One year into the pandemic: Short-term evolution of SARS-CoV-2 and emergence of new lineages

The COVID-19 pandemic was officially declared on March 11th, 2020. Since the very beginning, the spread of the virus has been tracked nearly in real-time by worldwide genome sequencing efforts. As of March 2021, more than 830,000 SARS-CoV-2 genomes have been uploaded in GISAID and this wealth of dat...

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Published inInfection, genetics and evolution Vol. 92; p. 104869
Main Authors González-Candelas, Fernando, Shaw, Marie-Anne, Phan, Tung, Kulkarni-Kale, Urmila, Paraskevis, Dimitrios, Luciani, Fabio, Kimura, Hirokazu, Sironi, Manuela
Format Journal Article
LanguageEnglish
Published Netherlands Elsevier B.V 01.08.2021
The Authors. Published by Elsevier B.V
Subjects
Biological Evolution
COVID-19
COVID-19 - epidemiology
COVID-19 - immunology
COVID-19 - virology
COVID-19 Vaccines - immunology
Diagnostic tests
Genetic Variation
Humans
Lineages
Review
SARS-CoV-2
SARS-CoV-2 - genetics
Vaccination
VACCINES
Variants
COVID-19
Variants
Lineages
SARS-CoV-2
Diagnostic tests
VACCINES
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Abstract The COVID-19 pandemic was officially declared on March 11th, 2020. Since the very beginning, the spread of the virus has been tracked nearly in real-time by worldwide genome sequencing efforts. As of March 2021, more than 830,000 SARS-CoV-2 genomes have been uploaded in GISAID and this wealth of data allowed researchers to study the evolution of SARS-CoV-2 during this first pandemic year. In parallel, nomenclatures systems, often with poor consistency among each other, have been developed to designate emerging viral lineages. Despite general fears that the virus might mutate to become more virulent or transmissible, SARS-CoV-2 genetic diversity has remained relatively low during the first ~ 8 months of sustained human-to-human transmission. At the end of 2020/beginning of 2021, though, some alarming events started to raise concerns of possible changes in the evolutionary trajectory of the virus. Specifically, three new viral variants associated with extensive transmission have been described as variants of concern (VOC). These variants were first reported in the UK (B.1.1.7), South Africa (B.1.351) and Brazil (P.1). Their designation as VOCs was determined by an increase of local cases and by the high number of amino acid substitutions harboured by these lineages. This latter feature is reminiscent of viral sequences isolated from immunocompromised patients with long-term infection, suggesting a possible causal link. Here we review the events that led to the identification of these lineages, as well as emerging data concerning their possible implications for viral phenotypes, reinfection risk, vaccine efficiency and epidemic potential. Most of the available evidence is, to date, provisional, but still represents a starting point to uncover the potential threat posed by the VOCs. We also stress that genomic surveillance must be strengthened, especially in the wake of the vaccination campaigns. •After months of human-to-human transmission divergent SARS-CoV-2 lineages have emerged.•The nomenclature is debated, but PANGO lineage names are: B.1.1.7, B.1.351 and P.1.•These lineages display a number of amino acid changes, especially in the S protein.•B.1.1.7, B.1.351 and P.1 may be more transmissible, their effect on disease severity is uncertain.•Some mutations in B.1.351 and P.1 may affect antibody binding or vaccine efficiency.
AbstractList The COVID-19 pandemic was officially declared on March 11th, 2020. Since the very beginning, the spread of the virus has been tracked nearly in real-time by worldwide genome sequencing efforts. As of March 2021, more than 830,000 SARS-CoV-2 genomes have been uploaded in GISAID and this wealth of data allowed researchers to study the evolution of SARS-CoV-2 during this first pandemic year. In parallel, nomenclatures systems, often with poor consistency among each other, have been developed to designate emerging viral lineages. Despite general fears that the virus might mutate to become more virulent or transmissible, SARS-CoV-2 genetic diversity has remained relatively low during the first ~ 8 months of sustained human-to-human transmission. At the end of 2020/beginning of 2021, though, some alarming events started to raise concerns of possible changes in the evolutionary trajectory of the virus. Specifically, three new viral variants associated with extensive transmission have been described as variants of concern (VOC). These variants were first reported in the UK (B.1.1.7), South Africa (B.1.351) and Brazil (P.1). Their designation as VOCs was determined by an increase of local cases and by the high number of amino acid substitutions harboured by these lineages. This latter feature is reminiscent of viral sequences isolated from immunocompromised patients with long-term infection, suggesting a possible causal link. Here we review the events that led to the identification of these lineages, as well as emerging data concerning their possible implications for viral phenotypes, reinfection risk, vaccine efficiency and epidemic potential. Most of the available evidence is, to date, provisional, but still represents a starting point to uncover the potential threat posed by the VOCs. We also stress that genomic surveillance must be strengthened, especially in the wake of the vaccination campaigns.
The COVID-19 pandemic was officially declared on March 11 , 2020. Since the very beginning, the spread of the virus has been tracked nearly in real-time by worldwide genome sequencing efforts. As of March 2021, more than 830,000 SARS-CoV-2 genomes have been uploaded in GISAID and this wealth of data allowed researchers to study the evolution of SARS-CoV-2 during this first pandemic year. In parallel, nomenclatures systems, often with poor consistency among each other, have been developed to designate emerging viral lineages. Despite general fears that the virus might mutate to become more virulent or transmissible, SARS-CoV-2 genetic diversity has remained relatively low during the first ~ 8 months of sustained human-to-human transmission. At the end of 2020/beginning of 2021, though, some alarming events started to raise concerns of possible changes in the evolutionary trajectory of the virus. Specifically, three new viral variants associated with extensive transmission have been described as variants of concern (VOC). These variants were first reported in the UK (B.1.1.7), South Africa (B.1.351) and Brazil (P.1). Their designation as VOCs was determined by an increase of local cases and by the high number of amino acid substitutions harboured by these lineages. This latter feature is reminiscent of viral sequences isolated from immunocompromised patients with long-term infection, suggesting a possible causal link. Here we review the events that led to the identification of these lineages, as well as emerging data concerning their possible implications for viral phenotypes, reinfection risk, vaccine efficiency and epidemic potential. Most of the available evidence is, to date, provisional, but still represents a starting point to uncover the potential threat posed by the VOCs. We also stress that genomic surveillance must be strengthened, especially in the wake of the vaccination campaigns.
The COVID-19 pandemic was officially declared on March 11th, 2020. Since the very beginning, the spread of the virus has been tracked nearly in real-time by worldwide genome sequencing efforts. As of March 2021, more than 830,000 SARS-CoV-2 genomes have been uploaded in GISAID and this wealth of data allowed researchers to study the evolution of SARS-CoV-2 during this first pandemic year. In parallel, nomenclatures systems, often with poor consistency among each other, have been developed to designate emerging viral lineages. Despite general fears that the virus might mutate to become more virulent or transmissible, SARS-CoV-2 genetic diversity has remained relatively low during the first ~ 8 months of sustained human-to-human transmission. At the end of 2020/beginning of 2021, though, some alarming events started to raise concerns of possible changes in the evolutionary trajectory of the virus. Specifically, three new viral variants associated with extensive transmission have been described as variants of concern (VOC). These variants were first reported in the UK (B.1.1.7), South Africa (B.1.351) and Brazil (P.1). Their designation as VOCs was determined by an increase of local cases and by the high number of amino acid substitutions harboured by these lineages. This latter feature is reminiscent of viral sequences isolated from immunocompromised patients with long-term infection, suggesting a possible causal link. Here we review the events that led to the identification of these lineages, as well as emerging data concerning their possible implications for viral phenotypes, reinfection risk, vaccine efficiency and epidemic potential. Most of the available evidence is, to date, provisional, but still represents a starting point to uncover the potential threat posed by the VOCs. We also stress that genomic surveillance must be strengthened, especially in the wake of the vaccination campaigns. •After months of human-to-human transmission divergent SARS-CoV-2 lineages have emerged.•The nomenclature is debated, but PANGO lineage names are: B.1.1.7, B.1.351 and P.1.•These lineages display a number of amino acid changes, especially in the S protein.•B.1.1.7, B.1.351 and P.1 may be more transmissible, their effect on disease severity is uncertain.•Some mutations in B.1.351 and P.1 may affect antibody binding or vaccine efficiency.
The COVID-19 pandemic was officially declared on March 11 th , 2020. Since the very beginning, the spread of the virus has been tracked nearly in real-time by worldwide genome sequencing efforts. As of March 2021, more than 830,000 SARS-CoV-2 genomes have been uploaded in GISAID and this wealth of data allowed researchers to study the evolution of SARS-CoV-2 during this first pandemic year. In parallel, nomenclatures systems, often with poor consistency among each other, have been developed to designate emerging viral lineages. Despite general fears that the virus might mutate to become more virulent or transmissible, SARS-CoV-2 genetic diversity has remained relatively low during the first ~ 8 months of sustained human-to-human transmission. At the end of 2020/beginning of 2021, though, some alarming events started to raise concerns of possible changes in the evolutionary trajectory of the virus. Specifically, three new viral variants associated with extensive transmission have been described as variants of concern (VOC). These variants were first reported in the UK (B.1.1.7), South Africa (B.1.351) and Brazil (P.1). Their designation as VOCs was determined by an increase of local cases and by the high number of amino acid substitutions harboured by these lineages. This latter feature is reminiscent of viral sequences isolated from immunocompromised patients with long-term infection, suggesting a possible causal link. Here we review the events that led to the identification of these lineages, as well as emerging data concerning their possible implications for viral phenotypes, reinfection risk, vaccine efficiency and epidemic potential. Most of the available evidence is, to date, provisional, but still represents a starting point to uncover the potential threat posed by the VOCs. We also stress that genomic surveillance must be strengthened, especially in the wake of the vaccination campaigns.
ArticleNumber 104869
Author González-Candelas, Fernando
Phan, Tung
Kulkarni-Kale, Urmila
Paraskevis, Dimitrios
Luciani, Fabio
Shaw, Marie-Anne
Kimura, Hirokazu
Sironi, Manuela
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  surname: González-Candelas
  fullname: González-Candelas, Fernando
  organization: Joint Research Unit Infection and Public Health FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio) and CIBER in Epidemiology and Public Health, Valencia, Spain
– sequence: 2
  givenname: Marie-Anne
  surname: Shaw
  fullname: Shaw, Marie-Anne
  organization: Leeds Institute of Medical Research at St James's, School of Medicine, University of Leeds, Leeds, United Kingdom
– sequence: 3
  givenname: Tung
  surname: Phan
  fullname: Phan, Tung
  organization: Division of Clinical Microbiology, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
– sequence: 4
  givenname: Urmila
  surname: Kulkarni-Kale
  fullname: Kulkarni-Kale, Urmila
  organization: Bioinformatics Centre, Savitribai Phule Pune University, Ganeshkhind, Pune 411007, Maharashtra, India
– sequence: 5
  givenname: Dimitrios
  surname: Paraskevis
  fullname: Paraskevis, Dimitrios
  organization: Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
– sequence: 6
  givenname: Fabio
  surname: Luciani
  fullname: Luciani, Fabio
  organization: University of New South Wales, Sydney 2052, New South Wales, Australia
– sequence: 7
  givenname: Hirokazu
  surname: Kimura
  fullname: Kimura, Hirokazu
  organization: Department of Health Science, Gunma Paz University Graduate School, Takasaki, Gunma 370-0006, Japan
– sequence: 8
  givenname: Manuela
  surname: Sironi
  fullname: Sironi, Manuela
  email: manuela.sironi@bp.LNF.it
  organization: Bioinformatics Unit, Scientific Institute IRCCS E. MEDEA, Bosisio Parini (LC), Italy
BackLink https://www.ncbi.nlm.nih.gov/pubmed/33915216$$D View this record in MEDLINE/PubMed
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Keywords COVID-19
Variants
Lineages
SARS-CoV-2
Diagnostic tests
VACCINES
Language English
License This is an open access article under the CC BY license.
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PublicationTitle Infection, genetics and evolution
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Snippet The COVID-19 pandemic was officially declared on March 11th, 2020. Since the very beginning, the spread of the virus has been tracked nearly in real-time by...
The COVID-19 pandemic was officially declared on March 11 , 2020. Since the very beginning, the spread of the virus has been tracked nearly in real-time by...
The COVID-19 pandemic was officially declared on March 11 th , 2020. Since the very beginning, the spread of the virus has been tracked nearly in real-time by...
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StartPage 104869
SubjectTerms Biological Evolution
COVID-19
COVID-19 - epidemiology
COVID-19 - immunology
COVID-19 - virology
COVID-19 Vaccines - immunology
Diagnostic tests
Genetic Variation
Humans
Lineages
Review
SARS-CoV-2
SARS-CoV-2 - genetics
Vaccination
VACCINES
Variants
Title One year into the pandemic: Short-term evolution of SARS-CoV-2 and emergence of new lineages
URI https://dx.doi.org/10.1016/j.meegid.2021.104869
https://www.ncbi.nlm.nih.gov/pubmed/33915216
https://search.proquest.com/docview/2520866807
https://pubmed.ncbi.nlm.nih.gov/PMC8074502
Volume 92
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