Geographical reconstruction of the SARS‐CoV‐2 outbreak in Lombardy (Italy) during the early phase

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.

COVID-19 outbreak in Italy: estimation of reproduction numbers over 2 months prior to phase 2

“…We consider that the distribution of the serial interval was expected to follow a gamma distribution with mean (±SD) of 6.50 ± 4.03 days as reported by the Imperial College COVID-19 Response Team Report 13 (March 30, 2020). We note that this value agrees very well with gamma distribution with mean 6.6 days (95% CI, 0.7 to 19) recently determined from the analysis of individual serial intervals in clusters in Lombardia (Italy) (Micheli et al 2020).…”

Genomic Surveillance of Circulating SARS-CoV-2 in South East Italy: A One-Year Retrospective Genetic Study

“…After the first detection of SARS-CoV-2 in Italy in January 2020 [3] in two Chinese tourists [4,5], there has been an intense viral circulation which mainly concerned Northern Italy [6,7] and, later, all the other Italian regions. To date, Italy has one of the highest rates of SARS-CoV-2 infection among the developed countries, with 4047 cases per 100,000 people and a significant case/fatality ratio of about 3.5% (data from https://coronavirus.jhu.edu/ map.html [8], accessed: 22 January 2021).…”

Lack of Association of Initial Viral Load in SARS-CoV-2 Patients with In-Hospital Mortality

“…However, another study carried out in Italy, with a cohort of more than 5,000 patients, did not reveal any significant differences between viral load and disease severity. 25 Another recent study, which included 205 patients and that performed a multivariate analysis, also found no differences in hospitalization length, the need for oxygen therapy, or mortality rates during follow-up. 9 …”