Continued Circulation of Highly Pathogenic H5 Influenza Viruses in Vietnamese Live Bird Markets in 2018–2021

Abstract

We isolated 77 highly pathogenic avian influenza viruses during routine surveillance in live poultry markets in northern provinces of Vietnam from 2018 to 2021. These viruses are of the H5N6 subtype and belong to HA clades 2.3.4.4g and 2.3.4.4h. Interestingly, we did not detect viruses of clade 2.3.4.4b, which in recent years have dominated in different parts of the world. The viruses isolated in this current study do not encode major determinants of mammalian adaptation (e.g., PB2-E627K or PB1-D701N) but possess amino acid substitutions that may affect viral receptor-binding, replication, or the responses to human antiviral factors. Several of the highly pathogenic H5N6 virus samples contained other influenza viruses, providing an opportunity for reassortment. Collectively, our study demonstrates that the highly pathogenic H5 viruses circulating in Vietnam in 2018–2021 were different from those in other parts of the world, and that the Vietnamese H5 viruses continue to evolve through mutations and reassortment.

Avian H6 Influenza Viruses in Vietnamese Live Bird Markets during 2018–2021

“…The PB2 sequences in one subgroup (shaded in blue in Figure S1 ) are most closely related to the PB2 sequences of previously reported H6 viruses. The PB2 sequences in the other subgroup (shaded in red in Figure S1 ) are most closely related to the PB2 sequences of highly pathogenic H5 avian influenza viruses (including viruses isolated during our surveillance studies [ 31 ]), indicating reassortment among avian influenza viruses.…”

“…From 2018 through to 2021, we collected a total of 3060 oropharyngeal and cloacal swabs from apparently healthy ducks and chickens at live bird markets in two provinces of northern Vietnam ([ 31 ], this study). Pooled samples were amplified in embryonated chicken eggs and tested for hemagglutination activity.…”

“…The N6 NA sequences of the viruses isolated in our study were similar to each other and most closely related to the NA sequences of other Vietnamese H6N6 viruses, except for the NA sequence of A/duck/Vietnam/HN6424/2020, which grouped with the NA sequences of Chinese H6N6 viruses (shown in red in the left panel of Figure 2 ). In the phylogenetic tree, the NA sequences of all H5N6 viruses isolated during our surveillance activities in Vietnam are shown ( Figure 2 , light blue; see [ 31 ]). The NA sequences of these viruses are not close to the NA sequences of the H6N6 viruses in the tree, indicating that the NA viral RNA segment was not recently exchanged between these viruses through reassortment.…”

“…The PA sequences (encoding the third subunit of the viral polymerase complex and the PA-X protein, another minor virulence factor) of the H6 viruses isolated in our study formed three groups ( Figure S3 ). The first group (shaded in red in Figure S3 ) is interspersed with the PA sequences of the highly pathogenic H5 viruses described in our earlier publication [ 31 ]. In the subgroups shaded in blue and yellow in Figure S3 , the PA sequences from our study grouped with the PA sequences of highly pathogenic H5 or other avian influenza viruses, providing additional confirmation of reassortment.…”

“…The National Institute of Health and Epidemiology of Vietnam conducts routine surveillance activities in live bird markets in two provinces of Northern Vietnam, Ha Noi and Quang Ninh. During these activities, 3060 oropharyngeal and cloacal swab samples (including the 2430 described in our previous publication [ 31 ]) were collected from apparently healthy birds between 2018 and 2021. All samples were stored in transport medium (DMEM containing 0.15% BSA, 100 IU/mL of penicillin-streptomycin, 0.5 μg/mL of amphotericin B, 100 μg/mL of gentamicin, 20 μg/mL of ciprofloxacin, and 0.02 M of HEPES) until further processing.…”