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Maximum-likelihood phylogenetic tree of SARS-CoV-2 whole-genome sequences of Lambda (lineage C.37). Tips are colored by region and clades with Argentine genomes are highlighted by grey rectangles. Nonsynonymous mutations associated with one or more of the Argentine clades are shown at the bottom of the rectangles. B.1.1.1 sequences were used as the outgroup. The SH-like/UFB values for the relevant groups are indicated for some groups. UFB: ultrafast bootstrap. The scale indicates the number of substitutions per site.
Source publication
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...
Citations
... Colombia was the main origin of Lambda lineages circulating in Central America, which might be related to the dominance of Lambda in the country's Pacific region 24 , and the whole Mu epidemic, originating from Colombia, was much more effective in spreading towards the north than to the south. Argentina and Chile were also observed as important routes of Lambda spreading towards the Caribbean and Mexico, which agreed with previous studies investigating the Lambda epidemic wave in these two countries 25,26 . Another identified pattern that emerged within South America is the preferential viral migration among neighboring countries located in the western side (Colombia, Ecuador, and Peru) or the eastern side (Brazil, Argentina, Paraguay, and Uruguay) of the Andes; while Chile, Bolivia and Venezuela seem to be strongly connected with both sides. ...
Latin America and Caribbean (LAC) regions were an important epicenter of the COVID-19 pandemic and SARS-CoV-2 evolution. Through the COVID-19 Genomic Surveillance Regional Network (COVIGEN), LAC countries produced an important number of genomic sequencing data that made possible an enhanced SARS-CoV-2 genomic surveillance capacity in the Americas, paving the way for characterization of emerging variants and helping to guide the public health response. In this study we analyzed approximately 300,000 SARS-CoV-2 sequences generated between February 2020 and March 2022 by multiple genomic surveillance efforts in LAC and reconstructed the diffusion patterns of the main variants of concern (VOCs) and of interest (VOIs) possibly originated in the Region. Our phylogenetic analysis revealed that the spread of variants Gamma, Lambda and Mu reflects human mobility patterns due to variations of international air passenger transportation and gradual lifting of social distance measures previously implemented in countries. Our results highlight the potential of genetic data to reconstruct viral spread and unveil preferential routes of viral migrations that are shaped by human mobility patterns.
... 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.
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.
