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(a) Number of cases reported in Argentina from EW44/2021 to EW31/2022. Note that in EW15/2022 (between the third and the fourth waves), Argentina modified the COVID-19 massive testing criterion and since then, testing in public hospitals is only performed in populations under a higher risk for severe disease (>50 years or comorbidities). Data from https://ourworldindata.org/coronavirus#explore-the-global-situation, accessed on 1 December 2023. The arrows are colored according to the variant present at each moment of the wave. (b) Frequency of variant detection analyzed by epidemiological week, 2021–2022. Data from Spike and complete genome sequencing of samples from cases that did not present epidemiological link with travel (n = 3431).
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The COVID-19 pandemic has lately been driven by Omicron. This work aimed to study the dynamics of SARS-CoV-2 Omicron lineages during the third and fourth waves of COVID-19 in Argentina. Molecular surveillance was performed on 3431 samples from Argentina, between EW44/2021 and EW31/2022. Sequencing, phylogenetic and phylodynamic analyses were perfor...
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Citations
... Nevertheless, the findings contribute to our understanding of the Omicron variant's genomic dynamics In Argentina, the first wave of COVID-19 occurred between August and November 2020, followed by a second wave from March to July 2021 [38]. Prior research has indicated that the emergence of the BA.1 variant in our country in December 2021 initiated the third wave of COVID-19, leading to a surge in cases in mid-January 2022 and ultimately supplanting the Delta variant by the end of January 2022 [6]. This nationwide study analyzed samples from 14 provinces. ...
... This nationwide study analyzed samples from 14 provinces. However, Cordoba, the second most populated province of Argentina, was not included [6]. Our data concerning the emergence of BA.1, the displacement of Delta, and the fourth wave initiated by BA.2 coincide with those reported by these authors. ...
... Our data concerning the emergence of BA.1, the displacement of Delta, and the fourth wave initiated by BA.2 coincide with those reported by these authors. However, we detected the presence of genomes of BA.5 in RFUC in April 2021 before the emergence of BA.4 in May 2021, with samples from patients across different neighborhoods in Cordoba city (Figures 1 and 2), while the emergence of both lineages was reported as simultaneous in Argentina [6]. This spreading pattern was first observed in South Africa, where the BA.4/BA.5 Omicron variants were first detected. ...
Understanding the evolutionary patterns and geographic spread of SARS-CoV-2 variants, particularly Omicron, is essential for effective public health responses. This study focused on the genomic analysis of the Omicron variant in Cordoba, Argentina from 2021 to 2022. Phylogenetic analysis revealed the dominant presence of BA.1 and BA.2 lineages, with BA.5 emerging earlier than BA.4, aligning with observations from other regions. Haplotype network analysis showed significant genetic divergence within Omicron samples, forming distinct clusters. In comparison to global datasets, we identified mutations in the Omicron genomes (A27S, Y145D, and L212I) situated within the NTD region of the Spike protein. These mutations, while not widespread globally, showed higher prevalence in our region. Of particular interest were the Y145D and L212I substitutions, previously unreported in Argentina. In silico analysis revealed that both mutations impact the binding affinity of T-cell epitopes to HLA type I and II alleles. Notably, these alleles are among the most common in the Argentinian population, with some associated with protection against and others with susceptibility to SARS-CoV-2 infection. These findings strongly suggest that these prevalent mutations likely influence the immunogenicity of the Spike protein and contribute to immune evasion mechanisms. This study provides valuable insights into the genomic dynamics of the Omicron variant in Cordoba, Argentina and highlights unique mutations with potential implications for COVID-19 vaccines.
... SARS-CoV-2 have mutated significantly since their first discovery. Notably, Omicron variant strain is the most highly mutated variant and has become the most predominant epidemic strain worldwide (13,14). Therefore, in this study, we comparatively analyzed the epidemiological characteristics and transmission dynamics Reporting of six cases of aggregated outbreaks of COVID-19 caused by 5 strains in Nanjing. ...
Background
SARS-CoV-2 strains have been of great concern due to their high infectivity and antibody evasion.
Methods
In this study, data were collected on indigenous aggregated outbreaks in Nanjing from January 2020 to December 2022, caused by five strains including the original strain, the Delta variant, and the Omicron variant (BA.2, BA.5.2, and BF.7). The basic epidemiological characteristics of infected individuals were described and then parametric analysis of transmission dynamics was performed, including the calculation of incubation period, serial interval (SI), the basic reproductive number (R0), and the household secondary attack rate (HSAR). Finally, we compared the trends of transmission dynamic parameters of different strains.
Results
The incubation period for the original strain, the Delta variant, Omicron BA.2, Omicron BA.5.2, and Omicron BF.7 were 6 d (95% CI: 3.5–7.5 d), 5 d (95% CI: 4.0–6.0 d), 3 d (95% CI: 3.0–4.0 d), 3 d (95% CI: 3.0–3.0 d), and 2 d (95% CI: 2.0–3.0 d), respectively; Also, the SI of the five strains were 5.69 d, 4.79 d, 2.7 d, 2.12 d, and 2.43 d, respectively. Notably, the incubation period and SI of the five had both a progressive shortening trend (p < 0.001); Moreover, R0 of the five were 2.39 (95% CI: 1.30–4.29), 3.73 (95% CI: 2.66–5.15), 5.28 (95% CI: 3.52–8.10), 5.54 (95% CI: 2.69–11.17), 7.39 (95% CI: 2.97–18.76), with an increasing trend gradually (p < 0.01); HSAR of the five were 25.5% (95% CI: 20.1–31.7%), 27.4% (95% CI: 22.0–33.4%), 42.9% (95% CI: 34.3–51.8%), 53.1% (95% CI: 45.0–60.9%), 41.4% (95% CI, 25.5–59.3%), also with an increasing trend (p < 0.001).
Conclusion
Compared to the original strain, the incubation period and SI decreased while R0 and HSAR increased, suggesting that transmission in the population was faster and the scope of the population was wider. Overall, it’s crucial to keep implementing comprehensive measures like monitoring and alert systems, herd immunization plans, and outbreak control.
... The dynamic nature of COVID-19 pandemic is characterized by the emergence and succession of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, categorized as variants of concern (VOCs), variants of interest (VOIs), and, more recently, variants being monitored (VBM) (1)(2)(3)(4)(5). ...
Introduction
The declaration of the end of the Public Health Emergency for COVID-19 on May 11th, 2023, has shifted the global focus led by WHO and CDC towards monitoring the evolution of SARS-CoV-2. Augmenting these international endeavors with local initiatives becomes crucial to not only track the emergence of new variants but also to understand their spread. We present a cost-effective digital PCR-based pooled sample testing methodology tailored for early variant surveillance.
Methods
Using 1200 retrospective SARS-CoV-2 positive samples, either negative or positive for Delta or Omicron, we assessed the sensitivity and specificity of our detection strategy employing commercial TaqMan variant probes in a 1:9 ratio of variant-positive to variant-negative samples.Results: The study achieved 100% sensitivity and 99% specificity in 10-sample pools, with an Area Under the Curve (AUC) exceeding 0.998 in ROC curves, using distinct commercial TaqMan variant probes.
Results
Thematic analysis of the interviews identified three major challenges faced by public health officials in promoting vaccination: dissemination of misinformation in media, political polarization of COVID and its contribution to vaccine acceptance and COVID fatigue, and assessment of the risks associated with disease severity versus vaccine safety considering limited public health resources.
Discussion
The employment of two separate TaqMan probes for both Delta and Omicron establishes dual validation routes, emphasizing the method’s robustness. Although we used known samples to model realistic emergence scenarios of the Delta and Omicron variants, our main objective is to demonstrate the versatility of this strategy to identify future variant appearances. The utilization of two divergent variants and distinct probes for each confirms the method’s independence from specific variants and probes. This flexibility ensures it can be tailored to recognize any subsequent variant emergence, given the availability of its sequence and a specific probe. Consequently, our approach stands as a robust tool for tracking and managing any new variant outbreak, reinforcing our global readiness against possible future SARS-CoV-2 waves.
... Year Authors Summary points 2023 Torres, et al., [56] The dynamics of the third and fourth waves of variants of the Omicron strain of CVID-19 in ARG are studied, based on phylogenetic and phylodynamic sequencing analyses, concluding that the different propagation dynamics would be due to various factors such as decreased immunity and increased population reinforced with vaccination or immunity to previous strains. 2023 Zhao, et al., [57] This article investigates the relationship between the acceptance of the COVID-19 vaccine by people with chronic diseases and the factors that correlate with their disagreement with vaccination. ...
Many studies have been performed in different regions of the world as a result of the COVID-19 pandemic. In this work, we perform a statistical study related to the number of vaccinated cases and the number of deaths due to COVID-19 in ten South American countries. Our objective is to group countries according to the aforementioned variables. Once the groups of countries are built, they are characterized based on common properties of countries in the same group and differences between countries that are in different groups. Countries are grouped using principal component analysis and K-means analysis. These methods are combined in a single procedure that we propose for the classification of the countries. Regarding both variables, the countries were classified into three groups. Political decisions, availability of resources, bargaining power with suppliers and health infrastructure among others are some of the factors that can affect both the vaccination process and the timely care of infected people to avoid death. In general, the countries acted in a timely manner in relation to the vaccination of their citizens with the exception of two countries. Regarding the number of deaths, all countries reached peaks at some point in the study period.
... Compared to the reference sequence hCoV-19/Wuhan/WIV04/2019 (GISAID accession number EPI_ISL_402124), the 1263 genome sequences displayed a total of 1631 amino acid changes in different viral genes (912 in ORF1a/1b, 268 in S, 121 in N, 114 in ORF3a, 94 in ORF7a, 47 in ORF8, 28 in M, 18 in ORF6, 17 in ORF7b, and 12 in E). In the Argentine sequences, all the C.37 lineage defining amino acid changes [41], shown in grey in Figure 4A, were found at a frequency higher than 95.9%. ...
... The Lambda variant is characterized by multiple lineage-specific deletions and amino acid substitutions in its viral genome, as shown in Figure 4A [41]. Specifically, the spike protein of the Lambda variant has a unique pattern of eight mutations (G75V, T76I, R246N, ∆247-253, L452Q, F490S, D614G, and T859N). ...
The second wave of COVID-19 occurred in South America in early 2021 and was mainly driven by Gamma and Lambda variants. In this study, we aimed to describe the emergence and local genomic diversity of the SARS-CoV-2 Lambda variant in Argentina, from its initial entry into the country until its detection ceased. Molecular surveillance was conducted on 9356 samples from Argentina between October 2020 and April 2022, and sequencing, phylogenetic, and phylogeographic analyses were performed. Our findings revealed that the Lambda variant was first detected in Argentina in January 2021 and steadily increased in frequency until it peaked in April 2021, with continued detection throughout the year. Phylodynamic analyses showed that at least 18 introductions of the Lambda variant into the country occurred, with nine of them having evidence of onward local transmission. The spatial–-temporal reconstruction showed that Argentine clades were associated with Lambda sequences from Latin America and suggested an initial diversification in the Metropolitan Area of Buenos Aires before spreading to other regions in Argentina. Genetic analyses of genome sequences allowed us to describe the mutational patterns of the Argentine Lambda sequences and detect the emergence of rare mutations in an immunocompromised patient. Our study highlights the importance of genomic surveillance in identifying the introduction and geographical distribution of the SARS-CoV-2 Lambda variant, as well as in monitoring the emergence of mutations that could be involved in the evolutionary leaps that characterize variants of concern.
... Therefore, we used this approach to detect the presence of three different Omicron sub-variants, including BA.1.1 (20 out of 27 isolates), BA.2 (5 out of 27), and BA.5.2 (2 out of 27). Such distribution matches the Argentinean epidemiology map during the sampling time (Torres et al., 2023). However, further research is warranted, as whole-genome sequencing (WGS) of SARS-CoV-2 using next-generation sequencing (NGS) technology remains the gold standard for tracking and identifying new variants, especially Phylogenetic analysis was performed on 602-base-pair-long nucleotide sequences of the SARS-CoV-2 Spike gene using the Neighbor Joining method with 1,000 bootstrap replicates. ...
Introduction
Pulmonary and extrapulmonary manifestations have been described after infection with SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19). The virus is known to persist in multiple organs due to its tropism for several tissues. However, previous reports were unable to provide definitive information about whether the virus is viable and transmissible. It has been hypothesized that the persisting reservoirs of SARS-CoV-2 in tissues could be one of the multiple potentially overlapping causes of long COVID.
Methods
In the present study, we investigated autopsy materials obtained from 21 cadaveric donors with documented first infection or reinfection at the time of death. The cases studied included recipients of different formulations of COVID-19 vaccines. The aim was to find the presence of SARS-CoV-2 in the lungs, heart, liver, kidneys, and intestines. We used two technical approaches: the detection and quantification of viral genomic RNA using RT-qPCR, and virus infectivity using permissive in vitro Vero E6 culture.
Results
All tissues analyzed showed the presence of SARS-CoV-2 genomic RNA but at dissimilar levels ranging from 1.01 × 10² copies/mL to 1.14 × 10⁸ copies/mL, even among those cases who had been COVID-19 vaccinated. Importantly, different amounts of replication-competent virus were detected in the culture media from the studied tissues. The highest viral load were measured in the lung (≈1.4 × 10⁶ copies/mL) and heart (≈1.9 × 10⁶ copies/mL) samples. Additionally, based on partial Spike gene sequences, SARS-CoV-2 characterization revealed the presence of multiple Omicron sub-variants exhibiting a high level of nucleotide and amino acid identity among them.
Discussion
These findings highlight that SARS-CoV-2 can spread to multiple tissue locations such as the lungs, heart, liver, kidneys, and intestines, both after primary infection and after reinfections with the Omicron variant, contributing to extending knowledge about the pathogenesis of acute infection and understanding the sequelae of clinical manifestations that are observed during post-acute COVID-19.
... As determined by viral sequencing, the most prevalent variant detected in our study was Delta, followed by Omicron, Gamma and Lambda. Each variant was prevalent in the period of highest circulation in Buenos Aires city and surroundings, according to data from Argentina [3,4,34]. ...
... A study conducted in the United States showed that breakthrough infections with Omicron variant were more likely, even in subjects with a booster dose, probably due to immune escape [46]. Overall, variants found in our study were coincident to the most frequently circulating variants in the community at each time, regardless of the type of vaccine and vaccination status [4,34]. ...
During the pandemic of COVID-19, numerous waves of infections affected the two hemispheres with different impacts on each country. Throughout these waves, and with the emergence of new variants, health systems and scientists have tried to provide real-time responses to the complex biology of SARS-CoV-2, dealing with different clinical presentations, biological characteristics, and clinical impact of these variants. In this context, knowing the extent period in which an infected individual releases infectious viral particles has important implications for public health. This work aimed to investigate viral RNA shedding and infectivity of SARS-CoV-2 beyond 10 days after symptom onset (SO). A prospective multicenter study was performed between July/2021 and February/2022 on 116 immunized strategic personnel with COVID-19 diagnosed by RT-qPCR, with asymptomatic (7%), mild (91%) or moderate disease (2%). At the time of diagnosis, 70% had 2 doses of vaccines, 26% had 2 plus a booster, and 4% had one dose. After day 10 from SO, sequential nasopharyngeal swabs were taken to perform RT-qPCR, viral isolation, and S gene sequencing when possible. Viral sequences were obtained in 98 samples: 43% were Delta, 16% Lambda, 15% Gamma, 25% Omicron (BA.1) and 1% Non-VOC/VOI, in accordance with the main circulating variants at each moment. SARS-CoV-2 RNA was detected 10 days post SO in 57% of the subjects. Omicron was significantly less persistent. Noteworthy, infective viruses could not be isolated in any of the samples. In conclusion, a 10-days isolation period was useful to prevent further infections, and proved valid for the variants studied. Recently, even shorter periods have been applied, as the Omicron variant is prevalent, and worldwide population is largely vaccinated. In the future, facing the possible emergence of new variants and considering immunological status, a return to 10 days may be necessary.
... On the other hand, the dispersal of variants across political borders has become significantly faster since traveling restrictions went down, which could dilute the power of a single country being responsible for starting the spread to a whole continent [58]. The first identification of BA.1 in other South American countries occurred mostly in December 2022 while BA.2 was usually first detected in February 2022 [59][60][61], both later dates than the observed in Brazil. Still, it is difficult to precise the introduction dates and the routes of spread across the continent, or even if Brazil was the source of introduction, because some regions are severely undersampled in comparison to the number of COVID-19 cases per habitant. ...
Brazil currently ranks second in absolute deaths by COVID-19, even though most of its population has completed the vaccination protocol. With the introduction of Omicron in late 2021, the number of COVID-19 cases soared once again in the country. We investigated in this work how lineages BA.1 and BA.2 entered and spread in the country by sequencing 2173 new SARS-CoV-2 genomes collected between October 2021 and April 2022 and analyzing them in addition to more than 18,000 publicly available sequences with phylodynamic methods. We registered that Omicron was present in Brazil as early as 16 November 2021 and by January 2022 was already more than 99% of samples. More importantly, we detected that Omicron has been mostly imported through the state of São Paulo, which in turn dispersed the lineages to other states and regions of Brazil. This knowledge can be used to implement more efficient non-pharmaceutical interventions against the introduction of new SARS-CoV variants focused on surveillance of airports and ground transportation.
The COVID-19 pandemic has caused more than 690 million infections and more than 6.9 million deaths worldwide. Despite the rapid and successful development of several effective vaccines against this infection, variants with an increased ability to transmit and evade immunity conferred by previous infections or vaccines have emerged among viral lineages. There are five variants of concern (VOCs) of SARS-CoV-2 that have circulated, with the Omicron variant being the last and the one that displaced the previous ones. In addition to the VOCs, several variants of interest (VOIs) have been identified. The five VOCs were found to circulate in Latin America (LA), and one of them, the Gamma VOC, emerged in Brazil. Additionally, two VOIs emerged in the region: the Lambda VOI and the Mu VOI, which emerged in Peru and Colombia, respectively. The World Health Organization (WHO) recommended genomic surveillance of these variants through whole-genome sequencing. This surveillance has been carried out unevenly among different countries and geographical regions of the world. LA, accounting for 8% of the world population and almost 12% of the total COVID-19 reported cases, contributed to only 3.4% of the viral genomic sequences, and great variability was observed among different countries. However, some countries adopted alternative rapid strategies to effectively conduct genomic surveillance, such as real-time PCR using variant-specific probes, or partial viral genome sequencing. In conclusion, even with somehow limited sequencing capacities, the LA region could describe the emergence distribution and evolution of the SARS-CoV-2 variants in real time.
Since its discovery in 2019, SARS-CoV-2 still makes the headline news [...]
