ArticlePathogens (Basel, Switzerland)2020
Genomic Diversity and Hotspot Mutations in 30,983 SARS-CoV-2 Genomes: Moving Toward a Universal Vaccine for the "Confined Virus"?
Article in Pathogens (Basel, Switzerland), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
47 citing papers in PubMed, 1 synthesis or guideline pooled it, 71 citations in OpenAlex.
- Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review.European journal of medical research · 2021Pooled it
- Germline-Targeting Strategies to Induce bNAbs against HIV-1.Current HIV research · 2026Review
- From Panels to Pathogen Networks: The Expanding Role of Targeted Sequencing in Veterinary Medicine.Biology · 2025Review
- Design and Characterization of Bispecific and Trispecific Antibodies Targeting SARS-CoV-2.Vaccines · 2025Article
- Emergence of the B.1.214.2 SARS-CoV-2 lineage with an Omicron-like spike insertion and a unique upper airway immune signature.BMC infectious diseases · 2024Article
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- Computational Drug Design Strategies for Fighting the COVID-19 Pandemic.Advances in experimental medicine and biology · 2024Article
- Identification of hACE2-interacting sites in SARS-CoV-2 spike receptor binding domain for antiviral drugs screening.Virus research · 2022Article
- A Preliminary Genomic Analysis of the Omicron Variants of SARS-CoV-2 in Central India During the third wave of the COVID-19 Pandemic.Archives of medical research · 2022Article
- SARS-CoV-2 Amino Acid Mutations Detection in Greek Patients Infected in the First Wave of the Pandemic.Microorganisms · 2022Article
- The first three waves of the Covid-19 pandemic hint at a limited genetic repertoire for SARS-CoV-2.FEMS microbiology reviews · 2022Article
- Ex vivo and in vivo suppression of SARS-CoV-2 with combinatorial AAV/RNAi expression vectors.Molecular therapy : the journal of the American Society of Gene Therapy · 2022Article
- SARS-CoV-2 Point Mutation and Deletion Spectra and Their Association with Different Disease Outcomes.Microbiology spectrum · 2022Article
- Long-term SARS-CoV-2-specific and cross-reactive cellular immune responses correlate with humoral responses, disease severity, and symptomatology.Immunity, inflammation and disease · 2022Article
- Identifying SARS-CoV-2 Lineage Mutation Hallmarks and Correlating Them With Clinical Outcomes in Egypt: A Pilot Study.Frontiers in molecular biosciences · 2022Article
- Role of the Microbiome in the Pathogenesis of COVID-19.Frontiers in cellular and infection microbiology · 2022Review
- Genomic Epidemiology of SARS-CoV-2 Divulge B.1, B.1.36, and B.1.1.7 as the Most Dominant Lineages in First, Second, and Third Wave of SARS-CoV-2 Infections in Pakistan.Microorganisms · 2021Article
- [Vaccine against COVID-19].Revista espanola de quimioterapia : publicacion oficial de la Sociedad Espanola de Quimioterapia · 2021Review
- Spatial Analysis of COVID-19 Vaccination: A Scoping Review.International journal of environmental research and public health · 2021Article
Corrections and comments
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Authors and funding
24 authors at 4 institutions in 1 country.
Funding
Abstract
The COVID-19 pandemic has been ongoing since its onset in late November 2019 in Wuhan, China. Understanding and monitoring the genetic evolution of the virus, its geographical characteristics, and its stability are particularly important for controlling the spread of the disease and especially for the development of a universal vaccine covering all circulating strains. From this perspective, we analyzed 30,983 complete SARS-CoV-2 genomes from 79 countries located in the six continents and collected from 24 December 2019, to 13 May 2020, according to the GISAID database. Our analysis revealed the presence of 3206 variant sites, with a uniform distribution of mutation types in different geographic areas. Remarkably, a low frequency of recurrent mutations has been observed; only 169 mutations (5.27%) had a prevalence greater than 1% of genomes. Nevertheless, fourteen non-synonymous hotspot mutations (>10%) have been identified at different locations along the viral genome; eight in ORF1ab polyprotein (in nsp2, nsp3, transmembrane domain, RdRp, helicase, exonuclease, and endoribonuclease), three in nucleocapsid protein, and one in each of three proteins: Spike, ORF3a, and ORF8. Moreover, 36 non-synonymous mutations were identified in the receptor-binding domain (RBD) of the spike protein with a low prevalence (<1%) across all genomes, of which only four could potentially enhance the binding of the SARS-CoV-2 spike protein to the human ACE2 receptor. These results along with intra-genomic divergence of SARS-CoV-2 could indicate that unlike the influenza virus or HIV viruses, SARS-CoV-2 has a low mutation rate which makes the development of an effective global vaccine very likely.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.