SARS-CoV-2 variant biology: immune escape, transmission and fitness

Nature Reviews Microbiology, Journal Year: 2023, Volume and Issue: unknown

Published: Jan. 18, 2023

In late 2020, after circulating for almost a year in the human population, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exhibited major step change its adaptation to humans. These highly mutated forms of SARS-CoV-2 had enhanced rates transmission relative previous variants and were termed 'variants concern' (VOCs). Designated Alpha, Beta, Gamma, Delta Omicron, VOCs emerged independently from one another, turn each rapidly became dominant, regionally or globally, outcompeting variants. The success VOC previously dominant variant was enabled by altered intrinsic functional properties virus and, various degrees, changes antigenicity conferring ability evade primed immune response. increased fitness associated with is result complex interplay biology context changing immunity due both vaccination prior infection. this Review, we summarize literature on transmissibility variants, role mutations at furin spike cleavage site non-spike proteins, potential importance recombination success, evolution T cells, innate population immunity. shows complicated relationship among antigenicity, virulence, which has unpredictable implications future trajectory disease burden COVID-19.

Language: Английский

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The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic

Science, Journal Year: 2022, Volume and Issue: 377(6609), P. 951 - 959

Published: July 26, 2022

Understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 is critical to preventing future zoonotic outbreaks before they become the next pandemic. The Huanan Seafood Wholesale Market Wuhan, China, was identified as a likely source of cases early reports, but later this conclusion became controversial. We show here that earliest known COVID-19 from December 2019, including those without reported direct links, were geographically centered on market. report live SARS-CoV-2–susceptible mammals sold at market late and within market, SARS-CoV-2–positive environmental samples spatially associated with vendors selling mammals. Although there insufficient evidence define upstream events, exact circumstances remain obscure, our analyses indicate emergence SARS-CoV-2 occurred through wildlife trade China epicenter

Language: Английский

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The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2

Science, Journal Year: 2022, Volume and Issue: 377(6609), P. 960 - 966

Published: July 26, 2022

Understanding the circumstances that lead to pandemics is important for their prevention. We analyzed genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in disease 2019 (COVID-19) pandemic. show SARS-CoV-2 before February 2020 likely comprised only two distinct viral lineages, denoted "A" and "B." Phylodynamic rooting methods, coupled with epidemic simulations, reveal these lineages were result at least separate cross-species transmission events into humans. The first zoonotic involved lineage B viruses around 18 November (23 October 8 December), introduction A occurred within weeks this event. These findings indicate it unlikely circulated widely humans define narrow window between when jumped cases COVID-19 reported. As other coronaviruses, emergence resulted from multiple events.

Language: Английский

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Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission

Nature Microbiology, Journal Year: 2022, Volume and Issue: 7(12), P. 2011 - 2024

Published: Nov. 10, 2022

Wildlife reservoirs of broad-host-range viruses have the potential to enable evolution viral variants that can emerge infect humans. In North America, there is phylogenomic evidence continual transmission severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from humans white-tailed deer (Odocoileus virginianus) through unknown means, but no We carried out an observational surveillance study in Ontario, Canada during November and December 2021 (n = 300 deer) identified a highly divergent lineage SARS-CoV-2 (B.1.641). This one most lineages so far, with 76 mutations (including 37 previously associated non-human mammalian hosts). From set five complete two partial deer-derived genomes we applied phylogenomic, recombination, selection mutation spectrum analyses, which provided for shared ancestry mink-derived virus. Our analysis also revealed epidemiologically linked human infection. Taken together, our findings provide sustained deer-to-human transmission.

Language: Английский

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The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK

Virus Evolution, Journal Year: 2022, Volume and Issue: 8(2)

Published: July 1, 2022

The first SARS-CoV-2 variant of concern (VOC) to be designated was lineage B.1.1.7, later labelled by the World Health Organization as Alpha. Originating in early autumn but discovered December 2020, it spread rapidly and caused large waves infections worldwide. Alpha is notable for being defined a long ancestral phylogenetic branch with an increased evolutionary rate, along which only two sequences have been sampled. genomes comprise well-supported monophyletic clade within rate typical SARS-CoV-2. epidemic continued grow despite restrictions on social mixing across UK imposition new restrictions, particular, English national lockdown November 2020. While these interventions succeeded reducing absolute number cases, impact non-pharmaceutical predominantly drive decline lineages that preceded We investigate sampled fall find one likely true intermediate sequence, providing information about order mutational events led explore alternate hypotheses can explain how acquired mutations yet remained largely unobserved region high genomic surveillance: under-sampled geographical location, non-human animal population, or chronically infected individual. conclude latter provides best explanation observed behaviour dynamics variant, although individual need not immunocompromised, persistently immunocompetent hosts also display higher within-host evolution. Finally, we compare branches mutation profiles other VOCs Delta appears outlier both terms locations its defining lack rapid branch. As variants, such Omicron, continue evolve (potentially through similar mechanisms), remains important origins variants identify ways potentially disrupt their evolution emergence.

Language: Английский

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Transmission of SARS-CoV-2 from humans to animals and potential host adaptation

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

Published: May 27, 2022

Abstract SARS-CoV-2, the causative agent of COVID-19 pandemic, can infect a wide range mammals. Since its spread in humans, secondary host jumps SARS-CoV-2 from humans to multiple domestic and wild populations mammals have been documented. Understanding extent adaptation these animal hosts is critical for assessing threat that spillback animal-adapted into poses. We compare genomic landscapes isolated species profiling mutational biases indicative potentially different selective pressures animals. focus on viral genomes mink ( Neovison vison ) white-tailed deer Odocoileus virginianus which independent outbreaks driven by onward animal-to-animal transmission reported. identify five candidate mutations animal-specific (NSP9_G37E, Spike_F486L, Spike_N501T, Spike_Y453F, ORF3a_L219V), one (NSP3a_L1035F), though they appear confer minimal advantage human-to-human transmission. No considerable changes mutation rate or evolutionary trajectory has resulted circulation thus far. Our findings suggest was required following human-to-animal spillover, highlighting ‘generalist’ nature as mammalian pathogen.

Language: 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, Journal Year: 2022, Volume and Issue: 39(4)

Published: March 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.

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

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: July 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.

Language: 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, Journal Year: 2023, Volume and Issue: 21(2)

Published: Feb. 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.

Language: Английский

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