Geographic reconstruction of the SARS-CoV-2 outbreak in Lombardy (Italy) during the early phase

The circulation of SARS-CoV-2 in Italy has been dominated by two large clusters of outbreaks in Northern part of the peninsula, source of alarming and prolonged infections in Lombardy region, in Codogno and Bergamo areas especially. The aim of the study was to expand understanding on the circulation of SARS-CoV-2 in the affected Lombardy areas. To this purpose, twenty full length genomes were collected from patients addressing to several Lombard hospitals from February 20th to April 4th, 2020. The obtained genome assemblies, available on the GISAD database and performed at the Referral Center for COVID-19 diagnosis, identified 2 main monophyletic clades, containing 9 and 52 isolates, respectively. The molecular clock analysis estimated a clusters divergence approximately one month before the first patient identification, supporting the hypothesis that different SARS-CoV-2 strains spread all over the world at different time, but their presence became evident only in late February along with Italian epidemic emergence. Therefore, the epidemiological reconstruction carried out by this work highlights multiple inputs of the virus into its initial circulation in Lombardy Region. However, a phylogenetic reconstruction robustness will be improved when other genomic sequences will be available, in order to guarantee a complete epidemiological surveillance.

Presence and vitality of SARS-CoV-2 virus in wastewaters and rivers

Wastewater-based epidemiology has been proposed to monitor the diffusion and trend of SARS-CoV-2 pandemic. In the present study, raw and treated samples from three wastewater treatment plants, and two river samples characterized the Milano Metropolitan Area, Italy, were surveyed for SARS-CoV-2 RNA positivity to real time PCR and infectiveness. Moreover, whole genome sequencing and phylogenetic analysis of isolated strains was performed. Raw wastewater samples resulted positive to PCR amplification, while treated water samples were always negative (four and two samples, respectively, sampled in two dates). Moreover, the rate of positivity in raw wastewater samples decreased after eight days, in congruence with the epidemiological trend estimated for the interested provinces. Virus infectiveness was always not significant, indicating the effectiveness of wastewater treatments, or the natural decay of viral vitality, which implied the absence of significant risk of infection from wastewaters. Samples from receiving rivers (two sites, sampled in the same dates as wastewaters) showed in some cases a positivity to PCR amplification, probably due to non-treated discharges, or the combined sewage overflows. Nevertheless, also for rivers vitality was negligible, indicating the absence of sanitary risks. Phylogenetic analysis of genome indicated that the isolated virus belongs to the most spread strain present in Europe and similar to another strain found in Lombardy.