Abstract
Since the 2009 influenza pandemic, Latin American (LA) countries have strengthened their influenza surveillance systems. We analyzed influenza genetic sequence data from the 2017 through 2018 Southern Hemisphere (SH) influenza season from selected LA countries, to map the availability of influenza genetic sequence data from, and to describe, the 2017 through 2018 SH influenza seasons in LA. We analyzed influenza A/H1pdm09, A/H3, B/Victoria and B/Yamagata hemagglutinin sequences from clinical samples from 12 National Influenza Centers (NICs) in ten countries (Argentina, Brazil, Chile, Colombia, Costa Rica, Ecuador, Mexico, Paraguay, Peru and Uruguay) with a collection date from epidemiologic week (EW) 18, 2017 through EW 43, 2018. These sequences were generated by the NIC or the WHO Collaborating Center (CC) at the U.S Centers for Disease Control and Prevention, uploaded to the Global Initiative on Sharing All Influenza Data (GISAID) platform, and used for phylogenetic reconstruction. Influenza hemagglutinin sequences from the participating countries (A/H1pdm09 n = 326, A/H3 n = 636, B n = 433) were highly concordant with the genetic groups of the influenza vaccine-recommended viruses for influenza A/H1pdm09 and influenza B. For influenza A/H3, the concordance was variable. Considering the constant evolution of influenza viruses, high-quality surveillance data-specifically genetic sequence data, are important to allow public health decision makers to make informed decisions about prevention and control strategies, such as influenza vaccine composition. Countries that conduct influenza genetic sequencing for surveillance in LA should continue to work with the WHO CCs to produce high-quality genetic sequence data and upload those sequences to open-access databases.
Highlights
Developing countries, including those in Latin American (LA), have contributed less surveillance data than developed countries to the global understanding of patterns of influenza circulation [1,2]
Clinical samples with a date of collection of May 1, 2017 through October 26, 2018, representing epidemiologic week (EW) 18, 2017 to EW 43, 2018, that were uploaded to the Global Initiative on Sharing All Influenza Data (GISAID) platform by October 28, 2018, were included in the analysis, based upon the fact that the South Hemisphere influenza season typically peaks in EW 18 and ends in EW 36 [8,9,10]
An additional n = 1,169 sequences were uploaded by the World Health Organization (WHO) Collaborating Center (CC) at the U.S CDC to GISAID from the samples collected by the participating countries (Table 1)
Summary
Developing countries, including those in Latin American (LA), have contributed less surveillance data than developed countries to the global understanding of patterns of influenza circulation [1,2]. The clinical samples should be tested using influenza-sensitive and specific methods, such as real-time reverse transcriptase polymerase chain reaction (rRT-PCR), and all epidemiologic and virologic data should be analyzed on a weekly basis and be publicly disseminated [3,4] As reflection of these advances in LA, there are currently more than 500 severe acute respiratory infection (SARI) sentinel sites conducting active influenza surveillance, 24 laboratories using molecular methods to detect influenza viruses, and more than 15 countries routinely sharing epidemiologic and virologic influenza surveillance data with the World Health Organization (WHO) on a routine basis [2]. As the technology of genetic sequencing has become more widely available, approximately 25% of LA NICs have incorporated this technique into their virologic surveillance as well (personal communication, Pan American Health Organization, January 2019), given that this technique can provide detailed genetic characterization of influenza viruses
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