Updated picture of SARS-CoV-2 variants and mutations

Abstract The worldwide burden of coronavirus disease 2019 (COVID-19) is still unremittingly prosecuting, with nearly 300 million infections and over 5.3 million deaths recorded so far since the origin of the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic at the end of the year 2019. The fight against this new highly virulent beta coronavirus appears one of the most strenuous and long challenges that humanity has ever faced, since a definitive treatment has not been identified so far. The adoption of potentially useful physical preventive measures such as lockdowns, social distancing and face masking seems only partially effective for mitigating viral spread, though efficacy and continuation of such measures on the long term is questionable, due to many social and economic reasons. Many COVID-19 vaccines have been developed and are now widely used, though their effectiveness is challenged by several aspects such as low uptake and limited efficacy in some specific populations, as well as by continuous emergence of new mutations in the SARS-CoV-2 genome, accompanying the origin and spread of new variants, which in turn may contribute to further decrease the effectiveness of current vaccines and treatments. This article is hence aimed to provide an updated picture of SARS-CoV-2 variants and mutations that have emerged from November 2019 to present time (i.e., early December 2021).

[1]  A. M. Kilpatrick,et al.  Estimates of reduced vaccine effectiveness against hospitalization, infection, transmission and symptomatic disease of a new SARS-CoV-2 variant, Omicron (B.1.1.529), using neutralizing antibody titers , 2021, medRxiv.

[2]  J. Nie,et al.  The significant immune escape of pseudotyped SARS-CoV-2 variant Omicron , 2021, Emerging microbes & infections.

[3]  A. Sigal,et al.  SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection , 2021, medRxiv.

[4]  S. Hoehl,et al.  Reduced Neutralization of SARS-CoV-2 Omicron Variant by Vaccine Sera and monoclonal antibodies , 2021, medRxiv.

[5]  M. Chawla-Sarkar,et al.  S glycoprotein diversity of the Omicron Variant , 2021, medRxiv.

[6]  J. Doudna,et al.  Rapid assessment of SARS-CoV-2–evolved variants using virus-like particles , 2021, Science.

[7]  Philip L. Tzou,et al.  The biological and clinical significance of emerging SARS-CoV-2 variants , 2021, Nature Reviews Genetics.

[8]  G. Lippi,et al.  Optimizing effectiveness of COVID-19 vaccination: will laboratory stewardship play a role? , 2021, Clinical chemistry and laboratory medicine.

[9]  D. Barh,et al.  Emergence of unique SARS-CoV-2 ORF10 variants and their impact on protein structure and function , 2021, International Journal of Biological Macromolecules.

[10]  Rezwanuzzaman Laskar,et al.  Differential mutation profile of SARS-CoV-2 proteins across deceased and asymptomatic patients , 2021, Chemico-Biological Interactions.

[11]  J. Derrick,et al.  Structural Evaluation of the Spike Glycoprotein Variants on SARS-CoV-2 Transmission and Immune Evasion , 2021, International journal of molecular sciences.

[12]  J. Dushoff,et al.  The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic , 2021, Current Biology.

[13]  G. Lippi,et al.  Anti-SARS-CoV-2 Antibodies Testing in Recipients of COVID-19 Vaccination: Why, When, and How? , 2021, Diagnostics.

[14]  J. Dushoff,et al.  Increased risk of SARS-CoV-2 reinfection associated with emergence of the Omicron variant in South Africa , 2021 .

[15]  OUP accepted manuscript , 2021, Virus Evolution.

[16]  Lanjuan Li,et al.  Patient-derived SARS-CoV-2 mutations impact viral replication dynamics and infectivity in vitro and with clinical implications in vivo , 2020, Cell discovery.

[17]  M. Kearney,et al.  Low genetic diversity may be an Achilles heel of SARS-CoV-2 , 2020, Proceedings of the National Academy of Sciences.

[18]  E. Callaway The coronavirus is mutating — does it matter? , 2020, Nature.

[19]  Y. Furuichi,et al.  RNA‐dependent RNA polymerase, RdRP, a promising therapeutic target for cancer and potentially COVID‐19 , 2020, Cancer science.

[20]  MingKun Li,et al.  Genomic diversity of SARS-CoV-2 in Coronavirus Disease 2019 patients , 2020, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[21]  G. Lippi,et al.  The novel coronavirus (2019-nCoV) outbreak: think the unthinkable and be prepared to face the challenge , 2020, Diagnosis.

[22]  F. Checchi,et al.  Deaths, late deaths, and role of infecting dose in Ebola virus disease in Sierra Leone: retrospective cohort study , 2016, British Medical Journal.

[23]  Robert J. Taylor,et al.  Global Mortality Estimates for the 2009 Influenza Pandemic from the GLaMOR Project: A Modeling Study , 2013, PLoS medicine.

[24]  J. Sanford,et al.  A new look at an old virus: patterns of mutation accumulation in the human H1N1 influenza virus since 1918 , 2012, Theoretical Biology and Medical Modelling.