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Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes.

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  • معلومة اضافية
    • المصدر:
      Publisher: MDPI Country of Publication: Switzerland NLM ID: 101509722 Publication Model: Electronic Cited Medium: Internet ISSN: 1999-4915 (Electronic) Linking ISSN: 19994915 NLM ISO Abbreviation: Viruses Subsets: MEDLINE
    • بيانات النشر:
      Original Publication: Basel, Switzerland : MDPI
    • الموضوع:
      Family Characteristics* ; Genome, Viral* ; Haplotypes*; Host Microbial Interactions/*genetics ; SARS-CoV-2/*genetics ; Spike Glycoprotein, Coronavirus/*genetics; COVID-19/epidemiology ; COVID-19/transmission ; COVID-19/virology ; Communicable Disease Control/methods ; Evolution, Molecular ; Humans ; Italy/epidemiology ; Mutation ; Phylogeny ; SARS-CoV-2/classification
    • نبذة مختصرة :
      In February 2020, the municipality of Vo', a small town near Padua (Italy) was quarantined due to the first coronavirus disease 19 (COVID-19)-related death detected in Italy. To investigate the viral prevalence and clinical features, the entire population was swab tested in two sequential surveys. Here we report the analysis of 87 viral genomes, which revealed that the unique ancestor haplotype introduced in Vo' belongs to lineage B, carrying the mutations G11083T and G26144T. The viral sequences allowed us to investigate the viral evolution while being transmitted within and across households and the effectiveness of the non-pharmaceutical interventions implemented in Vo'. We report, for the first time, evidence that novel viral haplotypes can naturally arise intra-host within an interval as short as two weeks, in approximately 30% of the infected individuals, regardless of symptom severity or immune system deficiencies. Moreover, both phylogenetic and minimum spanning network analyses converge on the hypothesis that the viral sequences evolved from a unique common ancestor haplotype that was carried by an index case. The lockdown extinguished both the viral spread and the emergence of new variants.
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    • Grant Information:
      STARS-CoG ISS-MYTH University of Padova and the Department of Molecular Medicine; MC_PC_19012 United Kingdom MRC_ Medical Research Council; PRID/SID 2020 University of Padova and the Department of Molecular Medicine; TOPP_SID19_01 University of Padova and the Department of Molecular Medicine; No 874735 (VEO) European Union's Horizon 2020 research and innovation programme; Misura Ricerca Covid 19, year 2020 Fondazione Umberto Veronesi; TOPP_PRIV20_01 University of Padova and the Department of Molecular Medicine; MR/R015600/1 United Kingdom MRC_ Medical Research Council
    • Contributed Indexing:
      Keywords: NGS sequencing; SARS-CoV-2; epidemiology; intra-host haplotypes; longitudinal analysis; minimum spanning network; phylogenetic analysis; viral genomics
    • الرقم المعرف:
      0 (Spike Glycoprotein, Coronavirus)
    • الموضوع:
      Date Created: 20220226 Date Completed: 20220309 Latest Revision: 20240906
    • الموضوع:
      20240906
    • الرقم المعرف:
      PMC8877413
    • الرقم المعرف:
      10.3390/v14020399
    • الرقم المعرف:
      35215992