Influenza and SARS-CoV-2 integrated surveillance laboratory testing algorithm

The integrated surveillance algorithm for influenza, SARS-CoV-2, and other respiratory viruses standardizes diagnostic, molecular, and genomic procedures within national surveillance systems. Its operational flow ranges from sample collection and transport at sentinel sites to detection by multiplex RT-PCR, subtyping or genotyping at National Influenza Centers (NICs), and genomic sequencing for phylogenetic analysis. 

The scheme establishes standardized criteria for sample selection, considering diagnostic quality, geographic, temporal, and clinical representativeness parameters, and ensuring strict compliance with biosafety standards and cold chain maintenance. It also includes procedures for the validation, release, and reporting of data to the international platforms FluNet and GISAID, in accordance with the International Health Regulations (IHR 2005) and the guidelines of the WHO Global Influenza Surveillance and Response System (GISRS). For more information: laboratoryresponse@paho.org