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

Article Multidisciplinary Sciences

SARS-CoV-2 infection in free-ranging white-tailed deer

Vanessa L. Hale et al.

Summary: Research shows that free-ranging white-tailed deer in northeast Ohio, USA are highly susceptible to SARS-CoV-2 infection, potentially enabling the virus to be transmitted in wildlife, opening up new pathways for evolution.

NATURE (2022)

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Article Multidisciplinary Sciences

Impact of ADAR-induced editing of minor viral RNA populations on replication and transmission of SARS-CoV-2

Johan Ringlander et al.

Summary: This study utilized deep sequencing to analyze RNA mutations in early-phase SARS-CoV-2 infected patients, and found that ADAR-induced RNA editing played an important role in these mutations. A->G mutations were abundant in minor viral populations and significantly associated with low viral load. Moreover, the frequency of these mutations increased in European consensus sequences and then decreased in autumn and early winter.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

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Article Multidisciplinary Sciences

Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer

Suresh V. Kuchipudi et al.

Summary: White-tailed deer, particularly in Iowa, have been found to be susceptible to SARS-CoV-2 infection and show evidence of human-to-deer transmission. This discovery highlights the need for a One Health approach to better understand the ecology, molecular evolution, and dissemination of the virus.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

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Article Multidisciplinary Sciences

SARS-CoV-2 Omicron variant: Antibody evasion and cryo-EM structure of spike protein-ACE2 complex

Dhiraj Mannar et al.

Summary: The newly reported Omicron variant shows new salt bridges and hydrogen bonds formed by mutated residues in the receptor binding domain, compensating for reduced ACE2 binding affinity. It also exhibits increased antibody evasion, which likely contributes to its rapid spread.

SCIENCE (2022)

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Article Virology

Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes

Debashree Chatterjee et al.

Summary: The emergence of SARS-CoV-2 variants plays a role in the waves of the COVID-19 pandemic. This study investigates the ACE2 binding and antigenicity of the Mu and A.2.5 Spike variants, revealing that they share some mutations with other emerging variants. The study also shows that these variants have improved binding to the ACE2 receptor and are similarly neutralized by vaccinated individuals' plasma.

VIRUSES-BASEL (2022)

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Article Cell Biology

Structural basis and mode of action for two broadly neutralizing antibodies against SARS-CoV-2 emerging variants of concern

Wenwe Li et al.

Summary: This study elucidates the structural basis and mode of action for two potent SARS-CoV-2 spike-neutralizing monoclonal antibodies. CV3-1 triggers shedding of the S1 subunit by binding to a loop structure in the receptor-binding domain (RBD), while CV3-25 inhibits membrane fusion by binding to an epitope in the stem helix region of the S2 subunit. Designing vaccine immunogens that incorporate conserved regions in the RBD and stem helix region could elicit pan-coronavirus protective immune responses.

CELL REPORTS (2022)

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Article Cell Biology

SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-week interval between doses

Debashree Chatterjee et al.

Summary: Continuous emergence of SARS-CoV-2 variants of concern (VOCs), such as Omicron, is raising concerns about decreased vaccine efficacy. A study on individuals who received their BNT162b2 mRNA vaccine 16 weeks apart found that a longer interval between doses enhances the recognition and neutralization of Omicron Spike compared to a shorter interval. However, it remains unknown if this difference provides any clinical benefit against Omicron.

CELL REPORTS (2022)

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Article Cell Biology

Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway

Jie Zhou et al.

Summary: SARS-CoV-2 has a wide range of host species, including humans, cats, dogs, and farmed mink. The molecular basis of mink and ferret adaptation to the virus involves specific spike mutations, which do not pose a significant threat to humans and have minimal impact on antigenicity. Certain SARS-CoV-2 variants may have a greater propensity to infect mustelid hosts.

CELL REPORTS (2022)

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Article Medicine, General & Internal

Transmission of SARS-CoV-2 delta variant (AY.127) from pet hamsters to humans, leading to onward human-to-human transmission: a case study

Hui-Ling Yen et al.

LANCET (2022)

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Article Multidisciplinary Sciences

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

Cedric C. S. Tan et al.

Summary: The spread of SARS-CoV-2 in mink and deer did not require significant adaptation, resulted in moderate changes to the virus's evolutionary trajectory, and has not led to viral mutations that greatly improve human transmission thus far.

NATURE COMMUNICATIONS (2022)

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Article Microbiology

Multiple Introductions of SARS-CoV-2 Alpha and Delta Variants into White-Tailed Deer in Pennsylvania

Andrew D. Marques et al.

Summary: White-tailed deer in Pennsylvania were found to have a high level of infection with SARS-CoV-2, indicating that they may serve as a potential reservoir for the virus to transmit back to humans. The variants of the virus in deer show significant differences from those in humans.

MBIO (2022)

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Article Microbiology

Whole-Genome Sequence of Cervid atadenovirus A from the Initial Cases of an Adenovirus Hemorrhagic Disease Epizootic of Black-Tailed Deer in Canada

Oliver Lung et al.

Summary: A complete 30416-nucleotide Cervid atadenovirus A genome was identified and analyzed from tissues of black-tailed deer in British Columbia, Canada that died in 2020. Unique nonsynonymous single-nucleotide polymorphisms in the E1B, Iva2, and E4.3 coding regions, as well as a deletion of 74 nucleotides, were found, which were not observed in isolates from moose and red deer.

MICROBIOLOGY RESOURCE ANNOUNCEMENTS (2022)

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Review Microbiology

Characteristics of SARS-CoV-2 and COVID-19

Ben Hu et al.

Summary: This review summarizes the research progress on SARS-CoV-2 and COVID-19, including virology characteristics, pathogenesis, and recent advances in treatment methods. Furthermore, it discusses in detail the potential wildlife hosts and zoonotic origin of this emerging virus.

NATURE REVIEWS MICROBIOLOGY (2021)

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Article Infectious Diseases

Target capture sequencing of SARS-CoV-2 genomes using the ONETest Coronaviruses Plus

Shing H. Zhan et al.

Summary: The study compared the performance of ONETest and ARTIC protocol in sequencing the SARS-CoV-2 genome in 70 respiratory samples. Results showed that ONETest provided more complete sequences with better coverage compared to ARTIC.

DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE (2021)

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Article Biochemistry & Molecular Biology

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

Changshuo Wei et al.

Summary: The study suggests that the rapid accumulation of mutations in the SARS-CoV-2 Omicron variant may have originated from humans jumping to mice and then back to humans, indicating an inter-species evolutionary trajectory.

JOURNAL OF GENETICS AND GENOMICS (2021)

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Article Virology

Susceptibility of White-Tailed Deer (Odocoileus virginianus) to SARS-CoV-2

Mitchell Palmer et al.

Summary: White-tailed deer are highly susceptible to infection by SARS-CoV-2, shedding infectious virus and transmitting it to other deer upon intranasal inoculation, providing important insights into the potential animal hosts of the virus.

JOURNAL OF VIROLOGY (2021)

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Article Multidisciplinary Sciences

Adaptation, spread and transmission of SARS-CoV-2 in farmed minks and associated humans in the Netherlands

Lu Lu et al.

Summary: In the first wave of the COVID-19 pandemic, SARS-CoV-2 was detected in mink farms in April 2020, leading to infections in minks and farm workers. The virus spread rapidly between mink farms, with a significant mutation in the Spike protein. Movement of people and distance between farms were significant predictors in viral dissemination between farms.

NATURE COMMUNICATIONS (2021)

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Article Multidisciplinary Sciences

Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants

Pengcheng Han et al.

Summary: Multiple SARS-CoV-2 variants, including Alpha, Beta, and Gamma, were studied in terms of their interactions with the human ACE2 receptor. The study identified key residues in the receptor-binding domain that affect binding affinity and demonstrated the potential of soluble ACE2 protein in preventing viral entry. The findings could contribute to the development of novel therapeutic and prophylactic agents targeting these emerging mutants.

NATURE COMMUNICATIONS (2021)

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Article Evolutionary Biology

Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2

Nicola De Maio et al.

Summary: The COVID-19 pandemic has prompted an unprecedented response from the sequencing community, leading to a study of mutation rates and selective pressures using sequence data from over 140,000 SARS-CoV-2 genomes. Two specific mutation rates, G -> U and C -> U, were found to be significantly higher than others, possibly attributed to APOBEC and ROS activity. Genomic context does have an effect on mutation rates, but its impact is limited.

GENOME BIOLOGY AND EVOLUTION (2021)

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Article Medicine, General & Internal

Emerging SARS-CoV-2 variants expand species tropism to murines

Huiping Shuai et al.

Summary: The study found that the SARS-CoV-2 variant B.1.1.7 and other N501Y-carrying variants can infect wildtype mice and rats, producing high viral loads and infectious virus particles in their respiratory tract. This suggests that these variants may have evolved to expand species tropism to murines.

EBIOMEDICINE (2021)

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Article Genetics & Heredity

Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic

Yatish Turakhia et al.

Summary: UShER is an efficient method that aids in real-time analysis of viral evolution during the COVID-19 pandemic by facilitating the addition of new SARS-CoV-2 genome sequences onto the existing phylogeny. The unprecedented accumulation of viral genome sequences is leading to a new era of 'genomic contact tracing' using viral genomes to trace local transmission dynamics. UShER addresses the challenge of placing new sequences onto the already large viral phylogeny, thus improving the speed of phylogenetic placement and data visualization for real-time contact tracing.

NATURE GENETICS (2021)

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Article Genetics & Heredity

Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie

Ales Varabyou et al.

Summary: A novel method identified potential recombinant SARS-CoV-2 genomes, aiding in the rapid analysis of novel isolates.

GENETICS (2021)

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Article Cell Biology

Isolation and characterization of cross-neutralizing coronavirus antibodies from COVID-19+subjects

Madeleine F. Jennewein et al.

Summary: The study identified 14 neutralizing antibodies against SARS-CoV-2, with 3 able to cross-neutralize SARS-CoV-1. The in vivo protective potential of antibodies is regulated by neutralization potency and epitope specificity. The study also suggests that epitopes in S2 can be used as blueprints for designing immunogens capable of eliciting cross-neutralizing coronavirus antibodies.

CELL REPORTS (2021)

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Article Microbiology

Extensive C->U transition biases in the genomes of a wide range of mammalian RNA viruses; potential associations with transcriptional mutations, damage- or host-mediated editing of viral RNA

Peter Simmonds et al.

Summary: The study found a preponderance of C->U transitions in diverse mammalian RNA viruses, suggesting a potential RNA editing process driving this phenomenon. The presence of genome scale RNA secondary structure was significantly associated with C->U/U->C transition asymmetries, indicating a possible RNA structure dependence of sites targeted for C->U mutations. These C->U mutations accounted for a significant portion of standing sequence variability of structured viruses, potentially driving their sequence diversification and longer-term evolution.

PLOS PATHOGENS (2021)

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Article Virology

Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool

Aine O'Toole et al.

Summary: The global virus genomics community has responded unprecedentedly to the SARS-CoV-2 pandemic, leading to significant advances in 'real-time' generation and sharing of genomic data. The development of new analytical methods, such as pangolin, has been necessary to handle the rapid growth in virus genome data production. Pangolin has processed nearly two million virus genomes, aiding in SARS-CoV-2 genomic epidemiology and providing researchers with valuable information about the pandemic's transmission lineages.

VIRUS EVOLUTION (2021)

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Article Multidisciplinary Sciences

SARS-CoV-2 exposure in wild white-tailed deer (Odocoileus virginianus)

Jeffrey C. Chandler et al.

Summary: Research indicates that white-tailed deer in the United States have been exposed to SARS-CoV-2, with 40% of samples testing positive for antibodies. This suggests that human infections of the novel coronavirus may have an impact on wildlife.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Article Biochemistry & Molecular Biology

Host-directed editing of the SARS-CoV-2 genome

Tobias Mourier et al.

Summary: The extensive sequence data from SARS-CoV-2 in 2020 pandemic has facilitated the study of viral genome evolution, revealing instances of directional mutation pressures exerted on the genome by host antiviral defense systems. It discusses three human defense mechanisms – APOBEC, ADAR, and ROS – and their potential implications on SARS-CoV-2 evolution.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2021)

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Article Multidisciplinary Sciences

Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans

Bas B. Oude Munnink et al.

Summary: Animal experiments have shown that various animals can be infected by SARS-CoV-2, with evidence of animal-to-human transmission within mink farms. Investigation into mink farm outbreaks revealed that the virus was initially introduced by humans and has since evolved, causing transmission between mink farms. Despite enhanced biosecurity measures and culling, transmission occurred between farms in three large clusters with unknown modes of transmission, resulting in a high percentage of infections among mink farm residents and employees.

SCIENCE (2021)

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Clinical and Pathological Findings in SARS-CoV-2 Disease Outbreaks in Farmed Mink (Neovison vison)

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

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