tetano
Editor, Senior Moderator
J Med Virol
. 2020 Aug 20.
doi: 10.1002/jmv.26447. Online ahead of print.
Geographical reconstruction of the SARS-CoV-2 outbreak in Lombardy (Italy) during the early phase
Valeria Micheli[SUP] 1 [/SUP], Sara Giordana Rimoldi[SUP] 1 [/SUP], Francesca Romeri[SUP] 1 [/SUP], Francesco Comandatore[SUP] 2 [/SUP], Alessandro Mancon[SUP] 1 [/SUP], Anna Gigantiello[SUP] 1 [/SUP], Matteo Perini[SUP] 2 [/SUP], Davide Mileto[SUP] 1 [/SUP], Cristina Pagani[SUP] 1 [/SUP], Alessandra Lombardi[SUP] 1 [/SUP], Maria Rita Gismondo[SUP] 1 [/SUP]
Affiliations
Abstract
The first identification of autochthonous transmission of SARS-CoV-2 in Italy was documented by the Laboratory of Clinical Microbiology, Virology and Bioemergencies of L. Sacco Hospital (Milano, Italy) on 20th February 2020 in a 38 years old male patient, who was found positive for pneumonia at the Codogno Hospital. Thereafter Lombardy has reported the highest prevalence of COVID-19 cases in the country, especially in Milano, Brescia and Bergamo provinces. The aim of this study was to assess the potential presence of different viral clusters belonging to the six main provinces involved in Lombardy COVID-19 cases in order to highlight peculiar province-dependent viral characteristics. A phylogenetic analysis was conducted on 20 full length genomes obtained from patients addressing to several Lombard hospitals from February 20th to April 4th, 2020, aligned with 41 Italian viral genome assemblies available on GISAID database as of 30th March, 2020: two main monophyletic clades, containing 8 and 53 isolates, respectively, were identified. Noteworthy, Bergamo isolates mapped inside the small clade harbouring M gene D3G mutation. The molecular clock analysis estimated a cluster divergence approximately one month before the first patient identification, supporting the hypothesis that different SARS-CoV-2 strains had spread worldwide at different times, but their presence became evident only in late February along with Italian epidemic emergence. Therefore, this epidemiological reconstruction suggests that virus initial circulation in Lombardy was ascribable to multiple introduction. The phylogenetic reconstruction robustness, however, will be improved when more genomic sequences are available, in order to guarantee a complete epidemiological surveillance. This article is protected by copyright. All rights reserved.
Keywords: Epidemiology; Evolution; Genetic variability; Pandemics; SARS coronavirus; Virus classification.
. 2020 Aug 20.
doi: 10.1002/jmv.26447. Online ahead of print.
Geographical reconstruction of the SARS-CoV-2 outbreak in Lombardy (Italy) during the early phase
Valeria Micheli[SUP] 1 [/SUP], Sara Giordana Rimoldi[SUP] 1 [/SUP], Francesca Romeri[SUP] 1 [/SUP], Francesco Comandatore[SUP] 2 [/SUP], Alessandro Mancon[SUP] 1 [/SUP], Anna Gigantiello[SUP] 1 [/SUP], Matteo Perini[SUP] 2 [/SUP], Davide Mileto[SUP] 1 [/SUP], Cristina Pagani[SUP] 1 [/SUP], Alessandra Lombardi[SUP] 1 [/SUP], Maria Rita Gismondo[SUP] 1 [/SUP]
Affiliations
- PMID: 32816316
- DOI: 10.1002/jmv.26447
Abstract
The first identification of autochthonous transmission of SARS-CoV-2 in Italy was documented by the Laboratory of Clinical Microbiology, Virology and Bioemergencies of L. Sacco Hospital (Milano, Italy) on 20th February 2020 in a 38 years old male patient, who was found positive for pneumonia at the Codogno Hospital. Thereafter Lombardy has reported the highest prevalence of COVID-19 cases in the country, especially in Milano, Brescia and Bergamo provinces. The aim of this study was to assess the potential presence of different viral clusters belonging to the six main provinces involved in Lombardy COVID-19 cases in order to highlight peculiar province-dependent viral characteristics. A phylogenetic analysis was conducted on 20 full length genomes obtained from patients addressing to several Lombard hospitals from February 20th to April 4th, 2020, aligned with 41 Italian viral genome assemblies available on GISAID database as of 30th March, 2020: two main monophyletic clades, containing 8 and 53 isolates, respectively, were identified. Noteworthy, Bergamo isolates mapped inside the small clade harbouring M gene D3G mutation. The molecular clock analysis estimated a cluster divergence approximately one month before the first patient identification, supporting the hypothesis that different SARS-CoV-2 strains had spread worldwide at different times, but their presence became evident only in late February along with Italian epidemic emergence. Therefore, this epidemiological reconstruction suggests that virus initial circulation in Lombardy was ascribable to multiple introduction. The phylogenetic reconstruction robustness, however, will be improved when more genomic sequences are available, in order to guarantee a complete epidemiological surveillance. This article is protected by copyright. All rights reserved.
Keywords: Epidemiology; Evolution; Genetic variability; Pandemics; SARS coronavirus; Virus classification.