Evolution of the SARS‐CoV‐2 omicron variants BA.1 to BA.5: Implications for immune escape and transmission

Reviews in Medical Virology, Journal Year: 2022, Volume and Issue: 32(5)

Published: July 20, 2022

Abstract The first dominant SARS‐CoV‐2 Omicron variant BA.1 harbours 35 mutations in its Spike protein from the original that emerged late 2019. Soon after discovery, rapidly to become worldwide and has since evolved into several variants. is of major public health concern owing high infectivity antibody evasion. This review article examines theories have been proposed on evolution including zoonotic spillage, infection immunocompromised individuals cryptic spread community without being diagnosed. Added complexity Omicron's are multiple reports recombination events occurring between co‐circulating variants with Delta other such as XE. Current literature suggests combination novel resulted having higher than Wuhan‐Hu‐1 variant. However, severity believed be less reduced syncytia formation lower multiplication human lung tissue. Perhaps most challenging studies indicate efficacy available vaccines against (8–127 times reduction) compared administration booster vaccine, however, compensates reduction improves by 12–35 fold. Concerningly though, broadly neutralising monoclonal antibodies, those approved FDA for therapeutic use previous variants, mostly ineffective exception Sotrovimab recent suggest BA.2 also resistant Sotrovimab. Currently two new BA.4 BA.5 emerging reported more transmissible immunity generated antibodies. As will likely continue emerge it important evolution, biological consequences mutations, existing well understood.

Language: Английский

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Evidence for a mouse origin of the SARS-CoV-2 Omicron variant

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2021, Volume and Issue: 48(12), P. 1111 - 1121

Published: Dec. 1, 2021

The rapid accumulation of mutations in the SARS-CoV-2 Omicron variant that enabled its outbreak raises questions as to whether proximal origin occurred humans or another mammalian host. Here, we identified 45 point acquired since divergence from B.1.1 lineage. We found spike protein sequence was subjected stronger positive selection than any reported variants known evolve persistently human hosts, suggesting a possibility host-jumping. molecular spectrum (i.e., relative frequency 12 types base substitutions) by progenitor significantly different for viruses evolved patients but resembled spectra associated with virus evolution mouse cellular environment. Furthermore, overlapped promote adaptation particularly through enhanced binding affinity cell entry receptor. Collectively, our results suggest jumped mice, rapidly accumulated conducive infecting host, then back into humans, indicating an inter-species evolutionary trajectory outbreak.

Language: Английский

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Deep mutational scans for ACE2 binding, RBD expression, and antibody escape in the SARS-CoV-2 Omicron BA.1 and BA.2 receptor-binding domains

PLoS Pathogens, Journal Year: 2022, Volume and Issue: 18(11), P. e1010951 - e1010951

Published: Nov. 18, 2022

SARS-CoV-2 continues to acquire mutations in the spike receptor-binding domain (RBD) that impact ACE2 receptor binding, folding stability, and antibody recognition. Deep mutational scanning prospectively characterizes impacts of on these biochemical properties, enabling rapid assessment new seen during viral surveillance. However, effects can change as virus evolves, requiring updated deep scans. We determined all single amino acid Omicron BA.1 BA.2 RBDs ACE2-binding affinity, RBD folding, escape from binding by LY-CoV1404 (bebtelovimab) monoclonal antibody. The some differ those measured ancestral Wuhan-Hu-1 background. These epistatic shifts largely resemble previously Alpha variant due convergent epistatically modifying N501Y substitution. variants show additional lineage-specific shifts, including examples phenomenon entrenchment causes Q498R substitutions present be more favorable background than earlier strains. In contrast, substitution Q493R exhibits no sign entrenchment, with derived state, R493, being unfavorable for Wuhan-Hu-1. Likely this reason, R493Q reversion has occurred sub-variants BA.4/BA.5 BA.2.75, where affinity buffer may potentiate concurrent antigenic change. Consistent prior studies, we find have reduced expression, identify candidate stabilizing ameliorate deficit. Last, our maps highlight a broadening sites compared datasets landscape inform ongoing efforts

Language: Английский

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Viral variant-resolved wastewater surveillance of SARS-CoV-2 at national scale

Nature Biotechnology, Journal Year: 2022, Volume and Issue: 40(12), P. 1814 - 1822

Published: July 18, 2022

Language: Английский

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Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic

Nature Reviews Genetics, Journal Year: 2022, Volume and Issue: 23(9), P. 547 - 562

Published: April 22, 2022

Language: Английский

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Spike and nsp6 are key determinants of SARS-CoV-2 Omicron BA.1 attenuation

Nature, Journal Year: 2023, Volume and Issue: 615(7950), P. 143 - 150

Published: Jan. 11, 2023

Language: Английский

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Wastewater analysis can be a powerful public health tool—if it’s done sensibly

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(6)

Published: Feb. 3, 2022

The coronavirus disease 2019 (COVID-19) pandemic sparked an explosion of interest in wastewater-based epidemiology (WBE; also known as wastewater monitoring or surveillance). Much has been said, the scientific literature and popular press alike, about public health value tracking severe acute respiratory syndrome 2 (SARS-CoV-2) wastewater. Emergence spread omicron variant recently pushed WBE for COVID-19 management back into headlines. Unfortunately, coverage potential is rarely balanced by a practical discussion limitations tradeoffs, especially when it comes to issues beyond technical challenges encountered lab. Sometimes makes sense way monitor outbreaks other threats, sometimes constraints argue spending scarce resources elsewhere. We grapple with such frequently while managing program Healthy Davis Together (HDT), multi-pronged pandemic-response initiative Davis, CA. Since launching September 2020, grown include in-house analysis collected on weekly, triweekly, daily basis from 70 sites distributed across City University California, (UC Davis) campus sewer systems influent their treatment plants. are glad that our data informing local mitigation efforts. Results UC dorm outflows supporting safe return students campus; results neighborhoods broader city areas helping officials understand spatial changes trends react accordingly. At same time, running campaign requires significant investments money, labor, expertise. Given much information gleaned not directly actionable, and/or duplicates sources, prudent consider these worthwhile. … [↵][1]1To whom correspondence may be addressed. Email: hbischel{at}ucdavis.edu. [1]: #xref-corresp-1-1

Language: Английский

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Learning from prepandemic data to forecast viral escape

Nature, Journal Year: 2023, Volume and Issue: 622(7984), P. 818 - 825

Published: Oct. 11, 2023

Abstract Effective pandemic preparedness relies on anticipating viral mutations that are able to evade host immune responses facilitate vaccine and therapeutic design. However, current strategies for evolution prediction not available early in a pandemic—experimental approaches require polyclonal antibodies test against 1–16 , existing computational methods draw heavily from strain prevalence make reliable predictions of variants concern 17–19 . To address this, we developed EVEscape, generalizable modular framework combines fitness deep learning model historical sequences with biophysical structural information. EVEscape quantifies the escape potential at scale has advantage being applicable before surveillance sequencing, experimental scans or three-dimensional structures antibody complexes available. We demonstrate trained 2020, is as accurate high-throughput variation SARS-CoV-2 other viruses including influenza, HIV understudied such Lassa Nipah. provide continually revised scores all strains predict probable further forecast emerging tool continuing development ( evescape.org ).

Language: Английский

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Persistent SARS-CoV-2 infection: significance and implications

The Lancet Infectious Diseases, Journal Year: 2024, Volume and Issue: 24(7), P. e453 - e462

Published: Feb. 7, 2024

SARS-CoV-2 causes persistent infections in a subset of individuals, which is major clinical and public health problem that should be prioritised for further investigation several reasons. First, infection often goes unrecognised, therefore might affect substantial number people, particularly immunocompromised individuals. Second, the formation tissue reservoirs (including non-respiratory tissues) underlie pathophysiology require new strategies diagnosis treatment. Finally, replication, setting suboptimal immune responses, possible source new, divergent virus variants escape pre-existing immunity on individual population levels. Defining optimal diagnostic treatment patients with replication monitoring viral evolution are urgent medical priorities.

Language: Английский

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Wastewater sequencing reveals community and variant dynamics of the collective human virome

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

Published: Oct. 28, 2023

Wastewater is a discarded human by-product, but its analysis may help us understand the health of populations. Epidemiologists first analyzed wastewater to track outbreaks poliovirus decades ago, so-called wastewater-based epidemiology was reinvigorated monitor SARS-CoV-2 levels while bypassing difficulties and pit falls individual testing. Current approaches overlook activity most viruses preclude deeper understanding virome community dynamics. Here, we conduct comprehensive sequencing-based 363 longitudinal samples from ten distinct sites in two major cities. Critical detection use viral probe capture set targeting thousands species or variants. Over 450 pathogenic 28 families are observed, which have never been detected such samples. Sequencing reads established pathogens emerging correlate clinical data sets SARS-CoV-2, influenza virus, monkeypox viruses, outlining public utility this approach. Viral communities tightly organized by space time. Finally, abundant yield sequence variant information consistent with regional spread evolution. We reveal landscape potential improve our outbreaks, transmission, effects on overall population health.

Language: Английский

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