Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control

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Authors

Abolnik, Celia
Strydom, Christine
Rauff, Dionne Linda
Wandrag, D.B.R. (Daniel)
Petty, Deryn

Journal Title

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Volume Title

Publisher

BioMed Central

Abstract

BACKGROUND : The threat of poultry-origin H6 avian influenza viruses to human health emphasizes the importance of monitoring their evolution. South Africa’s H6N2 epidemic in chickens began in 2001 and two co-circulating antigenic sub-lineages of H6N2 could be distinguished from the outset. The true incidence and prevalence of H6N2 in the country has been difficult to determine, partly due to the continued use of an inactivated whole virus H6N2 vaccine and the inability to distinguish vaccinated from non-vaccinated birds on serology tests. In the present study, the complete genomes of 12 H6N2 viruses isolated from various farming systems between September 2015 and February 2019 in three major chicken-producing regions were analysed and a serological experiment was used to demonstrate the effects of antigenic mismatch in diagnostic tests. RESULTS : Genetic drift in H6N2 continued and antigenic diversity in sub-lineage I is increasing; no sub-lineage II viruses were detected. Reassortment patterns indicated epidemiological connections between provinces as well as different farming systems, but there was no reassortment with wild bird or ostrich influenza viruses. The sequence mismatch between the official antigens used for routine hemagglutination inhibition (HI) testing and circulating field strains has increased steadily, and we demonstrated that H6N2 field infections are likely to be missed. More concerning, sublineage I H6N2 viruses acquired three of the nine HA mutations associated with human receptor-binding preference (A13S, V187D and A193N) since 2002. Most sub-lineage I viruses isolated since 2015 acquired the K702R mutation in PB2 associated with the ability to infect humans, whereas prior to 2015 most viruses in sub-lineages I and II contained the avian lysine marker. All strains had an unusual HA0 motif of PQVETRGIF or PQVGTRGIF. CONCLUSIONS : The H6N2 viruses in South African chickens are mutating and reassorting amongst themselves but have remained a genetically pure lineage since they emerged more than 18 years ago. Greater efforts must be made by government and industry in the continuous isolation and characterization of field strains for use as HI antigens, new vaccine seed strains and to monitor the zoonotic threat of H6N2 viruses.

Description

Additional file 1: Table S1a. Percentage nucleotide sequence identity in the HA genes of sub-lineage I viruses isolated since 2015.
Additional file 2: Table S1b. Percentage amino sequence identity in the HA proteins of all sub-lineage I viruses.
Additional file 3: Table S1c. Amino acid between-group distances.
Additional file 4: Figure S1. Alignment of the hemagglutinin protein sequences of South African H6N2 isolates from chickens.
Additional file 5: Table S2. Predicted glycosylation patterns in the surface glycoproteins of H6N2 influenza viruses isolated since 2015.
Additional file 6: Figure S2. Alignment of the neuraminidase protein sequences of South African H6N2 isolates from chickens.
Additional file 7: Figure S3. Alignment of the polymerase B2 (PB2) protein sequences of South African H6N2 isolates from chickens.

Keywords

Chickens, Evolution, Human markers, Serological diagnosis, South Africa (SA), H6N2 viruses, Avian influenza

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Citation

Abolnik C., Strydom C., Rauff D.L. et al. 2019, 'Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control', BMC Veterinary Research, 15, art. 455, pp. 1-20.