2). Precipitated F proteins were visualized using an antibody against the HA-tag (H6908), HRP-labeled secondary antibodies and chemiluminescence. In a, ConA staining is used as a loading control. Molecular masses of marker proteins are indicated
CedV F glycoprotein-mediated fusion activity. Syncytium formation in a MDCK-2 and b Vero76 cells co-expressing CedV F and G proteins was visualized by Giemsa staining at 30 h p.t.. Magnification, × 20. n = 3; c Quantitative reporter gene assay. At 24 h p.t., Vero76 cells expressing the T7 polymerase were layered on the cells expressing the indicated glycoproteins and incubated for 3 h at 37 °C. After cell lysis, luciferase activity was measured. Samples were tested in duplicates in three independent experiments. Reporter activity measured for the parental CedV F protein co-transfected with CedV G protein was set to 1 serving as a reference point for fusion activity. Bars represent the fusion activities of the different (mutant) CedV F proteins in relation to the fusion activity of the parental protein and include the standard error of the mean (SEM). Statistical analysis: unpaired Student’s t-test with Welch’s correction; (*) p ≤ 0.05; (**) p ≤ 0.005
Analysis of N-linked carbohydrates in CedV F protein expressed at the cell surface of MDCK-2 cells. Surface biotinylated CedV F proteins were immunoprecipitated using NeutrAvidin beads and either left untreated (lanes “−”) or digested with endo-β-N-acetylglucosaminidase H (Endo H; lanes “+”). Samples were separated by SDS-PAGE under reducing conditions, and blots were analyzed using an antibody against the HA-tag (H6908), HRP-labeled secondary antibodies and chemiluminescence. Molecular masses of marker proteins are indicated. n = 2
Background N-linked glycans on viral glycoproteins have been shown to be important for protein expression, processing and intracellular transport. The fusion glycoprotein F of Cedar virus (CedV) contains six potential N-glycosylation sites. Findings To investigate their impact on cell surface transport, proteolytic cleavage and biological activity, we disrupted the consensus sequences by conservative mutations (Asn to Gln) and found that five of the six potential N-glycosylation sites are actually utilized. The individual removal of N-glycan g1 (N66), g2 (N79) and g3 (N98) in the CedV F 2 subunit had no or only little effect on cell surface transport, proteolytic cleavage and fusion activity of CedV F. Interestingly, removal of N-linked glycan g6 (N463) in the F 1 subunit resulted in reduced cell surface expression but slightly increased fusogenicity upon co-expression with the CedV receptor-binding protein G. Most prominent effects however were observed for the disruption of N-glycosylation motif g4 (N413), which significantly impaired the transport of CedV F to the cell surface, thereby also affecting proteolytic cleavage and fusion activity. Conclusions Our findings indicate that the individual N-linked modifications, with the exception of glycan g4, are dispensable for processing of CedV F protein in transfection experiments. However, removal of g4 led to a phenotype that was strongly impaired concerning cell surface expression and proteolytic activation.
 
Consort-flow diagram to identify literature on the “Status of dyslipidemia in India” in the last two decades
a Lipid status of COVID-19 patients. The levels and distribution of lipoproteins in 75 COVID-19 positive patient serum samples. HDL levels are reduced, LDL and TC remain normal whereas most of the individuals have normal or increased TG and VLDL levels. b Test versus control. Lipid profile prevalence (%) in COVID-19 positive and control samples
a, b Levels and distribution of lipids in Males (58/75), and females (17/75)
a, b Levels and distribution of lipids in different age groups, young, < 40Y (10/66), middle, 40–60 Y (30/66), and old, > 60Y (26/66)
Prevalence (%) of abnormal total cholesterol, high-density lipoproteins, low-density lipoproteins, and triglyceride levels in the Indian population as documented in several studies across different parts of the country
Background Lipids play a central role in the virus life cycle and are a crucial target to develop antiviral therapeutics. Importantly, among the other lipoproteins, the ‘good cholesterol’ high-density lipoprotein (HDL) has been widely studied for its role in not only cardiovascular but several infectious diseases as well. Studies have suggested a role of serum lipids and lipoproteins including HDL, total cholesterol (TC), triglycerides (TG), and low-density lipoproteins (LDL) in several viral infections including COVID-19. This disease is currently a major public health problem and there is a need to explore the role of these host lipids/lipoproteins in virus pathogenesis. Methodology A total of 75 retrospective COVID-19 positive serum samples and 10 COVID-19 negative controls were studied for their lipid profiles including TC, HDL, LDL, and very-low-density lipoproteins (VLDL), and TG. Results Systematic literature search on dyslipidemia status in India shows that low HDL is the most common dyslipidemia. In this cohort, 65% (49) of COVID-19 patients had severely low HDL levels whereas 35% (26) had moderately low HDL and none had normal HDL levels. On the other hand, ~ 96% of samples had normal TC (72) and LDL (72) levels. VLDL and TG levels were also variable. In the controls, 100% of samples had moderately low HDL but none severely low HDL levels. Conclusion HDL likely plays a crucial role in COVID-19 infection and outcomes. The causal relationships between HDL levels and COVID-19 need to be studied extensively for an understanding of disease pathogenesis and management.
 
Background Bovine viral diarrhea virus 1 (BVDV-1) of the pestivirus genus is an economically crippling virus in the cattle industry; this positive RNA virus causes mucosal disease resulting in reproductive losses and other disease syndromes. The pathogenesis mechanism of the disease caused by BVDV infection is not well understood; for a better understanding of in vivo host BVDV-1 interactions, we conducted a transcriptomic study of infected cells at different times post-infection. Methods We compared the permissiveness and cellular response of a BVDV-1 cytopathogenic strain on Madin-Darby Bovine Kidney cells (MDBK) and bovine lung primary cells, a model closer to in vivo infection. Then a RNAseq analysis was realized on the infected bovine lung primary cells, at 10 hpi and 30 hpi (hours post-infection), to identify transcriptomic signatures. Results RNAseq analysis on BVDV-1 infected bovine primary cells showed 2,759 and 5,376 differentially expressed genes at respectively 10 hpi and 30 hpi with an absolute Fold Change ≥ 2. Among the different pathways deregulated, data analysis revealed a deregulation of Wnt signaling pathway, a conserved process that play a critical role in embryogenesis, cellular proliferation, and differentiation as well as in viral responses against viruses such as Influenza or Hepatitis C. We demonstrated here that the deregulation of the Wnt/βcatenin signaling pathway plays a role in viral replication of BVDV cp strain. Interestingly, we showed that the inhibition of this Wnt pathway using two inhibitors, FZM1 and iCRT14, induced a delay in onset of the establishment of a cytopathic effect of primary cells. Conclusions Thereby, this study highlighted a role of the Wnt signaling pathway in the BVDV-1 viral replication in bovine cells, suggesting an interesting option to explore as a new therapeutic target.
 
A Plane CT scan indicates less regular shape of liver, diffuse mass-like and nodular slightly hypodense lesions, some of which were fused. B Contrast-enhanced CT: significant ring enhancement in the arterial phase. C, D Continuous ring enhancement in the venous and delayed phases, local wall thinning and irritability in the right and left branches of the portal vein. Consider malignant tumors, a high possibility of hepatocellular carcinoma or cholangiocarcinoma, with local invasion of the right and left branches of the portal vein, hilar lymphadenopathy, and a small amount of ascites
A Abdominal ultrasound: size increased liver, and multiple hypoechoic masses observed. B–D Multiple hypoechoic masses in liver, the large intrahepatic mass is about 11.5 * 10.8 * 10.2 cm, located at the right, consider the possibility of liver cancer
A Plain MRI scan: increased liver volume with multiple nodules and mass shadows inside, showing slightly long T1 and slightly long T2 signals, liquefaction necrosis changes were observed in the center of the lesion, and some lesions appeared to be fused. B–D Contrast-enhanced scans showed mild enhancement of nodular mass shadows and ring-like enhancement changes. Consider malignant tumor combine with intrahepatic multiple metastases. The left branch of the portal vein was not clearly displayed, consider possible involvement. The right branch of the portal vein was suspect been locally invaded, the hepatic vein and the bile duct in the hilar area were not clearly displayed, the bile duct at the upper level was slightly dilated, the left upper quadrant was turbid, consider the possibility of local nodules
A Lymphoepithelioma-like carcinomas (staining, H&E; magnification, × 40). B High-power view of the same portion (staining, H&E; magnification, × 100). C Further high-power view revealed infiltrative growth of significant heterocyst nests in the liver tissue, which was morphologically consistent with malignant tumors, consider poorly differentiated carcinoma. (staining, H&E; magnification, × 200)
A Immunohistochemical results: CK7 foci (+), CK18 (weak + - +), CK19 (weak + - +), CK20 (−), CDX2 (weak + - +), AFP (−), Hepar1 (−), Arg-1 (−), GATA-3 (−), Vim (−), P40 a little (+), CD117 (−), CerbB2 (−), Ki-67 (+) 80–90%, EBV in situ hybridization: tumor cells EBER (+). Combining liver puncture with morphology, immunohistochemistry, and EBV in situ hybridization results, it was consistent with EB virus-associated poorly differentiated carcinoma (magnification, × 100). B Consider EBV infection-associated poorly differentiated cholangiocarcinoma (LELC morphology) magnification, × 200)
The clinical data of a patient with Epstein-barr virus (EBV) associated with cholangiocarcinoma was reported in this paper: a case of a 36-year-old female presented with abdominal pain and systemic skin yellowing combined with skin itching. Laboratory studies showed increase in alanine aminotransferase 242 U/L, aspartate aminotransferase 404 U/L, r-glutamyltransferase 1516 U/L, total bilirubin 308.2 µmol/L and CA199 (101.0 U/ml). AFP (4.5 ng/ml) was normal. CT revealed multiple space-occupying lesions in the liver. PET-CT revealed liver malignant tumor and lymph node metastasis. Liver puncture pathology revealed infiltrative growth of significant heterocyst nests in the liver tissue, which was morphologically consistent with malignant tumors, considering poorly differentiated carcinoma. Pathology suggestion: combining liver puncture with morphology, immunohistochemistry, and EBV in situ hybridization results, it was consistent with EB virus-associated poorly differentiated carcinoma, therefore, consider EBV infection-associated poorly differentiated cholangiocarcinoma (CCA) (LELC morphology). The patient underwent liver transplantation in Hangzhou Shulan Hospital on June 8, 2021 successfully. After surgery, the patient orally took tacrolimus for anti-rejection, entecavir for antiviral therapy, gemcitabine 1.2 g + cis-platinum 30 mg for chemotherapy. After following up for more than 5 months post liver transplantation, the condition of the patient deteriorated. The patient subsequently died. Based on the case of our patient and the review of existing literature, when the patient's serum CA199 increased, AFP did not change significantly, and there was no previous history of hepatitis B. CT revealed a low-density mass in the liver, ring enhancement in the arterial phase, and heterogeneous enhancement of the tumor in the delayed phase. Ring enhancement of the liver lesion mass was observed on MRI. Consider the might possibility of hepatic CCA. When patients showed recurrent tonsillitis at an early age, EBV virus infection should be vigilant and oropharyngeal tissue should persist, diagnosis of EBV-associated liver cancer should be considered. In particular, EBV infection-related liver cancer is relatively rare, the clinician should improve the recognition of the disease to strive for early diagnosis and therapy.
 
Background and aims The John Cunningham virus (JCV) is the established etiological agent of the polyomavirus-associated nephropathy among renal transplant recipients. In the present study, we aimed to determine the probable predictive factors leading to JCV replication in renal transplant patients. Material and methods Urine and plasma samples were collected from a total of 120 consecutive renal‐transplanted patients without preliminary screening from Jan 2018 to Mar 2019. After DNA extraction, the simultaneous detection and quantification of JCV and BK polyomavirus (BKV) were conducted using a Real-time quantitative PCR method. Moreover, statistical analyses were performed using the statistical software packages, SPSS version 21. Results The prevalence of JCV viruria and viremia among renal transplant recipients were 26 (21.67%) and 20 (16.67%), respectively. A significant association was observed between the JCV and two risk factors, diabetes mellitus ( P = 0.002) and renal stones ( P = 0.015). The prevalence of JCV viremia among recipients who were grafted near time to sampling was significantly higher ( P = 0.02). There was a statistically significant coexistence between BK and JC viruses among our patients ( P = 0.029). The frequency of JCV viruria in males was reported almost three times more than in females ( P = 0.005). The JCV shedding in urine was significantly associated with the tropical steroids like prednisolone acetate, which have been the standard regimen ( P = 0.039). Multivariable analysis revealed duration of post-transplantation (OR, 0.89; P = 0.038), diabetes mellitus (OR, 1.85; P = 0.034), and renal stone (OR 1.10; P = 0.04) as independent risk factors associated with JCV viremia post-renal transplantation. Conclusion It seems that the discovery of potential risk factors, including immunological and non-immunological elements, may offer a possible preventive or therapeutic approach in the JCV disease episodes. The results of this study may also help clarify the probable clinical risk factors involving in progressive multifocal leukoencephalopathy development.
 
Study selection process according to the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guideline
Forest plot of seroconversion proportions (prevalence) regarding the type of vaccine (A) and etiology of immunodeficiency (B) following the first dose of vaccine
Counter-enhanced funnel plots regarding the publication bias following the first dose (A), second dose (B), and third dose (C) of vaccination.
Forest plot of seroconversion proportions (prevalence) regarding the type of vaccine (A) and etiology of immunodeficiency (B) following the second dose of vaccine
Forest plot of seroconversion proportions (prevalence) following the third dose of vaccine
Background: Immunocompromised (IC) patients are at higher risk of more severe COVID-19 infections than the general population. Special considerations should be dedicated to such patients. We aimed to investigate the efficacy of COVID-19 vaccines based on the vaccine type and etiology as well as the necessity of booster dose in this high-risk population. Materials and methods: We searched PubMed, Web of Science, and Scopus databases for observational studies published between June 1st, 2020, and September 1st, 2021, which investigated the seroconversion after COVID-19 vaccine administration in adult patients with IC conditions. For investigation of sources of heterogeneity, subgroup analysis and sensitivity analysis were conducted. Statistical analysis was performed using R software. Results: According to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses, we included 81 articles in the meta-analysis. The overall crude prevalence of seroconversion after the first (n: 7460), second (n: 13,181), and third (n: 909, all population were transplant patients with mRNA vaccine administration) dose administration was 26.17% (95% CI 19.01%, 33.99%, I2 = 97.1%), 57.11% (95% CI: 49.22%, 64.83%, I2 = 98.4%), and 48.65% (95% CI: 34.63%, 62.79%, I2 = 94.4%). Despite the relatively same immunogenicity of mRNA and vector-based vaccines after the first dose, the mRNA vaccines induced higher immunity after the second dose. Regarding the etiologic factor, transplant patients were less likely to develop immunity after both first and second dose rather than patients with malignancy (17.0% vs 37.0% after first dose, P = 0.02; 38.3% vs 72.1% after second dose, P < 0.001) or autoimmune disease (17.0% vs 36.4%, P = 0.04; 38.3% vs 80.2%, P < 0.001). To evaluate the efficacy of the third dose, we observed an increasing trend in transplant patients after the first (17.0%), second (38.3%), and third (48.6%) dose. Conclusion: The rising pattern of seroconversion after boosting tends to be promising. In this case, more attention should be devoted to transplant patients who possess the lowest response rate.
 
Background At present, there are still no specific therapeutic drugs and appropriate vaccines for Dengue. Therefore, it is important to explore distinct clinical diagnostic indicators. Methods In this study, we combined differentially expressed genes (DEGs) analysis, weighted co-expression network analysis (WGCNA) and Receiver Operator Characteristic Curve (ROC) to screen a stable and robust biomarker with diagnosis value for Dengue patients. CIBERSORT was used to evaluate immune landscape of Dengue patients. Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and Gene set enrichment analysis (GSEA) were applied to explore potential functions of hub genes. Results CD38 and Plasma cells have excellent Area Under the Curve (AUC) in distinguishing clinical stages for Dengue patients, and activated memory CD4+ T cells and Monocytes have good AUC for this function. ZNF595 has acceptable AUC in discriminating dengue hemorrhagic fever (DHF) from dengue fever (DF) in whole acute stages. Analyzing any serotype, we can obtain consistent results. Negative inhibition of viral replication based on GO, KEGG and GSEA analysis results, up-regulated autophagy genes and the impairing immune system are potential reasons resulting in DHF. Conclusions CD38, Plasma cells, activated memory CD4+ T cells and Monocytes can be used to distinguish clinical stages for dengue patients, and ZNF595 can be used to discriminate DHF from DF, regardless of serotypes. Graphical abstract
 
Analytical sensitivity of the H5 RT-RAA assay. A dilution range from 10⁶ to 10¹ copies/μL of H5 subtype AIV cRNA was used to evaluate the detection limit of H5 RT-RAA assay. Negative represents negative control. 1–6: 10⁶ copies/μL–10¹ copies/μL; 7: negative control
Analytical specificity of the H5 RT-RAA assay. Detection signals were recorded by real-time fluorescence RT-RAA with four samples including H5 subtype AIVs (H5N1, H5N2 and H5N6), while no signals were detected from the 14 samples including other subtype AIVs, NDVs, IBVs and negative controls. 1: K144 (H5N1); 2: QD1 (H5N2); 3: G2324 (H5N6); 4: G2084 (H5N6)
Background The H5 subtype avian influenza virus (AIV) has caused huge economic losses to the poultry industry and is a threat to human health. A rapid and simple test is needed to confirm infection in suspected cases during disease outbreaks. Methods In this study, we developed a reverse transcription recombinase-aided amplification (RT-RAA) assay for the detection of H5 subtype AIV. Assays were performed at a single temperature (39 °C), and the results were obtained within 20 min. Results The assay showed no cross-detection with Newcastle disease virus or infectious bronchitis virus. The analytical sensitivity was 10 ³ RNA copies/μL at a 95% confidence interval according to probit regression analysis, with 100% specificity. Compared with published reverse transcription quantitative real-time polymerase chain reaction assays, the κ value of the RT-RAA assay in 420 avian clinical samples was 0.983 ( p < 0.001). The sensitivity for avian clinical sample detection was 97.26% (95% CI, 89.56–99.52%), and the specificity was 100% (95% CI, 98.64–100%). Conclusions These results indicated that our RT-RAA assay may be a valuable tool for detecting H5 subtype AIV.
 
53BP1 influences repair pathway choice. A DSB which has had initial repair factors recruited (MRN complex, ATM, MDC1) and adjacent to a nucleosome with ubiquitylated Lys15 of histone 2A (H2AK15ub) and mono- or di-methylated Lys20 of histone 4 (H4K20me1/2). B In G1 phase, 53BP1 binds to H2A15ub and H4K20me1/2 via its UDR motif and tudor domain respectively. RIF1 is recruited to 53BP1 via binding to ATM-phosphorylated residues. BRCA1 foci formation is inhibited in G1 via 53BP1 and RIF1, where the N terminus ATM target sites in 53BP1 are necessary for its ability to recruit and interact with RIF1 and PTIP. ATM-phosphorylation of 53BP1 leads to recruitment of other NHEJ-promoting factors such as PTIP and EXPAND1, and leads to blocking of end resection and promotion of NHEJ. C In G2/S phases, CtIP is recruited by and bound to the MRN complex. After CtIP is phosphorylated, BRCA1 binds, 53BP1-RIF1 are inhibited from binding to chromatin, and end resection and HDR are promoted. For all panels, colored fill indicates protein factors are conserved in vector mosquiotes, while while fill (CtIP, BRCA1) indicates repairs factors that appear to be absent in mosquitoes
Modified nuclease systems to bias HDR at specific DSBs. A Schematic of HDR factors tethered to Cas9 via peptide linker can promote strand-invasion (Cas9-yRAD2, Cas9-Brex27), end-resection (Cas9-CtIP, Cas9-MRE11, Cas9-UL12), or single-strand annealing (Cas9-RecA) at a DNA double-strand break. B Diagram of the REDIT system composed of Cas9, sgRNA, RNA aptamer with MS2 loop, MS2 coat protein (MCP), RecT, and either single-strand DNA (ssDNA) or double-stranded DNA (dsDNA) donors. C Visual representation of Cas9-hGem levels during cell cycle stages and Cas9-hGem construct. D Overview of S1mplex components: Cas9, sgRNA, RNA aptamer, streptavidin, biotin, and either ssDNA or dsDNA donors. E Cas9 tethered to PCV, an HUH endonuclease forming a covalent bond with ssODN donor. F A transcription factor DNA binding domain fused to Cas9 with a peptide linker binding to motifs presents donor DNA
Programmable gene editing systems such as CRISPR-Cas have made mosquito genome engineering more practical and accessible, catalyzing the development of cutting-edge genetic methods of disease vector control. This progress, however, has been limited by the low efficiency of homology-directed repair (HDR)-based sequence integration at DNA double-strand breaks (DSBs) and a lack of understanding about DSB repair in mosquitoes. Innovative efforts to optimize HDR sequence integration by inhibiting non-homologous end joining or promoting HDR have been performed in mammalian systems, however many of these approaches have not been applied to mosquitoes. Here, we review some of the most relevant steps of DNA DSB repair choice and highlight promising approaches that influence this choice to enhance HDR in the context of mosquito gene editing.
 
Distribution of HPV genotypes detected in participants. High risk HPV (HR-HPV) in dark color has a higher infection rate than low risk HPV (LR-HPV) in grey color
Distribution of HPV types in vaginal infection. a Distribution of HPV types with vaginal infection-positive in LSIL. b. Distribution of HPV types with vaginal infection-positive in HSIL. c. Distribution of HPV types with vaginal infection-positive in AGC. d. Distribution of HPV types with vaginal infection-positive in NILM
Background HPV (human papillomavirus) is an important cause of cervical cancer. Cervical-vaginal infection with pathogens, such as herpes simplex virus (HSV), bacterial vaginosis Trichomonas vaginalis and vaginal candidiasis could be a cofactor. This study aimed to assess the relationship between vaginal infection with HPV genotype and cytology test results and analyze the relationship between vaginal and HPV infections and cervical cancer. Methods We performed a district-based study to elucidate the relationship among the vaginal and HPV infections and cervical cancer. We collected the cervical exfoliation data of 23,724 women admitted to the Shanghai Zhoupu Hospital and received ThinPrep cytology test (TCT) and HPV detection between 2014 and 2019. Results Total vaginal infection rate was 5.3%, and the HPV-positive group had a slightly higher vaginal infection rate than the HPV-negative group (P < 0.01). The incidence rate of cervical intraepithelial neoplasia or cervical cancer with vaginal infection was higher than without vaginal infection (P < 0.001). Conclusion HPV/vaginal infection-positive women tended to have abnormal results of TCT. Women with vaginal infection were more likely to develop HPV infection. HSV combined with HPV infection was noted as a causal factor for HSIL.
 
Kinetics of ApoE and Zika E protein colocalization and evidence of their interaction in infected Huh7.5 cells. a Kinetics of the colocalization of the ApoE and Zika E proteins, from 6 to 48 h post-infection at an MOI of 1. Scale bars = 8 µm. b Pearson coefficients for the colocalization of ApoE and Zika E protein within the ROI in Huh7.5 cells were performed on 30 z-stacks per condition. ****: p value < 0.0001 in ANOVA tests. c Co-immunoprecipitation of ApoE and Zika E protein. NI: naive cells; Inf: infected cells; IP: immunoprecipitation; anti-ApoE: goat anti-ApoE Abs; anti-gp120: anti-HIV-1 gp120 Abs used as an isotype control for the immunoprecipitation assay
Detection of ApoE in ZIKV-induced ER membrane rearrangements in infected Huh7.5 cells. a Observation, by confocal microscopy, of the ApoE-Zika E protein channel with the ER marker calnexin in infected Huh7.5 cells and Pearson coefficient graph obtained from 30 z-stacks. Scale bars = 8 µm. b TEM observations of the characteristic membrane rearrangements induced by ZIKV infection in infected Huh7.5 cells. Thin black arrows: Zippered ER; thin white arrows: viral particles; bold black arrows: vesicle packets; asterisk: cytoplasmic vacuolization. Scale bars = 500 nm. c Immunogold labeling, on cryo-TEM sections, of ApoE and Zika E protein with 6 nm and 12 nm gold-conjugated Abs, respectively, in infected Huh7.5 cells. Insets show a high magnification of the area indicated by the thin arrow. Scale bars = 200 nm
ApoE and Zika E protein interact in ZIKV-induced ER rearrangements in infected HMC3 cells. a Western-blot analysis of the co-immunoprecipitation of ApoE and Zika E protein after 48 h post-infection. NI: naive cells; Inf: infected cells; IP: immunoprecipitation; anti-apoE: goat anti-ApoE Abs; anti-gp120: anti-HIV-1 gp120 Abs used as an isotype control for immunoprecipitation assays. b Assay of the colocalization of the ApoE-Zika E proteins with calnexin after 24 h of infection; Pearson coefficient for colocalization within the ROI in HMC3 cells performed on 30 z-stacks. Scale bars = 8 µm. c Characteristic membrane rearrangements were observed in infected HMC3 cells by TEM. White triangles: convoluted membranes; bold black arrow: vesicle packets. Scale bars = 500 nm. d Immunogold labeling of ApoE and Zika E protein with 10 nm and 6 nm gold-conjugated Abs, respectively, in infected HMC3 cells analyzed on cryo-TEM sections. Scale bar = 200 nm
ApoE is conserved on ZIKV extracellular particles secreted from infected Huh7.5 and HMC3 cells. a Immunogold labeling of ApoE (6 nm) and Zika E protein (12 nm) on particles secreted by infected Huh7.5 cells and concentrated by centrifugation on a sucrose cushion. b The same procedure was applied to supernatant from infected HMC3 cells. ApoE and Zika E protein were labeled with 10 nm and 6 nm gold beads, respectively
Neutralizing effect of anti-apoE Abs vs anti-Zika E protein Abs. a Example of FACS quantification of the number of cells positive for ZIKV envelope immunofluorescent labeling in the conditions tested. b Relative percentage of infected cells 48 h post-infection with particles previously incubated with various concentrations of Abs (indicated in μg/mL). The percentage of infection is relative to the corresponding isotype Abs. ****: p value < 0.0001 in ANOVA test
Background Zika virus (ZIKV), a member of the Flaviviridae family, has caused massive outbreaks of infection in tropical areas over the last decade and has now begun spreading to temperate countries. Little is currently known about the specific host factors involved in the intracellular life cycle of ZIKV. Flaviviridae viruses interact closely with host-cell lipid metabolism and associated secretory pathways. Another Flaviviridae, hepatitis C virus, is highly dependent on apolipoprotein E (ApoE) for the completion of its infectious cycle. We therefore investigated whether ZIKV also interacted with this protein. Methods ZIKV infections were performed on both liver and microglia derived cell lines in order to proceed to colocalization analysis and immunoprecipitation assays of ApoE and Zika envelope glycoprotein (Zika E). Transmission electron microscopy combined to immunogold labeling was also performed on the infected cells and related supernatant to study the association of ApoE and Zika E protein in the virus-induced membrane rearrangements and secreted particles, respectively. Finally, the potential of neutralization of anti-ApoE antibodies on ZIKV particles was studied. Result We demonstrated an interaction between ApoE and the Zika E protein. This specific interaction was observed in virus-induced host-cell membrane rearrangements, but also on newly formed intracellular particles. The partial neutralizing effect of anti-ApoE antibody and the immunogold labeling of the two proteins on secreted virions indicates that this interaction is conserved during ZIKV intracellular trafficking and release. Conclusions These data suggest that another member of the Flaviviridae also interacts with ApoE, indicating that this could be a common mechanism for the viruses from this family.
 
Background Viral antigen detection test is the most common method used to detect viruses in the field rapidly. However, due to the low sensitivity, it can only be used as an auxiliary diagnosis method for virus infection. Improving sensitivity is crucial for developing more accurate viral antigen tests. Nano luciferase (Nluc) is a sensitive reporter that has not been used in virus detection. Results In this study, we produced an intracellularly Nluc labeled detection antibody (Nluc-ch2C5) and evaluated its ability to improve the detection sensitivity of respiratory syndrome coronavirus 2 (SARS-CoV-2) antigens. Compared with the traditional horse-radish peroxidase (HRP) labeled antibody (HRP-ch2C5), Nluc-ch2C5 was 41 times more sensitive for inactivated SARS-CoV-2 virus by sandwich chemiluminescence ELISA. Then we applied Nluc-ch2C5 to establish an automatic magnet chemiluminescence immune assay (AMCA) for the SARS-CoV-2 viral spike protein, the limit of detection was 68 pfu/reaction. The clinical sensitivity and specificity reached 75% (24/32) and 100% (48/48) using 32 PCR-positive and 48 PCR-negative swab samples for clinical evaluation, which is more sensitive than the commercial ELSA kit and colloid gold strip kit. Conclusions Here, monoclonal antibody ch2C5 served as a model antibody and the SARS-CoV-2 served as a model pathogen. The Nluc labeled detecting antibody (Nluc-ch2C5) significantly improved the detection sensitivity of SARS-CoV-2 antigen. This labeling principle applies to other viral infections, so this labeling and test format could be expected to play an important role in detecting other virus antigens.
 
Objective The purpose of this study was to provide an updated estimate of the prevalences of different types of human papillomavirus (HPV) in females in Chaoshan District and to establish an internal quality control (IQC) method for excluding false-positive results in HPV detection by using the Levey–Jennings control chart. Method HPV types were detected in 23,762 cervical samples by using PCR membrane hybridization. The means and standard deviations (SDs) of the positive rates were calculated, the Levey–Jennings chart was plotted, and the rules for “out of control” and “warning” were established. A set of standardized IQC for HPV DNA tests was developed based on the values and Levey–Jennings charts. Result In 466 batches, the positive rate exceeded the 1 + 2SD rule 24 times, but there was no consecutive exceedance, which was considered “in control”. When the positive rate exceeded the 1 + 3SD rule 8 times with consecutive exceedance, it was considered “out of control”. Further examination revealed that detections showing “out of control” had an undesirable random error, indicating that contamination may occur due to improper operation. Conclusion This unique Levey–Jennings control chart is a practical method for eliminating false-positive results in HPV DNA detection and should be widely applicable in molecular diagnostic laboratories.
 
Census of patients admitted with coronavirus disease 2019 (COVID-19) with those who developed severe COVID-19 or were deceased across the first three surges of COVID-19 in Tehran, Iran
The number of patients who developed acute respiratory distress syndrome (ARDS) or acute cardiac injury (ACI) during the first three surges of coronavirus disease 2019 (COVID-19) in Tehran, Iran
Background A few studies compared the characteristics and outcomes of COVID-19 patients during the first and second surges of the disease. We aimed to describe the clinical features and outcomes of COVID-19 patients across the first, second, and third surges of the disease in Tehran, Iran. Method We conducted a retrospective cohort study of patients with COVID-19 admitted to Sina hospital in Tehran, Iran, during three surges of COVID-19 from February 16 to October 28, 2020. Result Surge 1 patients were younger with more prevalence of hypertension. They also presented with significantly higher oxygen saturation, systolic blood pressure, and respiratory rate on admission. Patients had higher levels of neutrophil to lymphocyte ratio, Urea, CRP, and ESR, in surge 2. The incidence of dyspnea, chest pain, and neurological manifestations followed a significant increasing trend from surge 1 to surge 3. There was no difference in severity and in-hospital mortality between the surges. However, the length of hospital stays and acute cardiac injury (ACI) was less in surge 1 and acute respiratory distress syndrome (ARDS) in surge 2 than in other surges. Conclusion Patients did not significantly differ in disease severity, ICU admission, and mortality between surges; however, length of hospital stay and ACI increased during surges, and the number of patients developing ARDS was significantly less in surge 2 compared to other peaks.
 
Phylogenetic placement of VZV sequence from co-infected CSF sample. Sequence alignments were done using the MAFFT algorithm and with other sequences from GenBank. Phylogenetic analysis was performed by Bayesian inference using the GTR + G + I substitution model. Sequences in the tree are designated by GenBank accession numbers and origins in brackets with the sequence from this study shown in a red font. Posterior probability support values are indicated at the nodes in the unrooted tree (A) and values greater than 0.9 are indicated in the rooted tree by black dots (B)
Phylogenetic comparison of circulating recombinant forms of HIV-1. Sequence alignments were done using the MAFFT algorithm and a concatenation of alignments of partial sequences from the gag, pol, vif, env and nef regions with other sequences from GenBank. Sequences in the tree are designated by GenBank accession numbers and assigned CRF, with the sequence from this study depicted by a red font. Black dots represent notes with posterior probability of 0.90 or greater and white dots represent those greater than 0.75
Background Encephalitis is a serious disease of the brain characterized by prodromal and specific neurological symptoms. HIV infections offer opportunistic viruses, such as Varicella-zoster virus (VZV), the chance to cause encephalitis in patients. There is a lack of information on the genetic diversity of VZV in Ghana and other parts of Africa which requires sequencing and characterization studies to address. The active evolution of HIV-1 in West Africa also requires continuous surveillance for the emergence of new genetic forms. Case presentation VZV was detected in the CSF sample of an 11-year-old patient presenting with symptoms of encephalitis by real-time PCR diagnostics. To identify possible unknown aetiological pathogens, next-generation sequencing was performed, and revealed an HIV-1 co-infection. Alignments of concatenated HIV-1 genome fragments in the gag, pol, vif, env and nef regions and a near-complete VZV genome were analyzed by Bayesian inference, and phylogenetic trees were generated. The VZV sequence belongs to clade 5 and the HIV-1 sequence is a member of the CRF02_AG predominant circulating recombinant form in Ghana. Conclusions Diagnostic tests for CSF HIV would be useful where possible in patients presenting with encephalitis due to VZV and other opportunistic viruses in Kumasi to shed light on the role of HIV in encephalitis cases in Ghana. This report reaffirms the role of the CRF02_AG circulating recombinant form in HIV infections in Ghana and also gives a preliminary genetic characterization of VZV in Kumasi, Ghana.
 
Expression and identification of CSFV Erns and BVDV tE2 proteins. A & C The recombinant CSFV Erns (A) or BVDV tE2 (C) protein expressed in E. Coli was analyzed by SDS-PAGE, with Coomassie blue staining. M, molecular marker; Lane 1, lysate of bacteria harboring the control plasmid pET-28a; Lane 2, the lysate of bacteria harboring the plasmid pET-Erns (A) or pET-tE2 (C); Lane 3, the purified CSFV Erns (A) or BVDV tE2 (C) protein. B & D Recombinant CSFV Erns (B) or BVDV tE2 (D) protein was confirmed by western blotting using an anti-His monoclonal antibody (upper) or a specific anti-virus polyclonal antibody (lower). M, molecular marker; Lane 1, lysate of bacteria harboring the control plasmid pET-28a; Lane 2, the lysate of bacteria harboring the plasmid pET-Erns (B) or pET-tE2 (D)
Optimizations of CSFV Erns and BVDV tE2 -based ELISA procedures. A & C Optimization of the concentration of coating antigen and the dilution of swine sera for CSFV Erns (A) or BVDV tE2 (C) -based ELISA using checkerboard titration test. B & D Optimization of the dilution of the secondary antibody for CSFV Erns (B) or BVDV tE2 (D) -based ELISA. P/N, positive control/negative control; ☆, the optimized condition for ELISA test
Validation of the specificity of CSFV Erns and BVDV tE2 -based indirect ELISAs. The specificities of CSFV Erns -based (A, C & E) and BVDV tE2 -based ELISAs (B, D & F) were validated using a panel of infected swine sera (A & B), including PCV2 (n = 9), PRRSV (n = 6), PEDV (n = 4), ASFV (n = 5), CSFV (n = 10), BVDV (n = 10) and negative control (n = 6); a panel of immunized rabbit sera (C & D), including CSFV (n = 4), BVDV (n = 4) and negative control (n = 4) or immunized mouse sera (E & F), including CSFV (n = 6), BVDV (n = 6) and negative control (n = 6)
The sensitivity of CSFV Erns and BVDV tE2 -based ELISAs. A Evaluation of the sensitivity of CSFV Erns -based ELISA using serially swine sera with different neutralizing antibody (NAb) titers. P1, P2 and P3, anti-CSFV positive sera; N1, CSFV-free serum. The number in brackets indicated the NAb titer. B Evaluation of the sensitivity of BVDV tE2 -based ELISA using serially swine sera with different NAb titers. P1, P2 and P3, anti-BVDV positive sera; N1, BVDV-free negative serum. The number in brackets indicated the NAb titer
Background Classical swine fever (CSF) virus is the causative agent of an economically important, highly contagious disease of pigs. CSFV is genetically and serologically related to bovine viral diarrhea virus (BVDV). BVDV infection in pigs can mimic CSF clinical signs, which cause difficulty in differentiation. Serological test for detection of virus specific antibodies is a valuable tool for diagnosis and surveillance of CSFV and BVDV infections in animals. The aim of this study was to develop the CSFV Erns and BVDV tE2 -based ELISAs to distinguishably test specific antibodies against CSFV and BVDV. Methods The CSFV Erns and truncated E2 (tE2, residues 690–865) of BVDV were expressed in E. coli and purified by Ni–NTA affinity chromatography, respectively. Employing Erns or tE2 protein as diagnostic antigen, indirect ELISAs were developed to distinguishably test specific antibodies against CSFV and BVDV. The specificity and sensitivity of ELISAs were evaluated using a panel of virus specific sera of pigs, immunized rabbits and immunized mice. A total 150 clinical serum samples from farm pigs were measured by the developed ELISAs and compared with virus neutralizing test (VNT). Results Indirect ELISA was established based on recombinant CSFV Erns or BVDV tE2 protein, respectively. No serological cross-reaction between antibodies against CSFV and BVDV was observed in sera of immunized rabbits, immunized mice or farm pigs by detections of the Erns and tE2 -based ELISAs. Compared to VNT, the CSFV Erns -based ELISA displayed a high sensitivity (93.3%), specificity (92.0%) and agreement rate (92.7%), and the sensitivity, specificity and agreement rate of BVDV tE2 -based ELISA was 92.3%, 95.2% and 94.7%, respectively. Conclusion The newly developed ELISAs are highly specific and sensitive and would be valuable tools for serological diagnosis for CSFV and BVDV infections.
 
Coxsackievirus A10 (CV-A10), the causative agent of hand, foot, and mouth disease (HFMD), caused a series of outbreaks in recent years and often leads to neurological impairment, but a clear understanding of the disease pathogenesis and host response remains elusive. Cellular microRNAs (miRNAs), a large family of non-coding RNA molecules, have been reported to be key regulators in viral pathogenesis and virus-host interactions. However, the role of host cellular miRNAs defensing against CV-A10 infection is still obscure. To address this issue, we systematically analyzed miRNA expression profiles in CV-A10-infected 16HBE cells by high-throughput sequencing methods in this study. It allowed us to successfully identify 312 and 278 miRNAs with differential expression at 12 h and 24 h post-CV-A10 infection, respectively. Among these, 4 miRNAs and their target genes were analyzed by RT-qPCR, which confirmed the sequencing data. Gene target prediction and enrichment analysis revealed that the predicted targets of these miRNAs were significantly enriched in numerous cellular processes, especially in regulation of basic physical process, host immune response and neurological impairment. And the integrated network was built to further indicate the regulatory roles of miRNAs in host-CV-A10 interactions. Consequently, our findings could provide a beneficial basis for further studies on the regulatory roles of miRNAs relevant to the host immune responses and neuropathogenesis caused by CV-A10 infection.
 
Background From the 1078 diarrhea stools tested in our survey from 2017 to 2020 in local area of China, PEDV was the key pathogen that was closely related to the death of piglets with diarrhea. In addition, coinfection of PEDV-positive samples with BVDV reached 17.24%. Although BVDV infection in swine is typically subclinical, the effect of PEDV and BVDV coinfection on disease severity and the potential molecular mechanism of coinfection with these two viruses remain unknown. Methods In this study, we developed a model of coinfection with porcine epidemic diarrhea virus (PEDV) and bovine viral diarrhea virus (BVDV) in PK15 cells, and a tandem mass tag (TMT) combined with LC–MS/MS proteomic approach was used to identify differential protein expression profiles. Additionally, we performed drug experiments to explore the inflammatory response induced by PEDV or BVDV mono- or coinfection. Results A total of 1094, 1538, and 1482 differentially expressed proteins (DEPs) were identified upon PEDV monoinfection, BVDV monoinfection and PEDV/BVDV coinfection, respectively. KEGG pathway analysis revealed that PEDV and BVDV coinfection led to a highly significantly enrichment of the inflammatory bowel disease (IBD) pathway. In addition, the NF-κB signaling pathway was more intensively activated by PEDV and BVDV coinfection, which induced higher production of inflammatory cytokines, than PEDV or BVDV monoinfection. Conclusions Our study indicated that cattle pathogens might play synergistic roles in the pathogenesis of porcine diarrhea, which might also improve our understanding of the pathogenesis of multiple infections in diarrhea.
 
Background Hepatitis C virus (HCV) infection increased the risk of hepatocellular carcinoma. Identification of host factors required for HCV infection will help to unveil the HCV pathogenesis. Adaptive mutations that enable the replication of HCV infectious clones could provide hints that the mutation-carrying viral protein may specifically interact with some cellular factors essential for the HCV life cycle. Previously, we identified D559G mutation in HCV NS5B (RNA dependent RNA polymerase) important for replication of different genotype clones. Here, we searched for the factors that potentially interacted with NS5B and investigated its roles in HCV infection. Methods Wild-type-NS5B and D559G-NS5B of HCV genotype 2a clone, J6cc, were ectopically expressed in hepatoma Huh7.5 cells, and NS5B-binding proteins were pulled down and identified by mass spectrometry. The necessity and mode of action of the selected cellular protein for HCV infection were explored by experiments including gene knockout or knockdown, complementation, co-immunoprecipitation (Co-IP), colocalization, virus infection and replication, and enzymatic activity, etc. Results Mass spectrometry identified a number of cellular proteins, of which protein phosphatase 2 regulatory subunit B’delta (PPP2R5D, the PP2A regulatory B subunit) was one of D559G-NS5B-pulled down proteins and selected for further investigation. Co-IP confirmed that PPP2R5D specifically interacted with HCV NS5B but not HCV Core and NS3 proteins, and D559G slightly enhanced the interaction. NS5B also colocalized with PPP2R5D in the endoplasmic reticulum. Knockdown and knockout of PPP2R5D decreased and abrogated HCV infection in Huh7.5 cells, respectively, while transient and stable expression of PPP2R5D in PPP2R5D-knockout cells restored HCV infection to a level close to that in wild-type Huh7.5 cells. Replicon assay revealed that PPP2R5D promoted HCV replication, but the phosphatase activity and catalytic subunit of PP2A were not affected by NS5B. Conclusions PPP2R5D interactes with HCV NS5B and is required for HCV infection in cultured hepatoma cells through facilitating HCV replication.
 
Background Coinfection with hepatitis C virus (HCV) is common in human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) patients due to shared routes of transmission. We aimed to investigate the characteristics of HCV subgenotypes among HIV/HCV-coinfected patients in Guangdong and explore the molecular transmission networks and related risk factors for HCV strains. Methods Plasma samples were obtained from 356 HIV/HCV-coinfected patients for HCV NS5B region sequencing. A neighbor-joining phylogenetic tree was constructed to affirm HCV subgenotypes. The transmission networks based on maximum likelihood phylogenetic tree were determined by Cluster Picker, and visualized using Cytoscape 3.2.1. Results A total of 302 HCV NS5B sequences were successfully amplified and sequenced from the 356 plasma samples. A neighbor-joining phylogenetic tree based on the 302 NS5B sequences revealed the profile of HCV subgenotypes circulating among HIV/HCV coinfection patients in Guangdong. Two predominant strains were found to be 6a (58.28%, 176/302) and 1b (18.54%, 56/302), followed by 3a (10.93%, 33/302), 3b (6.95%, 21/302), 1a (3.64%, 11/302), 2a (0.99%, 3/302) and 6n (0.66%, 2/302). A molecular transmission network of five major HCV genotypes was constructed, with a clustering rate of 44.04%. The clustering rates of subgenotypes 1a, 3a, 3b, 1b, and 6a were 18.18% (2/11), 42.42%, 52.38%, 48.21%, and 44.89%, respectively. Multivariate logistic regression analysis showed no significant effects from sex, age, transmission route, geographical region, baseline CD4 + T cell count or subgenotype (P > 0.05), except marital status. Married or cohabiting people (compared with unmarried people) had more difficulty forming transmission networks. Conclusions In summary, this study, based on HCV NS5B subgenotypes, revealed the HCV subtype diversity and distribution among HIV/HCV-coinfected patients in Guangdong. Marital status inclined to be the factor influencing HCV transmission networks formation.
 
Background Bovine parainfluenza virus type 3 (BPIV3) infection often causes respiratory tissue damage and immunosuppression and further results in bovine respiratory disease complex (BRDC), one of the major diseases in dairy cattle, caused huge economical losses every year. However, the pathogenetic and immunoregulatory mechanisms involved in the process of BPIV3 infection remain unknown. However, the pathogenetic and immunoregulatory mechanisms involved in the process of BPIV3 infection remain unknown. Proteomics is a powerful tool for high-throughput identification of proteins, which has been widely used to understand how viruses interact with host cells. Methods In the present study, we report a proteomic analysis to investigate the whole cellular protein alterations of MDBK cells infected with BPIV3. To investigate the infection process of BPIV3 and the immune response mechanism of MDBK cells, isobaric tags for relative and absolute quantitation analysis (iTRAQ) and Q-Exactive mass spectrometry-based proteomics were performed. The differentially expressed proteins (DEPs) involved in the BPIV3 invasion process in MDBK cells were identified, annotated, and quantitated. Results A total of 116 proteins, which included 74 upregulated proteins and 42 downregulated proteins, were identified as DEPs between the BPIV3-infected and the mock-infected groups. These DEPs included corresponding proteins related to inflammatory response, immune response, and lipid metabolism. These results might provide some insights for understanding the pathogenesis of BPIV3. Fluorescent quantitative PCR and western blotting analysis showed results consistent with those of iTRAQ identification. Interestingly, the upregulated protein MKK3 was associated with the p38 MAPK signaling pathway. Conclusions The results of proteomics analysis indicated BPIV3 infection could activate the p38 MAPK pathway to promote virus replication.
 
HBV preS region nucleotide entropy of CHB and HCC patients. A. Heat map show the nucleotide entropy in preS region of CHB and HCC patients. B. Comparison of nucleotide entropy in preS, preS1 and preS2 region between in CHB and HCC patients. C. Nucleotide points in preS region with different entropy between in CHB and HCC patients were described by volcano plot filtering. Entropy of all the nucleotide points in preS region were compared between in CHB and HCC patients. After logarithm, the p-values were presented in the y-lab direction. In the x-lab direction, the relative entropy ratios of CHB and HCC patients were also log-transformed and presented. Red spots represented nucleotide points with higher entropy in CHB patients, of which p-values and fold changes were upon specific threshhold. The green spots mean nucleotide points with opposite conditions
Classification results for HCC/CHB patients using SLR with different parameters. Classification results (accuracy, AUC, sensitivity and specificity) for all HCC/CHB patients as a function of penalization parameter λ in sparse logistic regression. The vertical lines show one SD in the CV studies
Comparison of entropy of the ten nucleotide points of HBV preS region selected by SLR model. Ten nucleotide points of HBV preS region were selected by SLR model for CHB/HCC classification and entropy between in CHB and HCC patients were compared. All of the ten nucleotide points showed significant divergence between in CHB and HCC patients
Classification results for HCC/CHB patients using SLR with different sample size. The vertical lines show one SD in the cross validation studies
Nucleotide and amino acid mapping for the identified mutation points. Functions of ten nucleotide points of HBV preS region selected by SLR model for CHB/HCC classification are also denoted
Background Chronic infection with hepatitis B virus (HBV) has been proved highly associated with the development of hepatocellular carcinoma (HCC). Aims The purpose of the study is to investigate the association between HBV preS region quasispecies and HCC development, as well as to develop HCC diagnosis model using HBV preS region quasispecies. Methods A total of 104 chronic hepatitis B (CHB) patients and 117 HBV-related HCC patients were enrolled. HBV preS region was sequenced using next generation sequencing (NGS) and the nucleotide entropy was calculated for quasispecies evaluation. Sparse logistic regression (SLR) was used to predict HCC development and prediction performances were evaluated using receiver operating characteristic curves. Results Entropy of HBV preS1, preS2 regions and several nucleotide points showed significant divergence between CHB and HCC patients. Using SLR, the classification of HCC/CHB groups achieved a mean area under the receiver operating characteristic curve (AUC) of 0.883 in the training data and 0.795 in the test data. The prediction model was also validated by a completely independent dataset from Hong Kong. The 10 selected nucleotide positions showed significantly different entropy between CHB and HCC patients. The HBV quasispecies also classified three clinical parameters, including HBeAg, HBVDNA, and Alkaline phosphatase (ALP) with the AUC value greater than 0.6 in the test data. Conclusions Using NGS and SLR, the association between HBV preS region nucleotide entropy and HCC development was validated in our study and this could promote the understanding of HCC progression mechanism.
 
PRISMA study selection flow diagram of included studies for analysis
Forest plot of pooled prevalence of NoV among individuals with gastroenteritis in Africa: The pooled prevalence represented by the X-axis, and the list of included papers represented by Y-axis, The red line represents the minimum possible prevalence value (0). The dashed line represents the mean pooled NoV prevalence estimate. The gray box represents the weight of each study contributing to the pooled prevalence estimate. The black dot at the center of the gray box represents the point prevalence estimate of each study and the horizontal line indicates the 95% confidence interval for estimates of each study. The blue diamond represents the 95% confidence interval of the pooled NoV prevalence estimate
GII NoVs among all eleven molecularly characterized samples: The pooled prevalence GII NoVs had been represented by the X-axis, and the list of included papers represented by Y-axis, The bold vertical line represents the minimum possible prevalence value (0). The dashed line represents the mean pooled GII NoV prevalence estimate. The gray box represents the weight of each study contributing to the pooled prevalence estimate. The black dot at the center of the gray box represents the point prevalence estimate of each study and the horizontal line indicates the 95% confidence interval for estimates of each study. The blue diamond represents the 95% confidence interval of the pooled GII NoV prevalence estimate
The distribution of NoV genotypes in Africa: The GII.4 is the leading among all the eleven molecularly characterized samples in our review which is followed by GII.6, GII.17. GI.3, GII.2, and others
Funnel plot symmetry to check the presence or absence of publication bias: left The pooled prevalence of NoVs in Africa from studies reporting between 2015 to 2021; right Egger’s publication bias plot. Each dot represents individual studies. The x-axis represents precision (reciprocal of the standard error of the estimate). The y-axis represents log transformed standardized effect (estimate divided by its standard error)
Background Noroviruses are the leading cause of acute gastroenteritis in all age groups globally. The problem is magnified in developing countries including Africa. These viruses are highly prevalent with high genetic diversity and fast evolution rates. With this dynamicity, there are no recent review in the past five years in Africa. Therefore, this review and meta-analysis aimed to assess the prevalence and genetic diversity of noroviruses in Africa and tried to address the change in the prevalence and genetic diverisity the virus has been observed in Africa and in the world. Methods Twenty-one studies for the pooled prevalence, and 11 out of the 21 studies for genetic characterization of norovirus were included. Studies conducted since 2006, among symptomatic cases of all age groups in Africa, conducted with any study design, used molecular diagnostic methods and reported since 2015, were included and considered for the main meta-analysis. PubMed, Cochrane Library, and Google Scholar were searched to obtain the studies. The quality the studies was assessed using the JBI assessment tool. Data from studies reporting both asymptomatic and symptomatic cases, that did not meet the inclusion criteria were reviewed and included as discussion points. Data was entered to excel and imported to STATA 2011 to compute the prevalence and genetic diversity. Heterogeneity was checked using I² test statistics followed by subgroup and sensitivity analysis. Publication bias was assessed using a funnel plot and eggers test that was followed by trim and fill analysis. Result The pooled prevalence of norovirus was 20.2% (95% CI: 15.91, 24.4). The highest (36.3%) prevalence was reported in Ghana. Genogroup II noroviruses were dominant and reported as 89.5% (95% CI: 87.8, 96). The highest and lowest prevalence of this genogroup were reported in Ethiopia (98.3%), and in Burkina Faso (72.4%), respectively. Diversified genotypes had been identified with an overall prevalence of GII. 4 NoV (50.8%) which was followed by GII.6, GII.17, GI.3 and GII.2 with a pooled prevalence of 7.7, 5.1, 4.6, and 4.2%, respectively. Conclusion The overall pooled prevalence of norovirus was high in Africa with the dominance of genogroup II and GII.4 genotype. This prevalence is comparable with some reviews done in the same time frame around the world. However, in Africa, an in increasing trained of pooled prevalence had been reported through time. Likewise, a variable distribution of non-GII.4 norovirus genotypes were reported as compared to those studies done in the world of the same time frame, and those previous reviews done in Africa. Therefore, continuous surveillance is required in Africa to support future interventions and vaccine programs.
 
Background The H9N2 virus can infect not only birds but also humans. The pathogenicity of H9N2 virus infection is determined by an excessive immune response in the lung. All-trans retinoic acid (ATRA), the active metabolite of vitamin A, plays an important regulatory role and has been widely used in the clinical practice. This study was aimed to investigate whether ATRA could regulate the immune response to H9N2 virus infection in the lungs of mice, thereby reducing the pathogenicity of the H9N2 virus in mice. Methods Mice were infected intranasally with H9N2 virus, and injected intraperitoneally with 0.2 mL of ATRA at low (1 mg/kg), medium (5 or 10 mg/kg), or high therapeutic dose (20 mg/kg), and toxic dose (40, 60, or 80 mg/kg), once per day for 10 days. Clinical signs, survival rates, and lung gross pathology were compared between the ATRA-treated H9N2-infected group, the ATRA group, and the H9N2-infected group, to investigate the effect of different doses of ATRA on the pathogenicity of H9N2 virus. Additionally, the viral load and cytokine concentration of lungs were measured at 3, 5, 7, and 9 days after infection, to investigate the potential mechanism of ATRA in affecting the pathogenicity of the H9N2 virus. Expression levels of cellular retinoic acid-binding protein 1 (CRABP1), cellular retinoic acid-binding protein 2 (CRABP2), and Retinoic acid-inducible gene-I (RIG-I) were detected using Western blotting. Results The ATRA-treated H9N2-infected mice showed more severe clinical signs compared with the H9N2-infected group. The medium and high therapeutic doses of ATRA reduced the survival rates, aggravated lung tissue damage, decreased the expression of interferon beta (IFN-β), and increased the concentrations of interleukin-1 beta (IL-1β), tumor necrosis factor alpha (TNF-α), and C-C motif chemokine ligand 2 (CCL2) in the lungs of the H9N2-infected mice. At the same time, the expression patterns of CRABP1, CRABP2, and RIG-I were changed in mice infected by H9N2 and treated with different concentrations of ATRA. Conclusions Our findings suggest that the therapeutic dose of ATRA can increase the pathogenicity of the H9N2 virus. Therefore, the consequences of those infected by influenza virus would be more severe after ATRA treatment.
 
Background Hepatitis B virus can induce hepatocellular carcinoma (HCC) by inducing a host immune response against infected hepatocytes. C-terminally truncated middle surface protein (MHBSt) has been reported to contribute to HCC through transcriptional activation in epidemiology studies, while the underlying mechanism of MHBSt-induced HCC is unknown. Methods In this study, a premature stop at codon 167 in MHBS (MHBSt¹⁶⁷) was investigated into eukaryotic expression plasmid pcDNA3.1(-). MHBSt¹⁶⁷ expressed plasmid was transfected into the L02 cell line, cell proliferation was analyzed by CCK-8 and high-content screening assays, the cell cycle was analyzed by flow cytometry, and epithelial-to-mesenchymal transition and autophagy were analyzed by immunoblotting and immunofluorescence. NF-κB activation and the MHBSt¹⁶⁷-induced immune response were analyzed by immunoblotting and immunofluorescence. IFN-α, IFN-β and IL-1α expression were analyzed by qPCR. Autophagy inhibitors were used to analyze the relationship between the immune response and autophagy. Results The results showed that MHBSt¹⁶⁷ promoted L02 cell proliferation, accelerated cell cycle progression from the S to G2 phase and promoted epithelial-to-mesenchymal transition through ER-stress, leading to autophagy and NF-κB activation and increased immune-related factor expression. The MHBSt¹⁶⁷-induced acceleration of cell proliferation and the cell cycle was abolished by autophagy or NF-κB inhibitors. Conclusion In summary, MHBSt¹⁶⁷ could promote cell proliferation, accelerate cell cycle progression, induce EMT and activate autophagy through ER-stress to induce the host immune response, supporting a potential role of MHBSt¹⁶⁷ in contributing to carcinogenesis.
 
Background Betanodaviruses, members of the Nodaviridae family, are the causative agents of viral nervous necrosis in fish, resulting in great economic losses worldwide. Methods In this study, we isolated a virus strain named seahorse nervous necrosis virus (SHNNV) from cultured big-belly seahorses Hippocampus abdominalis in Xiamen city, Fujian Province, China. Virus isolation, PCR detection, phylogenetic analysis, qRT-PCR, fluorescence in situ hybridization and histology were used for virus identification and analysis of virus histopathology. Furthermore, an artificial infection experiment was conducted for virulence testing. Results Brain and eye tissue homogenates of diseased big-belly seahorses were inoculated onto a grouper spleen (GS) cell monolayer at 28 °C. Tissue homogenates induced obvious cytopathic effects in GS cells. PCR and sequencing analyses revealed that the virus belonged to Betanodavirus and shared high sequence identity with red-spotted grouper nervous necrosis virus isolates. qRT-PCR and fluorescence in situ hybridization revealed that SHNNV mainly attacked the brain and eye. Histopathological examination revealed that the virus led to cytoplasmic vacuolation in the brain and retinal tissues. Infection experiments confirmed that SHNNV was highly infectious, causing massive death in big-belly seahorses. Conclusion A novel seahorse betanodavirus from the big-belly seahorse cultured in China was discovered. This finding will contribute to the development of efficient strategies for disease management in aquaculture.
 
Background Duck hepatitis A virus type 1 (DHAV-1) is one of the most serious pathogens endangering the duck industry. However, there are few studies on the regulation of the cell cycle by DHAV-1. Methods In this study, flow cytometry was applied to analyze the effect of DHAV-1 infection on the cell cycle of duck embryo fibroblasts (DEFs). Subsequently, we analyzed the effects of cell cycle phases on DHAV-1 replication by real-time reverse transcriptase quantitative PCR (real-time RT-qPCR). Results Flow cytometry data analysis found that DEFs in the S phase increased by 25.85% and 54.21% at 24 h and 48 h after DHAV-1 infection, respectively. The levels of viral RNA detected by real-time RT-qPCR were higher in the DEFs with synchronization in the S phase or G0/G1 phase than in the control group. However, there was no difference in viral copy number between the G2/M phase arrest and control groups. In addition, non-structural protein 3D of DHAV-1 significantly increased cells in the S phase, indicating that 3D protein is one of the reasons for the cell cycle arrest in the S phase. Conclusions In summary, DHAV-1 infection induces the cell cycle arrest of DEFs in the S phase. Both S phase and G0/G1 phase synchronization facilitate the replication of DHAV-1, and 3D protein is one of the reasons for the S phase arrest.
 
Top-cited authors
Burtram Clinton Fielding
  • University of the Western Cape
Eric Bergeron
  • Centers for Disease Control and Prevention
Nabil G Seidah
  • Institut de recherches cliniques de Montréal
Suzanne Benjannet
  • Institut de recherches cliniques de Montréal
Dewald Schoeman
  • University of the Western Cape