Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes
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. H...
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| Format: | Article |
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MDPI AG
2022-02-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/14/2/399 |
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| author | Laura Manuto Marco Grazioli Andrea Spitaleri Paolo Fontana Luca Bianco Luigi Bertolotti Martina Bado Giorgia Mazzotti Federico Bianca Francesco Onelia Giovanni Lorenzin Fabio Simeoni Dejan Lazarevic Elisa Franchin Claudia Del Vecchio Ilaria Dorigatti Giovanni Tonon Daniela Maria Cirillo Enrico Lavezzo Andrea Crisanti Stefano Toppo |
| author_facet | Laura Manuto Marco Grazioli Andrea Spitaleri Paolo Fontana Luca Bianco Luigi Bertolotti Martina Bado Giorgia Mazzotti Federico Bianca Francesco Onelia Giovanni Lorenzin Fabio Simeoni Dejan Lazarevic Elisa Franchin Claudia Del Vecchio Ilaria Dorigatti Giovanni Tonon Daniela Maria Cirillo Enrico Lavezzo Andrea Crisanti Stefano Toppo |
| author_sort | Laura Manuto |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T20:51:14Z |
| format | Article |
| id | doaj.art-1072e6cb6af84146b6868d3c744a4c4f |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-09T20:51:14Z |
| publishDate | 2022-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-1072e6cb6af84146b6868d3c744a4c4f2023-11-23T22:32:16ZengMDPI AGViruses1999-49152022-02-0114239910.3390/v14020399Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel HaplotypesLaura Manuto0Marco Grazioli1Andrea Spitaleri2Paolo Fontana3Luca Bianco4Luigi Bertolotti5Martina Bado6Giorgia Mazzotti7Federico Bianca8Francesco Onelia9Giovanni Lorenzin10Fabio Simeoni11Dejan Lazarevic12Elisa Franchin13Claudia Del Vecchio14Ilaria Dorigatti15Giovanni Tonon16Daniela Maria Cirillo17Enrico Lavezzo18Andrea Crisanti19Stefano Toppo20Department of Molecular Medicine, University of Padova, 35121 Padua, ItalyDepartment of Molecular Medicine, University of Padova, 35121 Padua, ItalyCenter for Omics Sciences, IRCCS San Raffaele Institute, 20132 Milan, ItalyResearch and Innovation Center, Edmund Mach Foundation, 38098 San Michele all’Adige, ItalyResearch and Innovation Center, Edmund Mach Foundation, 38098 San Michele all’Adige, ItalyDepartment of Veterinary Sciences, University of Torino, Grugliasco, 10095 Turin, ItalyDepartment of Molecular Medicine, University of Padova, 35121 Padua, ItalyDepartment of Molecular Medicine, University of Padova, 35121 Padua, ItalyDepartment of Molecular Medicine, University of Padova, 35121 Padua, ItalyDepartment of Molecular Medicine, University of Padova, 35121 Padua, ItalyEmerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, ItalyCenter for Omics Sciences, IRCCS San Raffaele Institute, 20132 Milan, ItalyCenter for Omics Sciences, IRCCS San Raffaele Institute, 20132 Milan, ItalyDepartment of Molecular Medicine, University of Padova, 35121 Padua, ItalyDepartment of Molecular Medicine, University of Padova, 35121 Padua, ItalyMRC Centre for Global Infectious Disease Analysis, Imperial College London, London SW7 2BX, UKCenter for Omics Sciences, IRCCS San Raffaele Institute, 20132 Milan, ItalyEmerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, ItalyDepartment of Molecular Medicine, University of Padova, 35121 Padua, ItalyDepartment of Molecular Medicine, University of Padova, 35121 Padua, ItalyDepartment of Molecular Medicine, University of Padova, 35121 Padua, ItalyIn 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.https://www.mdpi.com/1999-4915/14/2/399SARS-CoV-2epidemiologyviral genomicsintra-host haplotypeslongitudinal analysisNGS sequencing |
| spellingShingle | Laura Manuto Marco Grazioli Andrea Spitaleri Paolo Fontana Luca Bianco Luigi Bertolotti Martina Bado Giorgia Mazzotti Federico Bianca Francesco Onelia Giovanni Lorenzin Fabio Simeoni Dejan Lazarevic Elisa Franchin Claudia Del Vecchio Ilaria Dorigatti Giovanni Tonon Daniela Maria Cirillo Enrico Lavezzo Andrea Crisanti Stefano Toppo Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes Viruses SARS-CoV-2 epidemiology viral genomics intra-host haplotypes longitudinal analysis NGS sequencing |
| title | Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes |
| title_full | Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes |
| title_fullStr | Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes |
| title_full_unstemmed | Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes |
| title_short | Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes |
| title_sort | rapid sars cov 2 intra host and within household emergence of novel haplotypes |
| topic | SARS-CoV-2 epidemiology viral genomics intra-host haplotypes longitudinal analysis NGS sequencing |
| url | https://www.mdpi.com/1999-4915/14/2/399 |
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