SARS-CoV-2 variants, immune escape, and countermeasures

Frontiers of Medicine, Journal Year: 2022, Volume and Issue: 16(2), P. 196 - 207

Published: March 6, 2022

Language: Английский

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ViralFlow: A Versatile Automated Workflow for SARS-CoV-2 Genome Assembly, Lineage Assignment, Mutations and Intrahost Variant Detection

Viruses, Journal Year: 2022, Volume and Issue: 14(2), P. 217 - 217

Published: Jan. 23, 2022

The COVID-19 pandemic is driven by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) that emerged in 2019 and quickly spread worldwide. Genomic surveillance has become the gold standard methodology used to monitor study this fast-spreading virus its constantly emerging lineages. current deluge of SARS-CoV-2 genomic data generated worldwide put additional pressure on urgent need for streamlined bioinformatics workflows. Here, we describe a workflow developed our group process analyze large-scale Illumina amplicon sequencing data. This automates all steps reference-based analysis: processing, genome assembly, PANGO lineage assignment, mutation analysis screening intrahost variants. pipeline capable processing batch around 100 samples less than half an hour personal laptop or five minutes server with 50 threads. presented here available through Docker Singularity images, allowing implementation laptops small-scale analyses high capacity servers clusters. Moreover, low requirements memory CPU cores standardized results provided ViralFlow highlight it as versatile tool analysis.

Language: Английский

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Punt Politics as Failure of Health System Stewardship: Evidence from the COVID-19 Pandemic Response in Brazil and Mexico

The Lancet Regional Health - Americas, Journal Year: 2021, Volume and Issue: 4, P. 100086 - 100086

Published: Sept. 27, 2021

We present a new concept, Punt Politics, and apply it to the COVID-19 non-pharmaceutical interventions (NPI) in two epicenters of pandemic: Mexico Brazil. Politics refers national leaders federal systems deferring or deflecting responsibility for health decision-making sub-national entities without evidence coordination. The fragmentation authority overlapping functions federal, decentralized political make them more susceptible coordination problems than centralized, unitary systems. concept pandemics, which require system stewardship, using NPI data that we developed curated through Observatory Containment Americas illustrate Both countries suffer from protracted, high levels mortality inadequate pandemic responses, including little testing disregard scientific evidence. how populist leadership drove partisan politics contributed disabling an evidence-based response These cases combination decentralization is most conducive punting responsibility. discuss reduces functionality, providing lessons other future vaccine rollout.

Language: Английский

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Effectiveness of CoronaVac among healthcare workers in the setting of high SARS-CoV-2 Gamma variant transmission in Manaus, Brazil: A test-negative case-control study

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2021, Volume and Issue: unknown

Published: April 7, 2021

Abstract Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant, Gamma, emerged in the city of Manaus late 2020 during a large resurgence disease (COVID-19), and has spread throughout Brazil. The effectiveness vaccines settings with widespread Gamma variant transmission not been reported. Methods We performed matched test-negative case-control study to estimate an inactivated vaccine, CoronaVac, healthcare workers (HCWs) Manaus, where accounted for 86% genotyped SARS-CoV-2 samples at peak its epidemic. early analysis following administration least one vaccine dose two-dose schedule. primary outcome was symptomatic infection. Findings For at-least-one-dose analyses population was, respectively, 53,176 53,153 HCWs residing aged 18 years or older, complete information on age, residence, vaccination status. Among eligible analysis, 47,170 (89%) received CoronaVac 2,656 individuals (5%) underwent RT-PCR testing from 19 January, 2021 13 April, 2021. Of 3,195 tests, 885 (28%) were positive. 393 418 case- control pairs selected analyses, calendar time, neighbourhood. those who had both doses before sample collection date, average time second date 14 days (IQR 7-24). In associated 0.50-fold reduction (adjusted (VE), 49.6%, 95% CI 11.3 71.4) odds infection period more after receiving first dose. However, we estimated low VE 36.8%, -54.9 74.2) schedule against A finding that vaccinated much likely be infected than unvaccinated 0-13 (aOR 2.11, 1.36-3.27) suggests unmeasured confounding led downward bias estimate. Interpretation Evidence this mixed, affected by setting. Administration showed setting epidemic transmission. underscores need maintain non-pharmaceutical interventions while campaigns are being implemented. Funding Fundação Oswaldo Cruz (Fiocruz); Municipal Health Secretary Research Context searched PubMed articles published inception pandemic until April 3, 2021, no language restrictions, using search terms “P.1” AND “vaccine” “SARS-CoV-2”. Additionally, “CoronaVac” Early studies have found plasma convalescent COVID-19 patients sera reduced neutralisation P.1, compared strains isolated earlier pandemic. Pfizer BNT162b2 mRNA, Oxford-AstraZeneca ChAdOx1, only which such data date. No reported any reducing risk among exposed P.1 high Added value This finds 49.4% (95% 13.2 71.9) effective preventing prevalence Variant Concern. underpowered failed find significant (estimated 37.1%, -53.3 74.2). Implications all available evidence These findings suggestive but must strengthened observational other populations. Based evidence, there is implement sustained even as continue.

Language: Английский

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The spike glycoprotein of SARS-CoV-2: A review of how mutations of spike glycoproteins have driven the emergence of variants with high transmissibility and immune escape

International Journal of Biological Macromolecules, Journal Year: 2022, Volume and Issue: 208, P. 105 - 125

Published: March 15, 2022

Language: Английский

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