The evolution of SARS-CoV-2

Nature Reviews Microbiology, Journal Year: 2023, Volume and Issue: 21(6), P. 361 - 379

Published: April 5, 2023

Language: Английский

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Global landscape of SARS-CoV-2 genomic surveillance and data sharing

Nature Genetics, Journal Year: 2022, Volume and Issue: 54(4), P. 499 - 507

Published: March 28, 2022

Abstract Genomic surveillance has shaped our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. We performed a global landscape analysis on SARS-CoV-2 genomic and data using collection country-specific data. Here, we characterize increasing circulation the Alpha variant in early 2021, subsequently replaced by Delta around May 2021. sequencing availability varied markedly across countries, with 45 countries performing high level routine 96 sequencing. also observed marked heterogeneity percentage, technologies, turnaround time completeness released metadata regions income groups. A total 37% explicit reporting variants shared less than half their sequences concern (VOCs) public repositories. Our findings indicate an urgent need to increase timely full sharing sequences, standardization files support for limited bioinformatics capacity.

Language: Английский

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Molecular characteristics, immune evasion, and impact of SARS-CoV-2 variants

Signal Transduction and Targeted Therapy, Journal Year: 2022, Volume and Issue: 7(1)

Published: June 28, 2022

Abstract The persistent COVID-19 pandemic since 2020 has brought an enormous public health burden to the global society and is accompanied by various evolution of virus genome. consistently emerging SARS-CoV-2 variants harboring critical mutations impact molecular characteristics viral proteins display heterogeneous behaviors in immune evasion, transmissibility, clinical manifestation during infection, which differ each strain endow them with distinguished features populational spread. Several variants, identified as Variants Concern (VOC) World Health Organization, challenged efforts on control due rapid worldwide spread enhanced evasion from current antibodies vaccines. Moreover, recent Omicron variant even exacerbated anxiety continuous pandemic. Its significant medical treatment disease highlights necessity combinatory investigation mutational pattern influence dynamics against immunity, would greatly facilitate drug vaccine development benefit policymaking. Hence this review, we summarized characteristics, impacts focused parallel comparison different profile, transmissibility tropism alteration, effectiveness, manifestations, order provide a comprehensive landscape for research.

Language: Английский

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Impact of antigenic evolution and original antigenic sin on SARS-CoV-2 immunity

Journal of Clinical Investigation, Journal Year: 2023, Volume and Issue: 133(1)

Published: Jan. 2, 2023

Infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and vaccinations targeting the spike protein (S) offer protective immunity against disease 2019 (COVID-19). This may further be shaped by cross-reactivity common cold coronaviruses. Mutations arising in S that are associated altered intrinsic virus properties immune escape result continued circulation of SARS-CoV-2 variants. Potentially, vaccine updates will required to protect future variants concern, as for influenza. To potent protection variants, these second-generation vaccines need redirect epitopes not merely boost toward conserved domains preimmune individuals. For influenza, efficacy repeated vaccination is hampered original antigenic sin, an attribute memory leads greater induction antibodies specific first-encountered variant immunogen compared subsequent In this Review, recent findings on sin discussed context evolution. Unanswered questions directions highlighted, emphasis impact outcome design.

Language: Английский

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Co-infection with SARS-CoV-2 Omicron and Delta variants revealed by genomic surveillance

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

Published: May 18, 2022

Abstract Co-infections with different variants of SARS-CoV-2 are a key precursor to recombination events that likely drive evolution. Rapid identification such co-infections is required determine their frequency in the community, particularly populations at-risk severe COVID-19, which have already been identified as incubators for punctuated evolutionary events. However, limited data and tools currently available detect characterise associated recognised concern. Here we describe co-infection concern Omicron Delta two epidemiologically unrelated adult patients chronic kidney disease requiring maintenance haemodialysis. Both were co-circulating community at time detection. Genomic surveillance based on amplicon- probe-based sequencing using short- long-read technologies quantified subpopulations viruses respiratory samples. These findings highlight importance integrated genomic vulnerable provide diagnostic pathways recognise data.

Language: Английский

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Emerging evidence on Omicron (B.1.1.529) SARS‐CoV‐2 variant

Journal of Medical Virology, Journal Year: 2022, Volume and Issue: 94(5), P. 1876 - 1885

Published: Jan. 27, 2022

COVID's Omicron variant has sparked a slew of concerns across the globe. This review aims to provide brief overview what we know about right now. The new been discovered in 149 countries all six World Health Organization (WHO) regions since its discovery South Africa on November 24, 2021 and became dominant country less than 3 weeks. WHO warned that B.1.1.529 is spreading at an unprecedented rate, urged prepare for worst. Over course this time, researchers from around world have uncovered wealth information virus's epidemiology biological properties. Case numbers are increasing exponentially hard-hit areas such as Africa, United Kingdom, USA (overtaking delta variant), implying highly transmissible. Initial research provided some insights into efficacy vaccines against whether it produces major illness, however, much remains unknown, additional work needed investigate initial reports represent real-world situations.

Language: Английский

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An early warning system for emerging SARS-CoV-2 variants

Nature Medicine, Journal Year: 2022, Volume and Issue: 28(6), P. 1110 - 1115

Published: May 30, 2022

Language: Английский

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Global SARS-CoV-2 genomic surveillance: What we have learned (so far)

Infection Genetics and Evolution, Journal Year: 2023, Volume and Issue: 108, P. 105405 - 105405

Published: Jan. 18, 2023

The COVID-19 pandemic has brought significant challenges for genomic surveillance strategies in public health systems worldwide. During the past thirty-four months, many countries faced several epidemic waves of SARS-CoV-2 infections, driven mainly by emergence and spread novel variants. In that line, been a crucial toolkit to study real-time evolution, assessment optimization diagnostic assays, improve efficacy existing vaccines. pandemic, identification emerging lineages carrying lineage-specific mutations (particularly those Receptor Binding domain) showed how these might significantly impact viral transmissibility, protection from reinfection vaccination. So far, an unprecedented number genomes released databases (i.e., GISAID, NCBI), achieving 14 million genome sequences available as early-November 2022. present review, we summarise global landscape during first months circulation evolution. It demonstrates urgency importance sustained investment timely identify any potential pathogen or associated variants, which turn is key preparedness.

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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Progress and challenges in infectious disease surveillance and early warning

Medicine Plus, Journal Year: 2025, Volume and Issue: unknown, P. 100071 - 100071

Published: Jan. 1, 2025

Language: Английский

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