☆ 4.6 Review

The Remarkable Evolutionary Plasticity of Coronaviruses by Mutation and Recombination: Insights for the COVID-19 Pandemic and the Future Evolutionary Paths of SARS-CoV-2

VIRUSES-BASEL (2022)

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The Neighborhood of the Spike Gene Is a Hotspot for Modular Intertypic Homologous and Nonhomologous Recombination in Coronavirus Genomes

Marios Nikolaidis et al.

Summary: Research has shown that coronaviruses have a strong ability for intergenomic recombination, where they can exchange genetic material not only within the same subgenus but also across different CoV genera, other viruses, and even hosts. These events often occur at double crossovers surrounding the Spike ORF, indicating the instability and mobility of this genomic region.

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Pre-existing polymerase-specific T cells expand in abortive seronegative SARS-CoV-2

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Summary: Research suggests that some individuals can clear potential SARS-CoV-2 infection after exposure, with T cells playing a role in the process. Studying healthcare workers who tested negative for antibodies revealed that they had stronger and more diverse memory T cells, with a focus on RTC.

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Article Immunology

Novel Canine Coronavirus Isolated from a Hospitalized Patient With Pneumonia in East Malaysia

Anastasia N. Vlasova et al.

Summary: This study identified a novel canine-feline recombinant alphacoronavirus isolated from a child with pneumonia, suggesting recent zoonotic transmission and emphasizing the public health threat of animal CoVs. Better surveillance is needed to monitor these viruses and their potential impact on human health.

CLINICAL INFECTIOUS DISEASES (2022)

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Article Infectious Diseases

Prevention of host-to-host transmission by SARS-CoV-2 vaccines

Darius Mostaghimi et al.

Summary: As more people receive the SARS-CoV-2 vaccine worldwide, data is being generated to understand the vaccines' ability to reduce infection. Although randomized trials have shown that these vaccines greatly reduce symptomatic COVID-19, their effects on transmission between individuals are not well-known. This article discusses the available data on approved SARS-CoV-2 vaccines in reducing transmissibility by reducing primary infection, viral replication, transmission capacity, and symptomaticity. It also explores the potential of mucosal-targeted vaccine strategies to more effectively limit transmission compared to intramuscular vaccines. The population-level effects of approved vaccines on transmission are further examined through observational studies following clinical trials and vaccine distribution in real-world settings.

LANCET INFECTIOUS DISEASES (2022)

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Article Biochemistry & Molecular Biology

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Erik Volz et al.

Summary: The study suggests a positive selection for the SARS-CoV-2 spike protein variant D614G in the UK, but no evidence of differences in COVID-19 mortality or clinical severity in patients infected with this variant. 614G is associated with higher viral load and younger age of patients compared to 614D.

CELL (2021)

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Letter Immunology

The spike protein of SARS-CoV-2 variant A.30 is heavily mutated and evades vaccine-induced antibodies with high efficiency

Prerna Arora et al.

CELLULAR & MOLECULAR IMMUNOLOGY (2021)

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Article Biochemistry & Molecular Biology

Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult

Benoit Morel et al.

Summary: Inferring reliable phylogenies from virus sequence data is difficult due to the large number of sequences and low number of mutations; rooting the inferred phylogeny with external outgroups or applying novel computational methods is not credible; automatic classification of current sequences into subclasses for molecular species delimitation is also not possible due to sequences being too closely related.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

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SARS-CoV-2 spillover events

Peng Zhou et al.

SCIENCE (2021)

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Review Immunology

A focused review on technologies, mechanisms, safety, and efficacy of available COVID-19 vaccines

Parisa Ghasemiyeh et al.

Summary: It has been 20 months since the detection of COVID-19 cases in Wuhan, China, which rapidly spread worldwide and led to a pandemic. Different therapeutic options have been considered, but challenges remain in treating moderate to severe cases and those with underlying conditions. Public vaccination is believed to be the most efficient strategy to control morbidity and mortality.

INTERNATIONAL IMMUNOPHARMACOLOGY (2021)

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Article Microbiology

Atypical Divergence of SARS-CoV-2 Orf8 from Orf7a within the Coronavirus Lineage Suggests Potential Stealthy Viral Strategies in Immune Evasion

Russell Y. Neches et al.

Summary: Orf8 is one of the most puzzling genes in the SARS lineage of coronaviruses, showing distant sequence similarities with Orf7a and X4-like genes, with subtle conservation patterns in an immunoglobulin-like beta sandwich topology. Orf7a and Orf8 protein families exhibit different evolutionary trajectories within the coronavirus lineage, partly due to their interactions with the mammalian host cell. The high accuracy of the sequence space walk process and the idiosyncratic divergence patterns highlight the unique features of Orf8 in the evolution of the virus.

MBIO (2021)

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Article Microbiology

The coronavirus proofreading exoribonuclease mediates extensive viral recombination

Jennifer Gribble et al.

Summary: Recombination is essential for coronavirus diversity and the emergence of new strains. The mechanisms of CoV recombination are not well understood, but studies have shown extensive and diverse recombination products in CoVs during replication. The nsp14-ExoN protein is crucial for native recombination in CoVs, highlighting its potential as a target for inhibitors to control SARS-CoV-2 and future emerging zoonotic CoVs.

PLOS PATHOGENS (2021)

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Article Immunology

Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses

Saathvik R. Kannan et al.

Summary: The study revealed differences in the mutational profile between Delta and Delta Plus variants, with Delta Plus having more high-prevalence mutations and unique signature mutations. Structural analysis showed that these mutations can weaken the interactions between the virus and antibodies.

JOURNAL OF AUTOIMMUNITY (2021)

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Article Biochemistry & Molecular Biology

Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity

Wilfredo F. Garcia-Beltran et al.

Summary: New variants of SARS-CoV-2 show high resistance to vaccine neutralization, with some able to escape vaccine responses with just a few mutations, highlighting the importance of developing broadly protective measures against variants.

CELL (2021)

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Article Biochemistry & Molecular Biology

Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera

Daming Zhou et al.

Summary: The race to develop vaccines against SARS-CoV-2 variants, such as B.1.1.7, B.1.351, and P.1, is ongoing as these variants have mutations in the spike protein, potentially leading to immune escape. A structure-function analysis of B.1.351 revealed tighter ACE2 binding and widespread evasion from monoclonal antibody neutralization, particularly driven by the E484K mutation.

CELL (2021)

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Article Multidisciplinary Sciences

Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift

Elisabetta Cameroni et al.

NATURE (2021)

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HOW COVID VACCINES SHAPED 2021-IN EIGHT POWERFUL CHARTS

Smriti Mallapaty et al.

Summary: The vaccination of more than four billion people and limited access for many others were major factors this year, with Omicron's emergence further complicating the situation.

NATURE (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

SARS-CoV-2 spike D614G change enhances replication and transmission

Bin Zhou et al.

Summary: Research has shown that the D614G substitution in the spike protein of SARS-CoV-2 leads to increased binding and replication potential in humans, as well as significantly higher replication and transmissibility in different animal models, providing an explanation for the global prevalence of this variant in the COVID-19 pandemic.

NATURE (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.

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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 Biochemistry & Molecular Biology

Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen

Oscar A. MacLean et al.

Summary: The study suggests that SARS-CoV-2 has undergone limited significant adaptation to humans, with evidence of moderate positive selection concentrated in the early phases of the pandemic. In contrast, bat Sarbecoviruses show evidence of significant positive selection and an adaptive depletion in CpG composition. This indicates that the progenitor of SARS-CoV-2 likely acquired efficient human-human transmission capabilities through evolutionary history in bats, leading to the emergence of a relatively generalist virus.

PLOS BIOLOGY (2021)

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Review Virology

Interspecies Jumping of Bat Coronaviruses

Antonio C. P. Wong et al.

Summary: In the past two decades, there have been several interspecies jumping events of coronaviruses (CoV) between bats and other animals, resulting in major epidemics/pandemics and high fatality rates. The discovery of SARS-related CoVs in bats and civets, as well as genomic studies, have confirmed the transmission routes from bats to civets to humans. The MERS epidemic, with dromedaries as the reservoir, also highlights the potential risks of interspecies jumping events.

VIRUSES-BASEL (2021)

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Article Biochemistry & Molecular Biology

Antibody evasion by the P.1 strain of SARS-CoV-2

Wanwisa Dejnirattisai et al.

Summary: Ending the SARS-CoV-2 pandemic requires global vaccination. New virus strains with mutations impact antibody responses, but some variants are less resistant than others. A monoclonal antibody can neutralize different variants and partially restore neutralization potency for other public antibodies.

CELL (2021)

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Article Multidisciplinary Sciences

Neutralizing antibody vaccine for pandemic and pre-emergent coronaviruses

Kevin O. Saunders et al.

Summary: This study demonstrates that immunizing macaques with nanoparticles conjugated with the receptor-binding domain of SARS-CoV-2, adjuvanted with 3M-052 and alum, can elicit cross-neutralizing antibody responses against various coronaviruses and provide protection against SARS-CoV-2. Nucleoside-modified mRNAs encoding stabilized spike proteins also induce antibody responses against different coronaviruses, suggesting potential for developing vaccines against multiple betacoronaviruses in the future.

NATURE (2021)

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Article Medicine, General & Internal

Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant

S. A. Madhi et al.

Summary: The ChAdOx1 nCoV-19 vaccine did not provide significant protection against mild-to-moderate Covid-19 caused by the B.1.351 variant, with an efficacy of 10.4%. The incidence of serious adverse events was balanced between the vaccine and placebo groups.

NEW ENGLAND JOURNAL OF MEDICINE (2021)

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Article Multidisciplinary Sciences

Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain

Mohamed Raef Smaoui et al.

Summary: The interaction between the receptor-binding domain (RBD) of the SARS-CoV-2 spike glycoprotein and the ACE2 enzyme is crucial for the virus to enter cells, and current therapeutic efforts aim to affect this interaction. Analyzing spike protein mutations and toxicity potential provides insights for future vaccine development. Through computational exploration, potential mutations that can stabilize the spike protein and increase infectivity have been identified.

SCIENTIFIC REPORTS (2021)

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Article Biochemistry & Molecular Biology

Characterization of SARS-CoV-2 proteins reveals Orf6 pathogenicity, subcellular localization, host interactions and attenuation by Selinexor

Jin-Gu Lee et al.

Summary: This study identified Orf6 as a highly pathogenic protein in the SARS-CoV-2 genome and its interaction with key host proteins. The drug Selinexor was found to attenuate Orf6-induced cellular toxicity, suggesting it as a potential candidate for targeting Orf6 host protein interactions that lead to cytotoxicity.

CELL AND BIOSCIENCE (2021)

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Article Cell Biology

SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization

Markus Hoffmann et al.

Summary: Transmission of SARS-CoV-2 from humans to farmed mink and back raises concerns of genetic variants with potential increased threat to human health. Mutations in the spike protein of SARS-CoV-2 from mink allow efficient entry into human cells and inhibition by ACE2, while mutation Y453F reduces neutralization by certain antibodies authorized for COVID-19 therapy. Antibody responses induced by infection or specific treatments might not offer adequate protection against SARS-CoV-2 variants from mink.

CELL REPORTS (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 Microbiology

The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets

Thomas P. Peacock et al.

Summary: Efficient transmission of SARS-CoV-2 among infected ferrets is dependent on a functional furin cleavage site in the spike protein. The virus has a selective advantage in lung cells and primary human airway epithelial cells due to a polybasic insertion, but replication may be impaired in certain cell lines.

NATURE MICROBIOLOGY (2021)

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Article Immunology

A Synthetic Peptide CTL Vaccine Targeting Nucleocapsid Confers Protection from SARS-CoV-2 Challenge in Rhesus Macaques

Paul E. Harris et al.

Summary: This study tested the efficacy of a peptide-based vaccine targeting MHC class I epitopes on the SARS-CoV-2 nucleocapsid protein using a macaque model. The results showed that vaccinated animals had lower viral loads and better immune responses when challenged with SARS-CoV-2 compared to controls. The study demonstrates that this peptide vaccine can provide protection against SARS-CoV-2 infection in nonhuman primates.

VACCINES (2021)

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Article Immunology

Designing a SARS-CoV-2 T-Cell-Inducing Vaccine for High-Risk Patient Groups

Hans-Georg Rammensee et al.

Summary: The study involved two vaccinations of a healthy volunteer with SARS-CoV-2-derived peptides, resulting in CD4 T cell responses against some peptides after 19 days. These findings support the design of a T-cell-inducing vaccine for high-risk patients with weakened lymphocyte function.

VACCINES (2021)

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Article Biochemistry & Molecular Biology

Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic

Ben Jackson et al.

Summary: The study identified multiple independent origins of recombinant SARS-CoV-2 viruses in the United Kingdom, showing similarities to the B.1.1.7 variant but also some unique features. Evidence suggested that these viruses have the capability of transmission.

CELL (2021)

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Review Biochemistry & Molecular Biology

The origins of SARS-CoV-2: A critical review

Edward C. Holmes et al.

Summary: This article critically reviews the current scientific evidence to help clarify the origin of SARS-CoV-2. Recent debate has centered around two competing ideas: a laboratory escape scenario and zoonotic emergence.

CELL (2021)

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Article Immunology

Cutting Edge: Nucleocapsid Vaccine Elicits Spike-Independent SARS-CoV-2 Protective Immunity

William E. Matchett et al.

Summary: Vaccination with a human adenovirus type 5 vector expressing the SARS-CoV-2 nucleocapsid (N) protein can establish protective immunity and reduce weight loss and viral load in vaccinated Syrian hamsters and K18hACE2 mice. Vaccinated mice showed rapid N-specific T cell recall responses in the respiratory mucosa. This study supports the idea of including additional viral antigens in SARS-CoV-2 vaccines to broaden epitope coverage and immune effector mechanisms.

JOURNAL OF IMMUNOLOGY (2021)

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Article Virology

A Novel Potentially Recombinant Rodent Coronavirus with a Polybasic Cleavage Site in the Spike Protein

Xin Li et al.

Summary: The study conducted virus surveillance among rodents in rural and urban areas of South China, identifying three rodent coronaviruses, one of which was determined to be a potentially recombinant coronavirus with a polybasic cleavage site in the S protein. This new finding provides insight into the potential interspecies transmission of coronaviruses and highlights the importance of utilizing a One Health approach for virus discovery.

JOURNAL OF VIROLOGY (2021)

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Article Biochemistry & Molecular Biology

Stepwise Evolution and Exceptional Conservation of ORF1a/b Overlap in Coronaviruses

Han Mei et al.

Summary: The programmed frameshift element (PFE) is crucial for the propagation of coronaviruses, consisting of genomic features, overlapping reading frames, slippery sequences, and complex secondary structure elements that place severe constraints on the region. Evolutionary dynamics and exceptional conservation within the PFE region were demonstrated through comparative analysis of coronaviral genomic data from over 1,500,000 complete genomes and 55,000 raw read data sets.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

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Review Microbiology

SARS-CoV-2 variants, spike mutations and immune escape

William T. Harvey et al.

Summary: The evolution of SARS-CoV-2 has been characterized by the emergence of mutations and variants that impact virus characteristics. Manufacturers are preparing for possible updates to vaccines in response to changes in the virus population, and it is crucial to monitor genetic and antigenic changes alongside experiments to understand the impacts of mutations.

NATURE REVIEWS MICROBIOLOGY (2021)

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Editorial Material Biochemistry & Molecular Biology

Molnupiravir: coding for catastrophe

Brandon Malone et al.

Summary: Molnupiravir disrupts the accuracy of SARS-CoV-2 genome replication and prevents viral propagation by fostering error accumulation, a process known as 'error catastrophe'.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2021)

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Article Medicine, General & Internal

Pan-Sarbecovirus Neutralizing Antibodies in BNT162b2-Immunized SARS-CoV-1 Survivors

Chee-Wah Tan et al.

Summary: Survivors of SARS-CoV-1 infection who received the BNT162b2 mRNA vaccine produced potent cross-clade pan-sarbecovirus neutralizing antibodies, capable of neutralizing various variants of concern and potential human-infecting coronaviruses, indicating the feasibility of a pan-sarbecovirus vaccine strategy.

NEW ENGLAND JOURNAL OF MEDICINE (2021)

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Article Multidisciplinary Sciences

Cross-reactive CD4+ T cells enhance SARS-CoV-2 immune responses upon infection and vaccination

Lucie Loyal et al.

Summary: The study demonstrates that preexisting spike-cross-reactive T cells play a functional role in the immune response to SARS-CoV-2 infection and vaccination. Cross-reactive immunity may explain the rapid induction of immunity after primary SARS-CoV-2 immunization and the high rate of asymptomatic or mild COVID-19 cases.

SCIENCE (2021)

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Article Multidisciplinary Sciences

Chimeric spike mRNA vaccines protect against Sarbecovirus challenge in mice

David R. Martinez et al.

Summary: The emergence of SARS-CoV in 2003 and SARS-CoV-2 in 2019 has led to the development of universal vaccination strategies against the broader Sarbecovirus subgenus. Through the use of chimeric spike designs, high levels of broadly protective neutralizing antibodies have been induced against various high-risk Sarbecoviruses, showing potential for preventing SARS-like zoonotic coronavirus infections with pandemic potential.

SCIENCE (2021)

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Review Virology

Evolutionary trajectory of SARS-CoV-2 and emerging variants

Jalen Singh et al.

Summary: This review examines the origins of all known human coronaviruses, the evolutionary trajectory of SARS-CoV-2, and the emerging mutations within SARS-CoV-2 and variants of concern. It also highlights the impact of these mutations on virus transmission, pathogenicity, and neutralization by natural or vaccine-mediated immunity.

VIROLOGY JOURNAL (2021)

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Functions of Coronavirus Accessory Proteins: Overview of the State of the Art

Puxian Fang et al.

Summary: Coronavirus accessory proteins, though dispensable for replication in vitro, play crucial roles in regulating immunity, proliferation, and pathogenicity. Their function in virus infection and pathogenesis, particularly in interaction with host cells, is of significant interest.

VIRUSES-BASEL (2021)

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Article Multidisciplinary Sciences

Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains

Simon A. Rella et al.

Summary: The study suggests that a high vaccination rate can reduce the probability of emergence of vaccine-resistant strains, while a relaxation of non-pharmaceutical intervention measures when most of the population has been vaccinated may increase the risk of resistant strains. Therefore, maintaining transmission-reducing behaviors throughout the entire vaccination period is crucial to minimize the establishment of resistant strains.

SCIENTIFIC REPORTS (2021)

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Article Cell Biology

Combining spike- and nucleocapsid-based vaccines improves distal control of SARS-CoV-2

Tanushree Dangi et al.

Summary: Incorporating nucleocapsid as an antigen in SARS-CoV-2 vaccines can improve acute protection in both the lungs and brain, suggesting the inclusion of nucleocapsid in next-generation COVID-19 vaccines is warranted. This finding provides important insights for the development of future vaccines against COVID-19.

CELL REPORTS (2021)

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Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2

Juan Angel Patino-Galindo et al.

Summary: Through phylogenetic and recombination analyses, this study identified evidence of a recombination event in the receptor binding domain (RBD) of both SARS-CoV and SARS-CoV-2, resulting in increased binding affinity to the human ACE2 receptor. Structural modeling suggests that ancestors of SARS-CoV-2 may have acquired the ability to infect humans decades ago, with further mutations in the RBD enhancing binding affinity with the human receptor in SARS-CoV and SARS-CoV-2.

GENOME MEDICINE (2021)

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Article Biochemical Research Methods

The interplay of SARS-CoV-2 evolution and constraints imposed by the structure and functionality of its proteins

Lukasz Jaroszewski et al.

Summary: The mutation patterns in the SARS-CoV-2 virus genomes are closely linked to the structure and function of the proteins they encode, with highly mutated regions corresponding to more easily adaptable structural regions. Understanding these patterns is important for developing tools like antibodies, vaccines, and drugs to target conserved genomic regions due to natural selection.

PLOS COMPUTATIONAL BIOLOGY (2021)

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Article Microbiology

In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2

Agnieszka M. Szemiel et al.

Summary: This study selected drug-resistant SARS-CoV-2 populations with decreased sensitivity to remdesivir (RDV) in vitro, identifying a mutation in NSP12 that decreases RDV sensitivity. There is no evidence of widespread transmission of RDV-resistant mutants among globally circulating SARS-CoV-2 variants. Additionally, emerging SARS-CoV-2 variants showed substitutions at Spike sites corresponding to those identified in vitro, indicating their potential to arise without immune selection.

PLOS PATHOGENS (2021)

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Editorial Material Microbiology

SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse

Frank Konings et al.

Summary: A group convened and led by the Virus Evolution Working Group of the World Health Organization has announced a naming scheme to enable clear communication about SARS-CoV-2 variants of interest and concern.

NATURE MICROBIOLOGY (2021)

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Article Virology

Recombinant SARS-CoV-2 Genomes Circulated at Low Levels Over The First Year of The Pandemic

David VanInsberghe et al.

Virus Evolution (2021)

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A comparative recombination analysis of human coronaviruses and implications for the SARS-CoV-2 pandemic

Simon Pollett et al.

Summary: The study evaluated recombination in the evolution of human coronaviruses, finding evidence of recombination events in SARS-CoV-2, SARS-CoV-1, and other coronaviruses. Recombination breakpoints were more likely to occur in the non-ORF1 region of the genome containing structural genes, significantly affecting the temporal structure of the data. The findings underscore the importance of genomic surveillance to detect recombination, especially in SARS-CoV-2, which could potentially lead to immune evasion.

SCIENTIFIC REPORTS (2021)

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Review Public, Environmental & Occupational Health

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Melina Michelen et al.

Summary: Long COVID is a complex condition with prolonged and heterogeneous symptoms, including weakness, general malaise, fatigue, concentration impairment, and breathlessness. Approximately 37% of patients reported reduced quality of life, and 26% of studies presented evidence of reduced pulmonary function. There is an urgent need for further studies to explore the etiology, risk factors, and biomarkers of long COVID in different populations and settings.

BMJ GLOBAL HEALTH (2021)

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Review Biochemistry & Molecular Biology

Therapeutic targets and interventional strategies in COVID-19: mechanisms and clinical studies

Yu-Wen Zhou et al.

Summary: Due to limitations in current drug discovery efforts against SARS-CoV-2 and a lack of understanding of the biological mechanisms underlying COVID-19, alternative therapeutic targets are urgently needed. This study classified current COVID-19 therapeutic strategies into targeting the virus and targeting the host, focusing on repurposing drugs, emerging approaches, and promising potential targets.

SIGNAL TRANSDUCTION AND TARGETED THERAPY (2021)

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Article Multidisciplinary Sciences

Immunization with RBD-P2 and N protects against SARS-CoV-2 in nonhuman primates

So-Hee Hong et al.

Summary: A novel subunit vaccine was developed and shown to be effective in rodents and nonhuman primates. The addition of SARS-CoV-2 nucleocapsid protein enhanced the immune response of the vaccine, supporting the further development of RBD-P2 as a candidate vaccine against SARS-CoV-2.

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Article Biochemistry & Molecular Biology

Characterizing Transcriptional Regulatory Sequences in Coronaviruses and Their Role in Recombination

Yiyan Yang et al.

Summary: The study found that transcriptional regulatory sequences (TRS) in coronavirus genomes are conserved within different genera, with recombination hotspots frequently colocated with TRS-B sites.

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A nidovirus perspective on SARS-CoV-2

Anastasia A. Gulyaeva et al.

Summary: The two pandemics of respiratory distress diseases caused by zoonotic introductions of Severe acute respiratory syndrome-related coronaviruses in the 21st century have sparked unprecedented interest in coronavirus research, particularly in SARS-CoV and SARS-CoV-2. Comparative genomics of Nidovirales has played a crucial role in understanding the variations and conservations among different viruses within this vast order.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2021)

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Compositional diversity and evolutionary pattern of coronavirus accessory proteins

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Summary: Accessory proteins play crucial roles in coronavirus-host interactions. A standardized genome annotation tool, CoroAnnoter, was developed to study the composition, evolutionary patterns, and host interactions of accessory proteins in coronaviruses. Variations in the number of accessory proteins were observed among different coronaviruses, with SARS-CoV-2 and SARS-CoV having the most. Evolutionary analysis revealed conservation and diversity in the distribution of accessory proteins within and between different genera of coronaviruses. Additionally, comparison of virus-host interaction networks of SARS-CoV-2 and SARS-CoV accessory proteins showed shared antiviral signaling pathways and biological processes.

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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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Review Virology

Emerging coronaviruses: Genome structure, replication, and pathogenesis

Yu Chen et al.

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A new coronavirus associated with human respiratory disease in China

Fan Wu et al.

NATURE (2020)

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A pneumonia outbreak associated with a new coronavirus of probable bat origin

Peng Zhou et al.

NATURE (2020)

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Nucleocapsid proteins from other swine enteric coronaviruses differentially modulate PEDV replication

Suttipun Sungsuwan et al.

VIROLOGY (2020)

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Article Microbiology

The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2

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Recombinant Canine Coronaviruses Related to Transmissible Gastroenteritis Virus of Swine Are Circulating in Dogs

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Genetic interactions between an essential 3′ cis-acting RNA pseudoknot, replicase gene products, and the extreme 3′ end of the mouse coronavirus genome

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High fidelity of murine hepatitis virus replication is decreased in nsp14 exoribonuclease mutants

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Comparative analysis of twelve genomes of three novel group 2c and group 2d coronaviruses reveals unique group and subgroup features

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Rewiring the severe acute respiratory syndrome coronavirus (SARS-CoV) transcription circuit: Engineering a recombination-resistant genome

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Animal origins of the severe acute respiratory syndrome coronavirus: Insight from ACE2-S-protein interactions

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Nidovirales:: Evolving the largest RNA virus genome

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The Inverse relationship between evolutionary rate and age of mammalian genes is an artifact of increased genetic distance with rate of evolution and time of divergence

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Selective replication of coronavirus genomes that express nucleocapsid protein

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Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human

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Complete genomic sequence of human coronavirus OC43:: Molecular clock analysis suggests a relatively recent zoonotic coronavirus transmission event

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Recombinant avian infectious bronchitis virus expressing a heterologous spike gene demonstrates that the spike protein is a determinant of cell tropism

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RNA virus error catastrophe: Direct molecular test by using ribavirin

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Retargeting of coronavirus by substitution of the spike glycoprotein ectodomain: Crossing the host cell species barrier

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Natural genetic exchanges between vaccine and wild poliovirus strains in humans

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