1. Genetic sequencing pilot project in Latin America
PAHO / OMS

2. 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

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

4. 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

5. 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)

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

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

8. 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

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

10. 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.

11. 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 /2016-like

12. 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

13. 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

14. 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

15. 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

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

17. 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

18. MUCHAS GRACIAS THANK YOU OBRIGADA