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ABSTRACT: BACKGROUND: Pigs are well known source of human infectious disease. To better understand the spectrum of viruses present in pigs, we utilized the 454 Life Sciences GS-FLX high-throughput sequencing platform to sequence stool samples from healthy pigs. FINDINGS: Total nucleic acid was extracted from stool samples of healthy piglets and randomly amplified. The amplified materials were pooled and processed using a high-throughput pyrosequencing technique. The raw sequences were deconvoluted on the basis of the barcode and then processed through a standardized bioinformatics pipeline. The unique reads (348, 70 and 13) had limited similarity to known astroviruses, bocaviruses and parechoviruses. Specific primers were synthesized to assess the prevalence of the viruses in healthy piglets. Our results indicate extremely high rates of positivity. CONCLUSIONS: Several novel astroviruses, bocaviruses and Ljungan-like viruses were identified in stool samples from healthy pigs. The rates of isolation for the new viruses were high. The high detection rate, diverse sequences and categories indicate that pigs are well-established reservoirs for and likely sources of different enteric viruses.
Virology Journal 01/2013; 10(1):39. · 2.34 Impact Factor
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ABSTRACT: Using a high-throughput DNA sequencing method, one DNA sequence (contig01006), suspected to belong to a novel porcine bocavirus (PBoV), was found with a high rate of detection (19.6 %) in fecal samples from healthy piglets. Moreover, a novel PBoV (tentatively named PBoV3C) with a nearly complete genome sequence (5235 bp) was identified. PBoV3C exhibits typical genome characteristics of bocaviruses and shows the highest genomic sequence identity (78 % to 81 %) to PBoV3A/B (PBoV3/4-UK) and PBoV3D/E (PBoV3/4-HK), respectively. Phylogenetic and recombination analysis indicated high diversity, prevalence and complexity among the PBoVs. The phospholipase A2 (PLA2) site of VP1 and the secondary structure of VP2 of PBoV3C were also analyzed. Additionally, we propose a uniform method of PBoV nomenclature based on the VP1 gene.
Archives of Virology 07/2012; · 2.11 Impact Factor
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Yan Liu,
Zi-qian Xu,
Qing Zhang,
Miao Jin, Jie-mei Yu,
Jin-song Li,
Na Liu,
Shu-xian Cui,
Xiang-yu Kong,
Hong Wang,
Hui-ying Li,
Wei-xia Cheng,
Xue-jun Ma,
Zhao-jun Duan
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ABSTRACT: Rapid and broad diagnostic methods are needed for the identification of viral agents of gastroenteritis. In this study, we used Luminex xMAP technology to develop a multiplexed assay for the simultaneous identification of major enteric viral pathogens, including rotavirus A (RVA), noroviruses (NoVs) (including genogroups GI and GII), sapoviruses (SaV), human astrovirus (HAstV), enteric adenoviruses (EAds), and human bocavirus 2 (HBoV2). The analytical sensitivity allowed detection of 10(3) (EAds, HBoV2, and RVA) and 10(4) (NoV GI and GII, SaV, and HAstV) copies per reaction mixture. Compared to conventional PCR, the Luminex-based assay yielded greater than 75% sensitivity and 97% specificity for each virus, and the kappa correlation for detection of all viruses ranged from 0.75 to 1.00. In conclusion, this multiplexed Luminex-based assay provides a potentially rapid, high-throughput, and maneuverable diagnostic tool for major viral pathogens associated with gastroenteritis.
Journal of clinical microbiology 04/2012; 50(7):2384-9. · 4.16 Impact Factor
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ABSTRACT: Acute gastroenteritis (AGE) is one of the leading causes of death in children worldwide. Human bocavirus 2 (HBoV2) was recently identified in stool samples and is involved in the pathogenesis of AGE, but the current data were too limited to clarify this issue.
We conducted a case-control study on 632 children with diarrhea and 162 healthy controls in Lanzhou, China, to assess the role of HBoV2 in gastroenteritis.
Viruses known or suspected to be agents of AGE, including RV, HucV, AdV, AstV, and HBoVs, were detected. Viral loads of HBoV2 were quantified by Real-time PCR.
HBoV2 was detected in 129 (20.4%) and 20 (12.3%) of the gastroenteritis and control samples, respectively. The association between HBoV2 and gastroenteritis was weaker (OR = 1.269, CI= 0.704-2.288) than that between gastroenteritis and RV, HucV, AdV, or AstV, as determined by multivariate logistic regression analysis. The data also suggested that infection with HBoV2 did not exacerbate the clinical symptoms of gastroenteritis. Mean HBoV2 viral load in the case and control groups was fewer than 55 copies/ml extract.
HBoV2 exhibit different epidemiological features from HBoV1 and HBoV3. The data presented herein do not support a causative role for HBoV2 in AGE, despite its high prevalence in stool samples.
Journal of clinical virology: the official publication of the Pan American Society for Clinical Virology 09/2011; 52(3):251-3. · 3.12 Impact Factor
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ABSTRACT: A virus belonging to a new species in the genus Kobuvirus, family Picornaviridae, was first isolated in 2008 from apparently healthy pigs in Hungary and China. We report the complete genome sequence and the genetic organization of the novel porcine kobuvirus strain Y-1-CHI, which was identified in China. The RNA genome of strain Y-1-CHI contains 8210 nucleotides (nt) and has an organization similar to that of other picornaviruses. The full-length nucleotide sequence of Y-1-CHI was 88.62%, 58.66%, and 48.86% identical to those of S-1-HUN, U-1, and Aichi virus, respectively. No positive results were found in 454 stool samples from children with acute gastroenteritis. Dendrograms indicated that Y-1-CHI and S-1-HUN are most closely related to each other and belong to the same species. Our results suggest that members of this novel species have the typical genome characteristics of members of the genus Kobuvirus and may be distributed globally in swine.
Archives of Virology 01/2011; 156(5):747-51. · 2.11 Impact Factor
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ABSTRACT: Porcine sapoviruses (SaVs), which belong to the family Caliciviridae, have been considered potential zoonotic agents for human infection, and several cases have been reported in Asian countries. In this study, a total of 200 porcine fecal samples collected from Lulong county of China were tested. Among 200 samples, porcine sapoviruses were detected by RT-PCR in 17 samples (8.5%) showing their circulation in China. 14 out of 17 positive sapovirus strains were genetically related to the genogroup III (GIII) and were further divided into three different clusters or genotypes according to the phylogenetic analysis. In addition, the remaining three sapovirus strains belonged to GVII (one strain) and a potential novel genogroup (two strains) according to the phylogenetic analysis and the nucleotide identity and amino acid identity. These data suggested the genetic diversity of porcine sapoviruses in China.
Bing du xue bao = Chinese journal of virology / [bian ji, Bing du xue bao bian ji wei yuan hui] 05/2010; 26(3):255-9.
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ABSTRACT: From November 2008 to January 2009, a sharp increase of diarrhea in children in Guangdong province appeared, we randomly collected 53 stool specimens from out-patient children with dirrhea in 3 major hospitals (Guangzhou City Children's Hospital, Shenzhen Baoan District Maternal and Child Health Hospital, First Affiliated Hospital of Shantou University). Rotavirus and calicivirus were screened by ELISA and RT-PCR. We found 29 cases of rotavirus infection with diverse serotypes. Only four cases were identified as calicivirus infection. The result indicated that rotavirus was a major pathogen of this high incidence of diarrhea from November 2008 to January 2009 in Guangdong Province.
Bing du xue bao = Chinese journal of virology / [bian ji, Bing du xue bao bian ji wei yuan hui] 03/2010; 26(2):150-2.
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Jin-Song Li,
Wei-Xia Cheng,
Dong-Ping Yao,
Bei Lan, Jie-Mei Yu,
Yan Liu,
Yong-Qing Li,
Qing Zhang,
Miao Jin,
Zi-Qian Xu,
Dan-Di Li,
Zhao-Jun Duan
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ABSTRACT: To sequence the complete sequence of bocavirus I with sequence independent single primer amplification (SISPA-PCR).
To exclude the co-effection samples, all clinical samples of diarrhea cases were screened with special primers of rotavirus, astrovirus, adenovirus, calicivirus and bocavirus I. The virus were enriched through ultracentrifugation. Other nucleic acids, such as human and bacteria genomes, were degradated by DNase I and RNase. DNA of bocavirus was Amplificated with SISPA-PCR, then purificated, cloned and sequenced. The sequences were alighmented in nr with blastn and assembled with DNAstar.
A 4834bp sequence of bocavirus I were assembled.
SISPA-PCR is an economical and efficient technique for sequence a virus complete genome.
Zhonghua shi yan he lin chuang bing du xue za zhi = Zhonghua shiyan he linchuang bingduxue zazhi = Chinese journal of experimental and clinical virology 02/2010; 24(1):14-6.
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ABSTRACT: Rotavirus was detected in 52% of 2328 stool specimens collected from children with acute gastroenteritis admitted to three sentinel hospitals in Mainland China from January 2006 to December 2007. G3P[8] (42%) was the most common strain. Despite being common globally, only 18 (2%) G9-positive samples were identified. The VP7, VP4, VP6, and NSP4 genes were sequences for 13 of the G9 strains with G9P[8] being most common and showing the same origin as G9 strains reported in other countries. One G9P[6] strain was possibly derived by reassortment between earlier Chinese G9 strains and more recent local P[6] strains.
Vaccine 11/2009; 27 Suppl 5:F40-5. · 3.77 Impact Factor
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Jie-mei Yu,
Miao Jin,
Qing Zhang,
Hui-ying Li,
Dan-di Li,
Zi-qian Xu,
Jin-song Li,
Shu-xian Cui,
Su-hua Yang,
Na Liu,
Zhao-jun Duan
Emerging Infectious Diseases 06/2009; 15(5):823-5. · 6.79 Impact Factor
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Dong-liang Zhang,
Qing Zhang,
Dan-di Li,
Wei-xia Cheng,
Zi-qian Xu,
Miao Jin, Jie-mei Yu,
Lin Zhu,
Shu-xian Cui,
Pei-zhen Li,
Zhao-jun Duan
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ABSTRACT: To detect human parechovirus (HPeV) from stool samples of hospitalized children for acute gastroenteritis of undetectable etiology.
We conducted a real-time PCR to detect HPeV.
The results showed that 24 of 99 (24%) children with gastroenteritis of undetectable etiology were detected with HPeV. Four known HPeV types (HPeV1, 3, 4, 6) were detected in the present study. HPeV1 (50%) was frequently identified as the predominant strain and follow by HPeV3 (25%), HPeV4 (8.3%) and HPeV6 (4.2%). We were unable to type 3 samples.
HPeV was prevalent in hospitalized children for acute gastroenteritis of undetectable etiology in China. Further study is needed for clarifying the role of HPeV in gastroenteritis.
Zhonghua shi yan he lin chuang bing du xue za zhi = Zhonghua shiyan he linchuang bingduxue zazhi = Chinese journal of experimental and clinical virology 04/2009; 23(2):112-4.
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Yu Jin,
Wei-xia Cheng,
Xue-mei Yang,
Miao Jin,
Qing Zhang,
Zi-qian Xu, Jie-mei Yu,
Lin Zhu,
Su-hua Yang,
Na Liu,
Shu-xian Cui,
Zhao-yin Fang,
Zhao-jun Duan
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ABSTRACT: Gastroenteritis is a major cause of childhood morbidity and mortality worldwide. Rotavirus, human caliciviruses (HucV), adenovirus, and astrovirus are recognized as common etiologies of acute gastroenteritis.
To use antigen detection and molecular methods to determine the viral etiology of childhood diarrhea in Lanzhou, China, 2005-2007.
544 stool specimens were collected from children hospitalized with diarrhea. ELISA, RT-PCR, or PCR were used to detect viruses commonly causing diarrhea.
Group A rotavirus, norovirus, sapovirus, astrovirus, and adenovirus, were detected in 54.0%, 9.2%, 1.1%, 3.3%, and 4.4%, respectively. No group B or group C rotaviruses were detected. The relative contribution of these viruses changed greatly over 2 years. The percentage of rotavirus and adenovirus dropped from 61.2% and 5.4% to 47.6% and 1.4%, whereas HucV increased from 5.0% to 15.0%. G1 and P[8] were the predominant rotavirus strains, and P[6] was detected for the first time in this area. The predominant norovirus strain changed from GII3 to GII4, and the subtypes of GII4 changed from the Hunter strain to the variant 2006b strain.
The distribution of viruses and genotypes of individual viruses causing gastroenteritis in Lanzhou, China changed greatly during 2005-2007.
Journal of clinical virology: the official publication of the Pan American Society for Clinical Virology 03/2009; 44(3):238-41. · 3.12 Impact Factor
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Miao Jin,
Hua-ping Xie,
Zhao-jun Duan,
Na Liu,
Qing Zhang,
Bing-shan Wu,
Hui-ying Li,
Wei-xia Cheng,
Su-hua Yang, Jie-mei Yu,
Zi-qian Xu,
Shu-xian Cui,
Lin Zhu,
Ming Tan,
Xi Jiang,
Zhao-yin Fang
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ABSTRACT: Noroviruses are an important cause of acute gastroenteritis. Increasing data showed that the GII-4 strains are predominant worldwide and new GII-4 variants emerge every 1-2 years causing major epidemics. Surveillance of gastroenteritis in hospitalized children under 5 years of age in China is described. Among 1,110 specimens, 114 (10.3%) were positive for noroviruses, which was higher than adenoviruses (7.6%), astroviruses (3.5%), and sapoviruses (0.9%) and only lower than group A rotaviruses (40.6%). Thirty-eight of the 114 positive norovirus cases were co-infected with other enteric viruses. Five norovirus genotypes (GI-2, GI-4, GII-3, GII-4, and GII-14) were detected, with GII-4/2006b the most predominant type (64.9%). The reported recombinant of GII-3 capsid and GII-4 polymerase described previously was also detected frequently and a recombinant of GII-14 capsid and GII-6 polymerase was found for the first time. This study suggests that continual surveillance focusing on strain variation and dynamic change is important for understanding the epidemiology and development of a strategy for disease control and prevention.
Journal of Medical Virology 10/2008; 80(11):1997-2004. · 2.82 Impact Factor
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Wei-xia Cheng,
Yu Jin,
Zhao-jun Duan,
Zi-qian Xu,
Hong-mei Qi,
Qing Zhang, Jie-mei Yu,
Lin Zhu,
Miao Jin,
Na Liu,
Shu-xian Cui,
Hui-ying Li,
Zhao-yin Fang
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ABSTRACT: Human bocavirus (HBoV) was recently discovered in children with respiratory tract disease and gastroenteritis. The causative role of HBoV in human gastroenteritis remains uncertain, and, to our knowledge, no previous case-control study has studied the relationship between HBoV and gastroenteritis.
We conducted a case-control study that examined stool samples from 397 children with diarrhea and from 115 asymptomatic control subjects. HBoV was detected using polymerase chain reaction. Real-time polymerase chain reaction was used to quantify the HBoV loads in case and control groups. Common enteric viruses were examined using enzyme-linked immunosorbent assays, polymerase chain reaction, and reverse-transcription polymerase chain reaction.
At least 1 viral agent was discovered in 60.2% of cases. HBoV was detected in 14 samples, and 9 were coinfected with either rotavirus (7 of 14 samples) or human calicivirus (2 of 14). Many (8 [57.1%] of 14) of the HBoV infections occurred during September-December 2006. Most (12 [85.7%]) of the HBoV-infected children were 7-18 months of age. The percentage of children with HBoV infection did not differ significantly between case patients and control subjects (3.5% vs. 3.5%), and the statistical analysis did not support a correlation between HBoV infection and more-severe clinical symptoms. The viral load differences between the 2 groups were not statistically significant (P = .09, by log-normal Student's t test). In addition, the VP1/VP2 partial gene of HBoV from case patients and control subjects showed minimal sequence variation.
A single genetic lineage of HBoV was revealed in persons in China. Despite its high prevalence in stool samples, our study does not support a causative role of HBoV in gastroenteritis.
Clinical Infectious Diseases 08/2008; 47(2):161-7. · 9.15 Impact Factor
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Jie-Mei Yu,
Dan-Di Li,
Zi-Qian Xu,
Wei-Xia Cheng,
Qing Zhang,
Hui-Ying Li,
Shu-Xian Cui,
Miao-Jin,
Su-Hua Yang,
Zhao-Yin Fang,
Zhao-Jun Duan
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ABSTRACT: Human bocavirus (HBoV) was first identified in children with acute respiratory-tract infections, but recent studies have revealed that HBoV is also frequently detected in fecal specimens from children with gastroenteritis.
To investigate the prevalence of HBoV in children hospitalized with gastroenteritis in different areas of China.
Employing ELISA, RT-PCR or PCR, we evaluated 1216 fecal samples for common diarrheal agents from children aged less than 5-year-old hospitalized with acute gastroenteritis. MEGA software was used to construct phylogenetic trees of the VP1/VP2 partial sequences of the HBoV genome.
There were 67 HBoV-positive specimens, 52 (77.6%) were co-infected with rotavirus, norovirus, astrovirus, or enteric adenovirus. Statistical analysis of the clinical data indicated that children infected with both rotavirus and bocavirus did not have more severe clinical symptoms than children infected with rotavirus. The phylogenetic analysis of the VP1/VP2 partial sequences of the HBoV genome revealed a single genetic lineage.
Despite its high infection rate, there was no statistically significant a causual relationship between HBoV and gastroenteritis in children.
Journal of Clinical Virology 08/2008; 42(3):280-5. · 3.97 Impact Factor
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Dan-Di Li,
Shu-Xian Cui,
Qing Zhang,
Miao Jin, Jie-Mei Yu,
Dong-Liang Zhang,
Zi-Qian Xu,
Jing-Yu Tang,
Zhong Shan Wang,
Zhao-Yin Fang,
Zhao-Jun Duan
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ABSTRACT: Two Rotavirus G9P[8] strains (LL52696 and LL52727) were recognized during a sentinel-based survey in Lulong, China. Phylogenetic analysis of the VP7 gene showed that both strains isolated constituted a divergent genetic cluster distinct from the other G9 strains isolated in China. Analysis of VP4, VP6, and NSP4 genes revealed that these strains were closely related to Lulong strains. We hold that two strains were reassortant between G9 and Lulong predominant strains.
Bing du xue bao = Chinese journal of virology / [bian ji, Bing du xue bao bian ji wei yuan hui] 07/2008; 24(2):144-7.
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Dan-Di Li, Jie-Mei Yu,
Shu-Xian Cui,
Qing Zhang,
Xin-Hui Yuan,
Dong-liang Zhang,
Da-jiang Cao,
Su-Hua Yang,
Hui-Ying Li,
Zhong-Shan Wang,
Zhao-Jun Duan
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ABSTRACT: VP6- and NSP4- encoding genes of human group A rotavirus strain LL3354 with rare genotypes (G5P[6]), detected from China Lulong, was characterized by reverse transcription-PCR followed by sequencing and phylogenetic analysis. LL3354 joins the major cluster of SGI rotaviruses in the VP6 phylogenetic tree, However, It was identified as NSP4 genotype B. Our results provide evidence for independent segregation of the VP6- and NSP4-encoding genes in human group A rotaviruses.
Bioinformatics and Biomedical Engineering, 2008. ICBBE 2008. The 2nd International Conference on; 06/2008
