Genetic sequencing pilot project in Latin America

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Presentation transcript:

Genetic sequencing pilot project in Latin America PAHO / OMS

Background Strengthen genetic surveillance in the region Better understand patterns of viral evolution during the influenza season Contribute more information to vaccine strain selection Workshop of Influenza Bioinformatics – held by CDC, April 2017

Background 10 countries (12 NICs) Participating Countries: Argentina Brazil Chile Colombia Costa-Rica Ecuador Mexico Paraguay Peru Uruguay

Methodology 397 Hemagglutinin sequences of influenza A/H1, A/H3, B/Victoria and B/Yamagata Clinical samples – EW 18 to 35, 2017 Period of analysis: May – August / 2017 WHO protocol for amplification and sequencing (primers distributed by PAHO) Sequences generated by NIC or the WHO-CC at US-CDC uploaded to the Global Initiative on Sharing All Influenza Data (GISAID) platform

Table 1: Sequencing capacity and number of Hemagglutinin (HA) genetic sequences available in GISAID among participating National Influenza Centers, May 1 to August 31, 2017 Country Institution Total number of sequences uploaded to GISAID by the NIC Total number of sequences available in GISAID Total number of sequences (optimal for alignment) Argentina Instituto Nacional de Enfermedades Infecciosas, ANLIS C.G. Malbran 40 149 109 Brazil Fundação Oswaldo Cruz 54 46 36 Instituto Adolfo Lutz 30 75 71 Instituto Evandro Chagas 12 11 Chile Instituto de Salud Publica de Chile 33 73 Colombia Instituto Nacional de Salud 24 Costa-Rica Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud Ecuador Instituto Nacional de Investigación en Salud Pública 1 Mexico Instituto de Diagnostico y Referencia Epidemiologicos 27 32 16 Paraguay 5 Peru 19 Uruguay Departamento de Laboratorio de Salud Publica (n=197)

Evolutionary relationships among Influenza A (H1N1)pdm09, hemagglutinin gene, 2017 15 HA sequences from participating countries

Evolutionary relationships among Influenza A (H1N1)pdm09, hemagglutinin gene, 2017 15 HA sequences from participating countries Grouped within HA clade: 6B

Evolutionary relationships among Influenza A (H1N1)pdm09, hemagglutinin gene, 2017 15 HA sequences from participating countries Grouped within HA clade: 6B Among the 6B clade viruses: one major subclade: 6B.1 - Amino acid substitution S84N, S162N and I216T of HA1 Vaccine strain SH 2018 / NH 2018/2019 A/Michigan/45/2015-like

Evolutionary relationships among Influenza A (H3N2), hemagglutinin gene, 2017 239 HA sequences from participating countries

Evolutionary relationships among Influenza A (H3N2), hemagglutinin gene, 2017 239 HA sequences from participating countries Grouped within HA subclades: 3C.2a, 3C.2a1 and 3C.3a.

Evolutionary relationships among Influenza A (H3N2), hemagglutinin gene, 2017 239 HA sequences from participating countries Grouped within HA subclades: 3C.2a, 3C.2a1 and 3C.3a. Sequences clustered nearly equally in both subclades 3C.2a and 3C.2a1 Vaccine strain SH 2018 / NH 2018/2019 A/Singapore/INFIMH-16-0019/2016-like

Evolutionary relationships among Influenza A (H3N2), hemagglutinin gene, 2017 239 HA sequences from participating countries Grouped within HA subclades: 3C.2a, 3C.2a1 and 3C.3a. Sequences clustered nearly equally in both subclades 3C.2a and 3C.2a1 Among the 3C.2a clade viruses: one major subclade: - Amino acid substitution F193S of HA1

Evolutionary relationships among Influenza A (H3N2), hemagglutinin gene, 2017 239 HA sequences from participating countries Grouped within HA subclades: 3C.2a, 3C.2a1 and 3C.3a. Sequences clustered nearly equally in both subclades 3C.2a and 3C.2a1 Among the 3C.2a clade viruses: one major subclade: - Amino acid substitution F193S of HA1 Among the 3c.2a1clade viruses: two major subclades: Amino acid substitutions G479E Amino acid substitutions K92R and H311Q of HA1

Evolutionary relationships among Influenza B (Yamagata lineage), hemagglutinin gene, 2017 84 HA sequences from participating countries All influenza B Yamagata HA: Y3 clade Vaccine strain SH 2018 / NH 2018/2019 B/Phuket/3073/2013-like

Evolutionary relationships among Influenza B (Victoria lineage), hemagglutinin gene, 2017 16 HA sequences from participating countries All influenza B Victoria HA: V1A clade Among the V1A clade viruses: two major subclade: - Amino acid substitution I175V and V187A of HA1 - Amino acid deletions K162 and N163 of HA1. Vaccine strain SH 2018: B/Brisbane/60/2008 NH 2018/2019: B/Colorado/6/2017

Genetic groups of influenza viruses based upon hemagglutinin (HA) gene sequences from participating National Influenza Centers, May–August 2017

Next Steps Monthly upload of sequencing data to GISIAD: Deadline for all sequence upload: Aug 31, 2018 Preparation a peer-reviewed manuscript: Preliminary data from 2017 Strengthening of the project (1); in countries sequencing capacity (2); influenza genetic surveillance in the region (3) contribution with more information for the vaccine strains selection Strengthening of in country sequencing capacity Analysis of data updated until Aug, 2018 before the SH vaccine composition meeting

MUCHAS GRACIAS THANK YOU OBRIGADA flu@paho.org