The evolution of SARS-CoV-2

Nature Reviews Microbiology, Год журнала: 2023, Номер 21(6), С. 361 - 379

Опубликована: Апрель 5, 2023

Язык: Английский

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The Evolution and Biology of SARS-CoV-2 Variants

Cold Spring Harbor Perspectives in Medicine, Год журнала: 2022, Номер 12(5), С. a041390 - a041390

Опубликована: Апрель 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.

Язык: Английский

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Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function

Molecular Biology and Evolution, Год журнала: 2022, Номер 39(4)

Опубликована: Март 16, 2022

Among the 30 nonsynonymous nucleotide substitutions in Omicron S-gene are 13 that have only rarely been seen other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of at sites will likely impact (1) interactions between subunits Spike trimer and predisposition to shift from down up configurations, (2) with ACE2 receptors, (3) priming for membrane fusion. We show here that, based on both rarity these intrapatient sequencing reads patterns selection codon where occur related sarbecoviruses, prior emergence would predicted decrease fitness any virus which they occurred. further propose each clusters therefore cooperatively interact mitigate their individual costs, and, combination mutations, adaptively alter function Spike. Given evident epidemic growth advantages overall previously known lineages, it is crucial determine how such complex highly adaptive mutation constellations were assembled S-gene, why, despite unprecedented global genomic surveillance efforts, early stages this assembly process went completely undetected.

Язык: Английский

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SARS-CoV-2 evolution in the Omicron era

Nature Microbiology, Год журнала: 2023, Номер 8(11), С. 1952 - 1959

Опубликована: Окт. 16, 2023

Язык: Английский

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White-tailed deer ( Odocoileus virginianus ) may serve as a wildlife reservoir for nearly extinct SARS-CoV-2 variants of concern

Proceedings of the National Academy of Sciences, Год журнала: 2023, Номер 120(6)

Опубликована: Янв. 31, 2023

The spillover of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from humans to white-tailed deer (WTD) and its ability transmit raised concerns about the role WTD in epidemiology ecology virus. Here, we present a comprehensive cross-sectional study assessing prevalence, genetic diversity, evolution SARS-CoV-2 State New York (NY). A total 5,462 retropharyngeal lymph node samples collected free-ranging hunter-harvested during hunting seasons 2020 (Season 1, September December 2020, n = 2,700) 2021 2, 2021, 2,762) were tested by real-time RT–PCR (rRT-PCR). RNA was detected 17 (0.6%) Season 1 583 (21.1%) 2. Hotspots infection identified multiple confined geographic areas NY. Sequence analysis genomes 164 demonstrated presence lineages cocirculation three major variants concern (VOCs) (Alpha, Gamma, Delta) WTD. Our suggests occurrence events (human deer) Alpha Delta with subsequent deer-to-deer transmission adaptation viruses. Detection Gamma long after their broad circulation NY that may serve as wildlife reservoir for VOCs no longer circulating humans. Thus, implementation continuous surveillance programs monitor dynamics is warranted, measures minimize virus between animals are urgently needed.

Язык: Английский

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Transmission of SARS-CoV-2 in free-ranging white-tailed deer in the United States

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Июль 10, 2023

Abstract SARS-CoV-2 is a zoonotic virus with documented bi-directional transmission between people and animals. Transmission of from humans to free-ranging white-tailed deer ( Odocoileus virginianus ) poses unique public health risk due the potential for reservoir establishment where variants may persist evolve. We collected 8,830 respiratory samples across Washington, D.C. 26 states in United States November 2021 April 2022. obtained 391 sequences identified 34 Pango lineages including Alpha, Gamma, Delta, Omicron variants. Evolutionary analyses showed these viruses originated at least 109 independent spillovers humans, which resulted 39 cases subsequent local deer-to-deer three spillover back humans. Viruses repeatedly adapted recurring amino acid substitutions spike other proteins. Overall, our findings suggest that multiple were introduced, became enzootic, co-circulated deer.

Язык: Английский

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Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Апрель 25, 2023

Abstract The Papain-like protease (PLpro) is a domain of multi-functional, non-structural protein 3 coronaviruses. PLpro cleaves viral polyproteins and posttranslational conjugates with poly-ubiquitin protective ISG15, composed two ubiquitin-like (UBL) domains. Across coronaviruses, showed divergent selectivity for recognition cleavage despite sequence conservation. We show that SARS-CoV-2 binds human ISG15 K48-linked di-ubiquitin (K48-Ub 2 ) nanomolar affinity detect alternate weaker-binding modes. Crystal structures untethered complexes K48-Ub combined solution NMR cross-linking mass spectrometry revealed how the domains or are differently utilized in interactions PLpro. Analysis interface energetics predicted differential binding stabilities UBL/Ub were validated experimentally. emphasize substrate can be tuned to cleave specifically modifications while retaining capacity mono-Ub conjugates. These results highlight alternative druggable surfaces would inhibit function.

Язык: Английский

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SARS‐CoV‐2 in animals: susceptibility of animal species, risk for animal and public health, monitoring, prevention and control

EFSA Journal, Год журнала: 2023, Номер 21(2)

Опубликована: Фев. 1, 2023

Abstract The epidemiological situation of SARS-CoV-2 in humans and animals is continually evolving. To date, animal species known to transmit are American mink, raccoon dog, cat, ferret, hamster, house mouse, Egyptian fruit bat, deer mouse white-tailed deer. Among farmed animals, mink have the highest likelihood become infected from or further SARS-CoV-2. In EU, 44 outbreaks were reported 2021 farms seven MSs, while only six 2022 two thus representing a decreasing trend. introduction into usually via humans; this can be controlled by systematically testing people entering adequate biosecurity. current most appropriate monitoring approach for outbreak confirmation based on suspicion, dead clinically sick case increased mortality positive farm personnel genomic surveillance virus variants. analysis showed mink-specific clusters with potential spill back human population. companion cats, ferrets hamsters those at risk infection, which likely originates an human, has no very low impact circulation wild (including zoo animals), mostly carnivores, great apes been naturally cases wildlife so far. Proper disposal waste advised reduce risks spill-over wildlife. Furthermore, contact wildlife, especially if dead, should minimised. No specific recommended apart hunter-harvested clinical signs found-dead. Bats monitored as natural host many coronaviruses.

Язык: Английский

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Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Авг. 28, 2023

Abstract The zoonotic origin of the COVID-19 pandemic virus highlights need to fill vast gaps in our knowledge SARS-CoV-2 ecology and evolution non-human hosts. Here, we detected that was introduced from humans into white-tailed deer more than 30 times Ohio, USA during November 2021-March 2022. Subsequently, deer-to-deer transmission persisted for 2–8 months, disseminating across hundreds kilometers. Newly developed Bayesian phylogenetic methods quantified how is not only three-times faster compared rate observed but also driven by different mutational biases selection pressures. long-term effect this accelerated evolutionary remains be seen as no critical phenotypic changes were animal models using viruses. Still, has transmitted populations a relatively short duration, risk future may have serious consequences livestock.

Язык: Английский

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Tracing the origin of SARS-CoV-2 omicron-like spike sequences detected in an urban sewershed: a targeted, longitudinal surveillance study of a cryptic wastewater lineage

The Lancet Microbe, Год журнала: 2024, Номер 5(4), С. e335 - e344

Опубликована: Март 11, 2024

Язык: Английский

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