ArticlePloS one2021
Molecular characterization and the mutation pattern of SARS-CoV-2 during first and second wave outbreaks in Hiroshima, Japan.
Article in PloS one, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed, 35 citations in OpenAlex.
- Sustained applicability of SARS-CoV-2 variants identification by Sanger Sequencing Strategy on emerging various SARS-CoV-2 Omicron variants in Hiroshima, Japan.BMC genomics · 2024Article
- Positive selection underlies repeated knockout of ORF8 in SARS-CoV-2 evolution.Nature communications · 2024Article
- Article
- Despite low viral titer in saliva samples, Sanger-based SARS-CoV-2 spike gene sequencing is highly applicable for the variant identification.BMC medical genomics · 2023Article
- Structural basis of spike RBM-specific human antibodies counteracting broad SARS-CoV-2 variants.Communications biology · 2023Article
- Genomic surveillance of SARS-CoV-2 strains circulating in Iran during six waves of the pandemic.Influenza and other respiratory viruses · 2023Article
- Viable SARS-CoV-2 detected in the air of hospital rooms of patients with COVID-19 with an early infection.International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases · 2023Article
- Complete Genomic Characterisation and Mutation Patterns of Iraqi SARS-CoV-2 Isolates.Diagnostics (Basel, Switzerland) · 2022Article
- Article
- Transmission Dynamics and Genomic Epidemiology of Emerging Variants of SARS-CoV-2 in Bangladesh.Tropical medicine and infectious disease · 2022Article
- Whole-genome analysis and mutation pattern of SARS-CoV-2 during first and second wave outbreak in Gwangju, Republic of Korea.Scientific reports · 2022Article
- Human miRNAs to Identify Potential Regions of SARS-CoV-2.ACS omega · 2022Article
- Sequential dynamics of virological and serological changes in the serum of SARS-CoV-2 infected patients.Journal of medical virology · 2022Article
- Article
- Periodically aperiodic pattern of SARS-CoV-2 mutations underpins the uncertainty of its origin and evolution.Environmental research · 2022Article
- Mass Screening of SARS-CoV-2 Variants using Sanger Sequencing Strategy in Hiroshima, Japan.Scientific reports · 2022Article
- Molecular epidemiological features of SARS-CoV-2 in Japan, 2020-1.Virus evolution · 2022Article
- Hematological changes associated with COVID-19 infection.Journal of clinical laboratory analysis · 2022Review
- Analysis of co-occurring and mutually exclusive amino acid changes and detection of convergent and divergent evolution events in SARS-CoV-2.Computational and structural biotechnology journal · 2022Article
- Identifying Markers of Emerging SARS-CoV-2 Variants in Patients With Secondary Immunodeficiency.Frontiers in microbiology · 2022Review
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Authors and funding
16 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn this study, we performed molecular characterization of SARS-CoV-2 strains in Hiroshima and its mutation pattern between the first and second waves of the outbreak.
methodA total of 55 nasal swab samples from the first wave in Hiroshima and 13 from the second wave were examined quantitatively by RT-qPCR and qualitatively by nested PCR using specific primers. Four samples from each wave underwent next-generation sequencing and phylogenetic tree analysis including controls and all sequences retrieved in Japan from GISAID and GenBank. Subsequently, mutations were examined.
resultsViral load ranged 7.85 × 101-1.42 × 108 copies/ml. Of 68 samples, one was Asian type-O, 65 were European type-GR, and 2 were undetectable. Phylogenetic tree analysis indicated that Japan was infected with various Asian strains (L, S, V, O) from January through April. By second week of March, European strains (G, GH, GR) had appeared, and GR strains became predominant after mid-March. The first case in Hiroshima was classified as Asian strain O, and the rest were GR strains. Then, second wave of GR strains appeared independently with 11-15 base mutations. Comparing the first- and second-wave GR strains, mutation rate was 1.17-1.36 × 10-3 base substitutions per site per year; in addition, amino acid changes occurred at S1361P and P3371S in ORF1a, A314V in ORF1b, and P151L in N. All seven GR strains were D614G variants with R202K and G203R mutations in N. A single-nucleotide insertion in ORF8 that causes a defect in ORF8 protein was found in one isolate (S66) from the second wave.
conclusionOur findings reveal the evolutionary hierarchy of SARS-CoV-2 in Japan. The predominant D614G variants and a new form of ORF8 deletion in Hiroshima provide the clue for role of viral factor in local outbreaks of SARS-CoV-2.
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