Genesis and spread of multiple reassortants during the 2016/2017 H5 avian influenza epidemic in Eurasia

Abstract

Highly pathogenic avian influenza (HPAI) viruses of the H5 A/goose/Guangdong/1/96 lineage can cause severe disease in poultry and wild birds, and occasionally in humans. In recent years, H5 HPAI viruses of this lineage infecting poultry in Asia have spilled over into wild birds and spread via bird migration to countries in Europe, Africa, and North America. In 2016/2017, this spillover resulted in the largest HPAI epidemic on record in Europe and was associated with an unusually high frequency of reassortments between H5 HPAI viruses and cocirculating low-pathogenic avian influenza viruses. Here, we show that the seven main H5 reassortant viruses had various combinations of gene segments 1, 2, 3, 5, and 6. Using detailed time-resolved phylogenetic analysis, most of these gene segments likely originated from wild birds and at dates and locations that corresponded to their hosts' migratory cycles. However, some gene segments in two reassortant viruses likely originated from domestic anseriforms, either in spring 2016 in east China or in autumn 2016 in central Europe. Our results demonstrate that, in addition to domestic anseriforms in Asia, both migratory wild birds and domestic anseriforms in Europe are relevant sources of gene segments for recent reassortant H5 HPAI viruses. The ease with which these H5 HPAI viruses reassort, in combination with repeated spillovers of H5 HPAI viruses into wild birds, increases the risk of emergence of a reassortant virus that persists in wild bird populations yet remains highly pathogenic for poultry.

Keywords: emerging infectious diseases; highly pathogenic avian influenza; phylogenetic analysis; poultry; wild birds.

Fig. 1.

Bayesian time-resolved phylogenetic trees for gene segments 1 to 4 of H5NX HPAI viruses sampled between May 2016 and July 2017 and for which whole genomes were sequenced. Distinct clades (groups) in the trees are given different colored branches. The number of distinct groups differs per gene segment: four for segment 1, three for segment 2, five for segment 3, and one for segment 4. Furthermore, all eight segments of each virus are represented as eight parallel bars at the tips of each tree, with the colors in each segment's bar corresponding to the branches of the individual gene sequences to indicate reassortment. The final bar represents the geographic locations of the sequences in the tree.

Fig. 2.

Bayesian time-resolved phylogenetic trees for gene segments 5 to 8 of H5NX HPAI viruses sampled between May 2016 and July 2017 and for which whole genomes were sequenced. For segment 6, there are separate phylogenetic trees for subtypes N8 and N5. Distinct clades (groups) in the trees are given different colored branches. The number of distinct groups differs per gene segment: five for segment 5, two for segment 6, and one for segments 7 and 8. Furthermore, all eight segments of each virus are represented as eight parallel bars at the tips of each tree, with the colors in each segment’s bar corresponding to the branches of the individual gene sequences to indicate reassortment. The final bar represents the geographic locations of the sequences in the tree.

Fig. 3.

Supernetwork of 2016/2017 H5 HPAI viruses, based on full-genome sequences, generated by using maximum-likelihood (ML) phylogenetic trees of sorted sequences according to segments. The eight ML trees of the segments were used to calculate a supernetwork. Each reassortant is indicated by a different color and assembled into four groups. The seven most common reassortants are numbered 1 to 7. Less common reassortants (total: four) are indicated in gray. Each circle represents full genome of HPAI virus, and the edges represent their phylogenetic relationship. Details as names, collection dates, and coordinates are given in SI Appendix, Table S8.

Fig. 4.

Overview of the main reassortments described in this manuscript. Group designations and colors correspond to those in Fig. 3. The positions of the reassortants correspond to the estimated dates of origin in Table 1. Dotted lines join the gene segments that are related.

Fig. 5.

Geographical distribution of detected H5NX HPAI viruses with full-genome sequences between the second quarter of 2016 and the second quarter of 2017. Viruses were detected from the east coast of Asia to the northwest coast of Europe, southern to northern Africa, and in south Asia. A–C show magnified maps of (A) the northwest coast of Europe, (B) southern Africa, and (C) the east coast of Asia. Lambert conformal conic projection. Light green: reassortant 1; dark green: reassortant 2; red: reassortant 3; purple: reassortant 4; orange: reassortant 5; light blue: reassortant 6; dark blue: reassortant 7; circle: Wild-ans; square: Wild-ans-long; pentagon: Wild-other; rhomboid: Dom-ans; triangle: Dom-gal. Map image credit: Copyright © 1995–2020 Esri. All rights reserved. Published in the United States of America.