Use of complete SARS-CoV-2 genomes to estimate the Rt in Peru during March – April 2020

Abstract

Understanding the current SARS-CoV-2 pandemics dynamics using a multidisciplinary approach is essential to improve evidence-based policies. In our study, we estimated the SARS-CoV-2 effective reproductive number (Rt) in Peru using information from 69 complete genomes sequenced by INS-Peru and available in the GISAID public database. The tendency of Rt within March and April 2020 was similar to independent epidemiological reports. The Rt value decreased (Rt<1) during the first weeks of the pandemics in Peru but increases (Rt>1) before the beginning of April. More genomic information from Peruvian samples, available in public databases, that also represent the broad geographic diversity of Peru will allow better estimations based on genetic data and will complement epidemiological information.