The Evolution and Biology of SARS-CoV-2 Variants

Cold Spring Harbor Perspectives in Medicine, Journal Year: 2022, Volume and Issue: 12(5), P. a041390 - a041390

Published: April 20, 2022

Our understanding of the still unfolding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic would have been extremely limited without study genetics and evolution this new human coronavirus. Large-scale genome-sequencing efforts provided close to real-time tracking global spread diversification SARS-CoV-2 since its entry into population in late 2019. These data underpinned analysis origins, epidemiology, adaptations population: principally immune evasion increasing transmissibility. SARS-CoV-2, despite being a pathogen, was highly capable human-to-human transmission. During rapid humans, has evolved independent forms, so-called "variants concern," that are better optimized for The most important adaptation bat progenitor both SARS-CoV-1 infection (and other mammals) is use angiotensin-converting enzyme (ACE2) receptor. Relaxed structural constraints provide plasticity SARS-related spike protein permitting it accommodate significant amino acid replacements antigenic consequence compromising ability bind ACE2. Although bulk research justifiably concentrated on viral as main determinant changes transmissibility, there accumulating evidence contribution regions proteome virus-host interaction. Whereas levels community transmission recombinants genetically distinct variants at present low, when divergent cocirculate, recombination between clades detected, risk viruses with properties emerge. Applying computational machine learning methods genome sequence sets generate experimentally verifiable predictions will serve an early warning system novel variant surveillance be future vaccine planning. Omicron, latest concern, focused attention step change events, "shift," opposed incremental "drift" antigenicity. Both increase transmissibility shift Omicron led readily causing infections fully vaccinated and/or previously infected. Omicron's virulence, while reduced relative concern replaced, Delta, very much premised past exposure individuals clear signal boosted vaccination protects from disease. Currently, proven itself dangerous pathogen unpredictable evolutionary capacity, leading too great not ensure all world screened by sequencing, protected through available affordable vaccines, non-punitive strategies place detecting responding concern.

Language: Английский

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Recombination in Coronaviruses, with a Focus on SARS-CoV-2

Viruses, Journal Year: 2022, Volume and Issue: 14(6), P. 1239 - 1239

Published: June 7, 2022

Recombination is a common evolutionary tool for RNA viruses, and coronaviruses are no exception. We review here the evidence recombination in SARS-CoV-2 reconcile nomenclature recombinants, discuss their origin fitness, speculate how recombinants could make difference future of COVID-19 pandemics.

Language: Английский

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Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination

Med, Journal Year: 2022, Volume and Issue: 3(12), P. 848 - 859.e4

Published: Oct. 20, 2022

Language: Английский

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Real-time genomic surveillance for enhanced control of infectious diseases and antimicrobial resistance

Frontiers in Science, Journal Year: 2024, Volume and Issue: 2

Published: April 25, 2024

This article advocates for mobilizing pathogen genomic surveillance to contain and mitigate health threats from infectious diseases antimicrobial resistance (AMR), building upon successes achieved by large-scale genome sequencing analysis of SARS-CoV-2 variants in guiding COVID-19 monitoring public responses adopting a One Health approach. Capabilities laboratory-based epidemic alert systems should be enhanced fostering (i) universal access real-time whole sequence (WGS) data pathogens inform clinical practice, infection control, policies, vaccine drug research development; (ii) integration diagnostic microbiology data, testing asymptomatic individuals, epidemiological into programs; (iii) stronger cross-sectorial collaborations between healthcare, health, animal environmental using approaches, toward understanding the ecology transmission pathways AMR across ecosystems; (iv) international collaboration interconnection networks, harmonization laboratory methods, standardization methods global reporting, including on variant or strain nomenclature; (v) responsible sharing databases, platforms according FAIR (findability, accessibility, interoperability, reusability) principles; (vi) system implementation its cost-effectiveness different settings. Regional policies governance initiatives foster concerted development efficient utilization protect humans, animals, environment.

Language: Английский

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Culture and identification of a “Deltamicron” SARS‐CoV‐2 in a three cases cluster in southern France

Journal of Medical Virology, Journal Year: 2022, Volume and Issue: 94(8), P. 3739 - 3749

Published: April 25, 2022

Multiple SARS-CoV-2 variants have successively, or concomitantly spread worldwide since the summer of 2020. A few co-infections with different were reported and genetic recombinations, common among coronaviruses, suspected based on co-detection signature mutations in a given genome. Here we report three infections southern France Delta 21J_AY.4-Omicron 21K/BA.1 "Deltamicron" recombinant. The hybrid genome harbors two lineages, supported by mean sequencing depth 1163-1421 reads nucleotide diversity 0.1%-0.6%. It is composed near full-length spike gene (from codons 156-179) an Omicron variant 21J/AY.4 lineage backbone. Importantly, cultured isolate this recombinant sequenced its was observed scanning electron microscopy. As it misidentified current screening quantitative polymerase chain reaction (qPCR), designed implemented for routine diagnosis specific duplex qPCR. Finally, structural analysis suggested content could optimize viral binding to host cell membrane. These findings prompt further studies virological, epidemiological, clinical features

Language: Английский

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Detection and prevalence of SARS-CoV-2 co-infections during the Omicron variant circulation in France

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Oct. 23, 2022

Abstract From December 2021-February 2022, an intense and unprecedented co-circulation of SARS-CoV-2 variants with high genetic diversity raised the question possible co-infections between how to detect them. Using 11 mixes Delta:Omicron isolates at different ratios, we evaluated performance 4 sets primers used for whole-genome sequencing developed unbiased bioinformatics method detection involving genetically distinct lineages. Applied on 21,387 samples collected 6, 2021 February 27, 2022 from random genomic surveillance in France, detected 53 The prevalence Delta Omicron (BA.1) lineages BA.1 BA.2 were estimated 0.18% 0.26%, respectively. Among 6,242 hospitalized patients, intensive care unit (ICU) admission rates 1.64%, 4.81% 15.38% Omicron, Delta/Omicron No BA.1/BA.2 reported among ICU admitted patients. co-infected a total 21 patients (39.6%) not vaccinated. Although rare this study, their proper is crucial evaluate clinical impact risk emergence potential recombinants.

Language: Английский

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Evidence of co-infections during Delta and Omicron SARS-CoV-2 variants co-circulation through prospective screening and sequencing

Clinical Microbiology and Infection, Journal Year: 2022, Volume and Issue: 28(11), P. 1503.e5 - 1503.e8

Published: July 2, 2022

To describe Delta/Omicron SARS-CoV-2 variants co-infection detection and confirmation during the fifth wave of COVID-19 pandemics in France 7 immunocompetent epidemiologically unrelated patients.

Language: Английский

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Systematic detection of co-infection and intra-host recombination in more than 2 million global SARS-CoV-2 samples

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Jan. 15, 2024

Abstract Systematic monitoring of SARS-CoV-2 co-infections between different lineages and assessing the risk intra-host recombinant emergence are crucial for forecasting viral evolution. Here we present a comprehensive analysis more than 2 million raw read datasets submitted to European COVID-19 Data Portal identify recombination. Co-infection was observed in 0.35% investigated cases. Two independent procedures were implemented detect We show that sensitivity is predominantly determined by density lineage-defining mutations along genome, thus used an expanded list mutually exclusive defining specific variant combinations increase statistical power. call attention multiple challenges rendering detection difficult provide guidelines reduction false positives arising from chimeric sequences produced during PCR amplification. Additionally, three recombination hotspots Delta – Omicron BA.1 recombinants.

Language: Английский

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The emergence of SARS-CoV-2 Omicron subvariants: current situation and future trends

Infezioni in Medicina, Journal Year: 2022, Volume and Issue: 30(4)

Published: Dec. 1, 2022

The SARS-CoV-2 Omicron variant (B.1.1.529) has been the most recent of concern (VOC) established by World Health Organization (WHO). Because its greater infectivity and immune evasion, this quickly became dominant type circulating worldwide. Our literature review thoroughly explains current state emergence, particularly comparing different omicron subvariants, including BA.2, BA.1, BA.3. Such elaboration would be based on structural variations, mutations, clinical manifestation, transmissibility, pathogenicity, vaccination effectiveness. notable difference between three subvariants is insufficiency deletion (Δ69-70) in spike protein, which results a lower detection rate (S) gene target known as failure (SGTF). Furthermore, BA.2 had stronger affinity to human Angiotensin-converting Enzyme (hACE2) receptor than other sub-lineages. Regarding number BA.1.1 (40), followed BA.3, BA.3 with 39, 34, 31 respectively. In addition, have transmissibility sub-lineages (BA.1 BA.1.1). These characteristics are primarily responsible for Omicron's vast geographical spread high contagiousness rates,

Language: Английский

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Global asymptotic stability, extinction and ergodic stationary distribution in a stochastic model for dual variants of SARS-CoV-2

Mathematics and Computers in Simulation, Journal Year: 2022, Volume and Issue: 204, P. 302 - 336

Published: Aug. 29, 2022

Language: Английский

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