End-to-end integration of SARS-CoV-2 and influenza sentinel surveillance: revised interim guidance

Overview

This guidance provides interim guidance for the integration of SARS-CoV-2 and influenza virologic and genomic surveillance, from sentinel site case enrolment and sampling to the eventual sharing of the virus sequence data, a process known as end-to-end surveillance. This guidance builds on experiences and lessons learned as countries adapted their influenza surveillance systems in the context of the COVID-19 pandemic and reviews new evidence to provide guidance on end-to-end surveillance. The guidance includes new algorithms and strategies to adapt sentinel systems to make them resilient and agile for addressing global and national surveillance needs for influenza and COVID-19. It highlights the need to link sentinel surveillance systems to inform policy and adjust the national public health response to the COVID-19 pandemic. It incorporates inputs from Member States and international experts solicited before and during a virtual consultation in October 2021. It is intended for public health professionals involved in disease and laboratory surveillance at the national level. It is also a guide for WHO staff involved in influenza and COVID-19 sentinel surveillance integration. 

This interim guidance is an update and replaces two previous documents:

Maintaining surveillance of influenza and monitoring of SARS-CoV-2 (published 8 November 2020) and Operational considerations to expedite genomic sequencing component of GISRS surveillance of influenza SARS-CoV-2 (published 16 February 2021).

It complements the Guidance for surveillance of SARS-CoV-2 variants (published 9 August 2021) and the Public health surveillance for COVID-19 (interim guidance, published 16 December 2020).