Severe acute respiratory syndrome coronavirus 2 Genome sequencing. Severe acute respiratory syndrome coronavirus 2

During the course of a surveillance period from June 2020 to May 2021, we will collect nasopharyngeal swab (NPS) samples from 60-80 hospitalized individuals in the city of Cordoba (Argentina) that are positive for SARS-CoV-2 or influenza respiratory infections. Sequencing of viral genomes will provide SARS-CoV-2 genomic data that will be extremely valuable to understand the epidemiology and evolution of the virus in Cordoba and compare with the viral strains circulating elsewhere in the country and other countries in the region. Nanopore sequencing technology will be used during this study with the overall aim to validate and establish protocols for generating viral diagnostic and sequence data locally at the collection sites. We expect to detect a 5% or higher proportion of COVID19 patients with influenza virus co-infection as the city of Cordoba enters into the flu season. We expect co-infections to reveal different disease outcomes compared to single infections of either SARS-CoV-2 or influenza virus infections. The Southern Hemisphere will give us the opportunity to have a first look of what could be expected later in the year when the Northern Hemisphere enters into the flu season (although it is impossible to predict how the summer months, social distancing, and reduced travel will affect the incidence of both influenza and COVID19 in the population later in the year).