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The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic

CURRENT BIOLOGY (2021)

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Article Virology

Synonymous mutations and the molecular evolution of SARS-CoV-2 origins

Hongru Wang et al.

Summary: This study analyzed the synonymous divergence between SARS-CoV-2 and related strains, finding that the divergence between bat-derived viruses and SARS-CoV-2 is larger in the RBD compared to GD410721. This supports the hypothesis of recombination between the strains.

VIRUS EVOLUTION (2021)

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Article Infectious Diseases

Preliminary report of an outbreak of SARS-CoV-2 in mink and mink farmers associated with community spread, Denmark, June to November 2020

Helle Daugaard Larsen et al.

Summary: During June-November 2020, SARS-CoV-2-infected mink were found in 290 out of 1,147 Danish mink farms. In North Denmark Region, 30% of individuals associated with mink farms tested positive for SARS-CoV-2, and approximately 27% of SARS-CoV-2 strains in the community were linked to mink. Despite measures taken, the virus spread was not effectively controlled, leading to the government ordering the culling of all Danish mink as they pose a potential virus reservoir that challenges pandemic control.

EUROSURVEILLANCE (2021)

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Article Infectious Diseases

Infection sustained by lineage B.1.1.7 of SARS-CoV-2 is characterised by longer persistence and higher viral RNA loads in nasopharyngeal swabs

Paolo Calistri et al.

Summary: A targeted surveillance in the Abruzzo region of Italy detected 313 persons affected by lineage B.1.1.7, with statistically significant differences in viral load and persistence compared to other lineages. In individuals infected with B.1.1.7 lineage, lower values of C-T associated with the detection of the N protein encoding gene and longer persistence of SARS-CoV-2 RNA in nasopharyngeal swabs were observed.

INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES (2021)

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Article Medicine, General & Internal

Single-dose administration and the influence of the timing of the booster dose on immunogenicity and efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine: a pooled analysis of four randomised trials

Merryn Voysey et al.

Summary: The AZD1222 vaccine has been approved for emergency use in the UK with an interval of 4-12 weeks between doses. Analysis shows that the vaccine is efficacious with two doses and provides immunoprotection after the first dose before the second dose is administered.

LANCET (2021)

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Article Multidisciplinary Sciences

Detection of a SARS-CoV-2 variant of concern in South Africa

Houriiyah Tegally et al.

Summary: The article describes a newly emerged lineage of SARS-CoV-2, 501Y.V2, characterized by eight mutations in the spike protein, which may result in increased transmissibility or immune escape. This lineage originated in South Africa and quickly became dominant in Eastern Cape, Western Cape, and KwaZuluNatal provinces within weeks.

NATURE (2021)

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Article Multidisciplinary Sciences

SARS-CoV-2 evolution during treatment of chronic infection

Steven A. Kemp et al.

Summary: Chronic infection with SARS-CoV-2 can lead to viral evolution and increased resistance to neutralizing antibodies in immunosuppressed individuals treated with convalescent plasma. During convalescent plasma therapy, there were significant shifts in the viral population structure and sensitivity, suggesting strong selection pressure on the virus during treatment.

NATURE (2021)

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Article Physics, Multidisciplinary

The effectiveness of backward contact tracing in networks

Sadamori Kojaku et al.

Summary: Contact tracing is crucial for epidemic control, with backward tracing being more effective than forward tracing due to biases from contact heterogeneity. By strategically executed contact tracing, a substantial fraction of transmissions can be prevented with higher efficiency compared to case isolation alone, calling for a revision of current contact-tracing strategies to leverage all forms of bias. Incorporating backward and deep tracing in a digital context while maintaining privacy-preserving requirements is particularly crucial.

NATURE PHYSICS (2021)

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Letter Medicine, General & Internal

Serum Neutralizing Activity Elicited by mRNA-1273 Vaccine

Kai Wu et al.

NEW ENGLAND JOURNAL OF MEDICINE (2021)

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Article Multidisciplinary Sciences

Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England

Nicholas G. Davies et al.

Summary: A new variant of SARS-CoV-2 has emerged in England, with a higher reproduction number and potential for large resurgences of COVID-19 cases. Without stringent control measures, it is projected that COVID-19 hospitalizations and deaths in England for the first 6 months of 2021 will exceed those in 2020. The variant has spread globally and exhibited similar transmission increases in Denmark, Switzerland, and the United States.

SCIENCE (2021)

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Article Multidisciplinary Sciences

SARS-CoV-2 within-host diversity and transmission

Katrina A. Lythgoe et al.

Summary: The study found that SARS-CoV-2 infections in clinical samples in the UK are characterized by low levels of within-host diversity and a narrow bottleneck at transmission. Most variants are either lost or occasionally fixed at the point of transmission, with shared diversity not persisting.

SCIENCE (2021)

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Article Multidisciplinary Sciences

Epidemiological and evolutionary considerations of SARS-CoV-2 vaccine dosing regimes

Chadi M. Saad-Roy et al.

Summary: Given vaccine dose shortages and logistical challenges, various deployment strategies are being proposed to increase population immunity levels to SARS-CoV-2. While focusing on one dose may decrease infections in the short term, the long-term outcomes depend on the relative immune robustness of this approach. Under conditions of partial population immunity, a one-dose policy may increase the potential for antigenic evolution.

SCIENCE (2021)

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Article Multidisciplinary Sciences

Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape

Kevin R. McCarthy et al.

Summary: The translation above discusses zoonotic pandemics caused by animal viruses spilling over into highly susceptible human populations, specifically focusing on the evolution of coronaviruses in human hosts and the impact of recurrent deletions in the spike glycoprotein on antibody epitopes. These studies help understand the antigenic evolution and adaptive evolution of SARS-CoV-2.

SCIENCE (2021)

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Article Medicine, General & Internal

Risk of mortality in patients infected with SARS-CoV-2 variant of concern 202012/1: matched cohort study

Robert Challen et al.

Summary: The study found that the mortality hazard ratio associated with infection with VOC-202012/1 compared with previously circulating variants was 1.64, indicating an increase in deaths from 2.5 to 4.1 per 1000 detected cases in comparatively low risk group of covid-19 patients in the community. This suggests that infection with VOC-202012/1 may lead to substantial additional mortality compared with previously circulating variants, impacting healthcare capacity planning and control policies.

BMJ-BRITISH MEDICAL JOURNAL (2021)

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Article Biology

Population Genomics Insights into the First Wave of COVID-19

Maria Vasilarou et al.

Summary: Computational analyses of SARS-CoV-2 genomes revealed evidence of positive selection regions co-localized with regions from recombination events with nonhuman hosts, suggesting the involvement of pangolin coronavirus in the evolution of SARS-CoV-2. Additionally, there were indications of recombination events with coronavirus genomes from other hosts like hedgehogs and sparrows, and even within human hosts. The study also estimated a demographic scenario involving exponential growth of SARS-CoV-2 populations in European, Asian, and Northern American cohorts, supporting observed polymorphism patterns in the genomes.

LIFE-BASEL (2021)

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Article Biochemistry & Molecular Biology

Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant

Xianding Deng et al.

Summary: A new SARS-CoV-2 variant named B.1.427/B.1.429 was identified in California, with increased transmissibility and carrying three mutations in spike protein, including L452R substitution. The variant emerged in May 2020 and became predominant in sequenced cases from September 2020 to January 2021. In vivo viral shedding was increased and antibody neutralization decreased, calling for further investigation.

CELL (2021)

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Article Multidisciplinary Sciences

Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7

Nicholas G. Davies et al.

Summary: Studies have shown that the SARS-CoV-2 B.1.1.7 lineage is more transmissible and may cause more severe illness compared to pre-existing variants.

NATURE (2021)

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Article Multidisciplinary Sciences

Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

Erik Volz et al.

Summary: Genetic and testing data from England indicate that the SARS-CoV-2 variant B.1.1.7 has a transmission advantage over other lineages, showing a rapid expansion during autumn 2020. Analysis of S gene target failures (SGTF) in community-based diagnostic PCR testing suggests that B.1.1.7 is more transmissible than non-variant of concern lineages and has a significant transmission advantage, with a reproduction number 50% to 100% higher. Additionally, cases of B.1.1.7 appear to include a larger share of under 20-year-olds compared to non-variant cases.

NATURE (2021)

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Letter Medicine, General & Internal

Effectiveness of the BNT162b2 Covid-19 Vaccine against the B.1.1.7 and B.1.351 Variants

Laith J. Abu-Raddad et al.

NEW ENGLAND JOURNAL OF MEDICINE (2021)

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Editorial Material Multidisciplinary Sciences

The emerging plasticity of SARS-CoV-2

Kevin D. McCormick et al.

SCIENCE (2021)

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Article Multidisciplinary Sciences

Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

Nuno R. Faria et al.

Summary: A new variant of concern, P.1, with 17 mutations including three spike protein mutations associated with increased binding to human ACE2 receptors, emerged in Manaus, Brazil between November 2020 and January 2021. Molecular analysis suggests P.1 may be 1.7- to 2.4-fold more transmissible and that previous infection may provide 54 to 79% protection against P.1 infection compared to other lineages. Enhanced global genomic surveillance of such variants is crucial for pandemic response.

SCIENCE (2021)

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Article Microbiology

A human coronavirus evolves antigenically to escape antibody immunity

Rachel T. Eguia et al.

Summary: This study investigates the evolution of human coronavirus 229E and finds that as the virus evolves, mutations in the spike protein can escape neutralization by antibodies in old human sera. The results suggest that viral evolution may impact immunity, highlighting the need for periodic updates to coronavirus vaccines.

PLOS PATHOGENS (2021)

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Article Public, Environmental & Occupational Health

Postvaccination SARS-CoV-2 Infections Among Skilled Nursing Facility Residents and Staff Members - Chicago, Illinois, December 2020-March 2021

Richard A. Teran et al.

MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT (2021)

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Article Multidisciplinary Sciences

Modelling the impact of shutdowns on resurging SARS-CoV-2 transmission in Canada

Victoria Ng et al.

Summary: This study utilized an age-stratified agent-based model to explore the impact of shutdowns on controlling SARS-CoV-2 transmission in Canada. The results suggest that implementing shutdowns quickly, for a sufficient duration, targeting multiple sectors, and in response to low community transmission can reduce the total number of shutdown days. Shutdowns should be used as a last resort when other public health measures are insufficient, and the time bought by shutdowns should be used to enhance less disruptive public health interventions.

ROYAL SOCIETY OPEN SCIENCE (2021)

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Article Immunology

Concerns about SARS-CoV-2 evolution should not hold back efforts to expand vaccination

Sarah Cobey et al.

Summary: When vaccines are in limited supply, expanding the number of people who receive the vaccine by dose-sparing strategies may reduce disease and mortality, although it could potentially increase the risk of vaccine-escape variants. Preliminary evidence suggests that such strategies could slow the rate of viral escape, as long as vaccination provides some protection against escape variants.

NATURE REVIEWS IMMUNOLOGY (2021)

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Article Virology

Synonymous mutations and the molecular evolution of SARS-CoV-2 origins

Hongru Wang et al.

Summary: Human SARS-CoV-2 is genetically closer to bat-derived viruses than pangolin-derived strains, supporting the recombination hypothesis. However, the high synonymous divergence between pangolin strain and SARS-CoV-2 suggests a recombination event into bat-derived viruses. Additionally, there is a significant increase in nonsynonymous mutations in current pandemic strains, indicating a negative impact on viral fitness.

VIRUS EVOLUTION (2021)

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Article Biochemistry & Molecular Biology

Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals

Alba Grifoni et al.

CELL (2020)

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Article Biochemistry & Molecular Biology

On the evolutionary epidemiology of SARS-CoV-2

Troy Day et al.

CURRENT BIOLOGY (2020)

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Article Biology

Evidence for transmission of COVID-19 prior to symptom onset

Lauren C. Tindale et al.

ELIFE (2020)

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Article Biology

De-Escalation by Reversing the Escalation with a Stronger Synergistic Package of Contact Tracing, Quarantine, Isolation and Personal Protection: Feasibility of Preventing a COVID-19 Rebound in Ontario, Canada, as a Case Study

Biao Tang et al.

BIOLOGY-BASEL (2020)

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Article Multidisciplinary Sciences

SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls

Nina Le Bert et al.

NATURE (2020)

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Review Infectious Diseases

A systematic review and meta-analysis of published research data on COVID-19 infection fatality rates

Gideon Meyerowitz-Katz et al.

INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES (2020)

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Article Multidisciplinary Sciences

Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates

Joana Damas et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

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Article Biochemistry & Molecular Biology

Case Study: Prolonged Infectious SARS-CoV-2 Shedding from an Asymptomatic Immunocompromised Individual with Cancer

Victoria A. Avanzato et al.

CELL (2020)

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Letter Medicine, General & Internal

Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host

Bina Choi et al.

NEW ENGLAND JOURNAL OF MEDICINE (2020)

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Article Multidisciplinary Sciences

No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2

Lucy van Dorp et al.

NATURE COMMUNICATIONS (2020)

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Article Biochemistry & Molecular Biology

Superspreading events in the transmission dynamics of SARS-CoV-2: Opportunities for interventions and control

Benjamin M. Althouse et al.

PLOS BIOLOGY (2020)

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Review Multidisciplinary Sciences

Emerging infectious diseases and biological invasions: a call for a One Health collaboration in science and management

Nick H. Ogden et al.

ROYAL SOCIETY OPEN SCIENCE (2019)

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Article Biochemical Research Methods

Nextstrain: real-time tracking of pathogen evolution

James Hadfield et al.

BIOINFORMATICS (2018)

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Article Biology

Why does drug resistance readily evolve but vaccine resistance does not?

David A. Kennedy et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2017)

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Article Multidisciplinary Sciences

Risk factors for the evolutionary emergence of pathogens

H. K. Alexander et al.

JOURNAL OF THE ROYAL SOCIETY INTERFACE (2010)

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Article Evolutionary Biology

Invasion thresholds and the evolution of nonequilibrium virulence

James J. Bull et al.

EVOLUTIONARY APPLICATIONS (2008)

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Article Ecology

Applying population-genetic models in theoretical evolutionary epidemiology

Troy Day et al.

ECOLOGY LETTERS (2007)

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Article Genetics & Heredity

A single positively selected West Nile viral mutation confers increased virogenesis in American crows

Aaron C. Brault et al.

NATURE GENETICS (2007)

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Article Multidisciplinary Sciences

Superspreading and the effect of individual variation on disease emergence

JO Lloyd-Smith et al.

NATURE (2005)

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