Co-circulation of both low and highly pathogenic avian influenza H5 viruses in current poultry epidemics in Taiwan

Abstract

Highly pathogenic avian influenza (HPAI) A(H5) viruses belonging to clade 2.3.4.4c of the A/goose/Guangdong/1/96-like (Gs/GD) lineage caused severe global outbreaks in domestic birds from 2014 to 2015, that also represented the first incursions of Gs/GD viruses into Taiwan and the USA. However, few studies have investigated the circulation of clade 2.3.4.4c viruses after 2015. Here, we describe Gs/GD clade 2.3.4.4c and Mexican-like H5N2 viruses that were isolated in Taiwan during active surveillance conducted in chicken farms from February to March 2019. Phylogenetic analysis demonstrated two distinct genome constellations of the clade 2.3.4.4c H5 viruses, with the internal genes of one of the new genotypes closely related to a virus isolated from a pintail (Anas acuta) in Taiwan, providing the first direct evidence that migratory birds play a role in importing viruses into Taiwan. Our study also confirmed the co-circulation of Gs/GD clade 2.3.4.4c and Mexican-like H5 lineage viruses in Taiwan, presenting a rare case where Gs/GD viruses developed sustained transmission alongside another enzootic H5 lineage, raising the possibility that homosubtypic immunity may mask virus transmission, potentially frustrating detection, and the implementation of appropriate control measures. To eradicate H5 viruses from poultry in Taiwan, further studies on the effect of co-circulation in poultry of low pathogenic avian influenza and HPAI viruses are needed. Furthermore, only with continued surveillance efforts globally can we fully discern dispersal patterns and risk factors of virus transmission both to and within Taiwan.

Ecological factors associated with persistent circulation of multiple highly pathogenic avian influenza viruses among poultry farms in Taiwan during 2015-17

“…In particular, a new re-assorted HPAI H5N5 with HA gene belonging to clade 2.3.4.4 descendent with Taiwan local strains, was identified since September, 2019. Thirdly, our viral sequencing data from the field collections during 2019 provided the directly scientific support of gene exchange between the domestic poultry and wild birds [ 53 ]. Fourth, avian influenza virus monitoring in migratory birds has been performed in Taiwan since 1998 and was recently expanded to include the dead wild birds collected by the citizen scientists [ 13 ].…”

Avian influenza overview May – August 2020

“…In the same study, Li et al (2020) also reported codetection in March 2019 of another A(H5N2) virus on the same farm as one of the above described novel reassortant HPAI A(H5N2) viruses. This virus belonged for all its gene segments to the Mexican-like LPAI A(H5N2) virus lineage, recurrently detected in Taiwan since 2003 and responsible for the emergence in 2012 of a directly related HPAI virus.…”

“…For this same genotype, the polymerase gene segments were derived from a Eurasian LPAI virus gene pool for PB2 and PA, and from a north American LPAI virus gene pool for PB1. Whereas, for the genotype detected in March 2019, all internal gene segments (except M) were distinct from known A(H5) virus sequences detected in Taiwan, but clustered with other Eurasian LPAI viruses.In the same study,Li et al (2020) also reported codetection in March 2019 of another A(H5N2) virus on the same farm as one of the above described novel reassortant HPAI A(H5N2) viruses. This virus belonged for all its gene segments to the Mexican-like LPAI A(H5N2) virus lineage, recurrently detected in Taiwan since 2003 and responsible for the emergence in 2012 of a directly related HPAI virus.…”

“…In contrast to the last report, only one case of HPAI A(H5N2) on a medium-sized poultry farm was reported to the OIE between 16 May and 15 August. The Taiwanese lineages of HPAI A(H5N2) (clade 2.3.4.4) differ from the Eurasian HPAI A(H5N2) lineage (Li et al, 2020); the latter belonging to clade 2.3.4.4b, which has been detected, with different genotypes, in Egypt and Russia as well as in Asian countries between 2016 and 2019 (EFSA et al, 2019a) and in Bulgaria in 2020.…”

“…an active surveillance programme implemented in Taiwan during the first quarter of 2019, two chicken farms were detected with A(H5) viruses from faecal swabs collected in February and March 2019. From these viruses,Li et al (2020) characterised two distinct novel reassortant genotypes of HPAI A(H5N2) A/goose/Guangdong/1/1996-lineage viruses, one on each farm. For both genotypes, the HA and NA genes were most closely related to those of a clade 2.3.4.4c HPAI A(H5N2) virus identified in 2016 in Taiwan, and their M gene segments were related to those of earlier isolates of clade 2.3.4.4 A(H5Nx) viruses.The genotype identified from the February 2019 case also derived its NP and NS gene segments from the previously mentioned clade 2.3.4.4c A(H5N2) detected in 2016.…”