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. 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 variant

SARS-CoV-2 antibody dynamics and transmission from community-wide serological testing in the Italian municipality of Vo'

none36In February and March 2020, two mass swab testing campaigns were conducted in Vo', Italy. In May 2020, we tested 86% of the Vo' population with three immuno-assays detecting antibodies against the spike and nucleocapsid antigens, a neutralisation assay and Polymerase Chain Reaction (PCR). Subjects testing positive to PCR in February/March or a serological assay in May were tested again in November. Here we report on the results of the analysis of the May and November surveys. We estimate a seroprevalence of 3.5% (95% Credible Interval (CrI): 2.8-4.3%) in May. In November, 98.8% (95% Confidence Interval (CI): 93.7-100.0%) of sera which tested positive in May still reacted against at least one antigen; 18.6% (95% CI: 11.0-28.5%) showed an increase of antibody or neutralisation reactivity from May. Analysis of the serostatus of the members of 1,118 households indicates a 26.0% (95% CrI: 17.2-36.9%) Susceptible-Infectious Transmission Probability. Contact tracing had limited impact on epidemic suppression.restrictedDorigatti, Ilaria; Lavezzo, Enrico; Manuto, Laura; Ciavarella, Constanze; Pacenti, Monia; Boldrin, Caterina; Cattai, Margherita; Saluzzo, Francesca; Franchin, Elisa; Del Vecchio, Claudia; Caldart, Federico; Castelli, Gioele; Nicoletti, Michele; Nieddu, Eleonora; Salvadoretti, Elisa; Labella, Beatrice; Fava, Ludovico; Guglielmo, Simone; Fascina, Mariateresa; Grazioli, Marco; Alvisi, Gualtiero; Vanuzzo, Maria Cristina; Zupo, Tiziano; Calandrin, Reginetta; Lisi, Vittoria; Rossi, Lucia; Castagliuolo, Ignazio; Merigliano, Stefano; Unwin, H Juliette T; Plebani, Mario; Padoan, Andrea; Brazzale, Alessandra R; Toppo, Stefano; Ferguson, Neil M; Donnelly, Christl A; Crisanti, AndreaDorigatti, Ilaria; Lavezzo, Enrico; Manuto, Laura; Ciavarella, Constanze; Pacenti, Monia; Boldrin, Caterina; Cattai, Margherita; Saluzzo, Francesca; Franchin, Elisa; Del Vecchio, Claudia; Caldart, Federico; Castelli, Gioele; Nicoletti, Michele; Nieddu, Eleonora; Salvadoretti, Elisa; Labella, Beatrice; Fava, Ludovico; Guglielmo, Simone; Fascina, Mariateresa; Grazioli, Marco; Alvisi, Gualtiero; Vanuzzo, Maria Cristina; Zupo, Tiziano; Calandrin, Reginetta; Lisi, Vittoria; Rossi, Lucia; Castagliuolo, Ignazio; Merigliano, Stefano; Unwin, H Juliette T; Plebani, Mario; Padoan, Andrea; Brazzale, Alessandra R; Toppo, Stefano; Ferguson, Neil M; Donnelly, Christl A; Crisanti, Andre