Determining the Phylogenetic and Phylogeographic Origin of Highly Pathogenic Avian Influenza (H7N3) in Mexico

Lu, Lingyun; Lycett, Samantha; Brown, Andrew J. Leigh

doi:10.1371/journal.pone.0107330

Cited by 28 publications

(39 citation statements)

References 46 publications

(53 reference statements)

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“…This result is especially relevant for surveillance projects conducting surveillance for highly pathogenic strains in wild birds (74). Given the degree of reassortment in AIVs observed here, surveillance sites for strains of interest (e.g., HPH5N1, HPH7N3, and LPH7N9) are ideally situated within migratory routes, although gene segments from any one of these viruses may be found in other flyways (61,(75)(76)(77). While targeted surveillance efforts are necessary for rapid responses to disease threats, continued longitudinal studies examining the persistence and evolutionary patterns at regional sites are essential for elucidating the natural history of these viruses in their wild bird hosts (78,79).…”

Section: Discussionmentioning

confidence: 86%

Spread and Persistence of Influenza A Viruses in Waterfowl Hosts in the North American Mississippi Migratory Flyway

Fries

Nolting

Bowman

et al. 2015

J Virol

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While geographic distance often restricts the spread of pathogens via hosts, this barrier may be compromised when host species are mobile. Migratory waterfowl in the order Anseriformes are important reservoir hosts for diverse populations of avian-origin influenza A viruses (AIVs) and are assumed to spread AIVs during their annual continental-scale migrations. However, support for this hypothesis is limited, and it is rarely tested using data from comprehensive surveillance efforts incorporating both the temporal and spatial aspects of host migratory patterns. We conducted intensive AIV surveillance of waterfowl using the North American Mississippi Migratory Flyway (MMF) over three autumn migratory seasons. Viral isolates (n ‫؍‬ 297) from multiple host species were sequenced and analyzed for patterns of gene dispersal between northern staging and southern wintering locations. Using a phylogenetic and nucleotide identity framework, we observed a larger amount of gene dispersal within this flyway rather than between the other three longitudinally identified North American flyways. Across seasons, we observed patterns of regional persistence of diversity for each genomic segment, along with limited survival of dispersed AIV gene lineages. Reassortment increased with both time and distance, resulting in transient AIV constellations. This study shows that within the MMF, AIV gene flow favors spread along the migratory corridor within a season, and also that intensive surveillance during bird migration is important for identifying virus dispersal on time scales relevant to pandemic responsiveness. In addition, this study indicates that comprehensive monitoring programs to capture AIV diversity are critical for providing insight into AIV evolution and ecology in a major natural reservoir. IMPORTANCEMigratory birds are a reservoir for antigenic and genetic diversity of influenza A viruses (AIVs) and are implicated in the spread of virus diversity that has contributed to previous pandemic events. Evidence for dispersal of avian-origin AIVs by migratory birds is rarely examined on temporal scales relevant to pandemic or panzootic threats. Therefore, characterizing AIV movement by hosts within a migratory season is important for implementing effective surveillance strategies. We conducted surveillance following birds along a major North American migratory route and observed that within a migratory season, AIVs rapidly reassorted and gene lineages were dispersed primarily within the migratory corridor. Patterns of regional persistence were observed across seasons for each gene segment. We show that dispersal of AIV gene lineages by migratory birds occurs quickly along migratory routes and that surveillance for AIVs threatening human and animal health should focus attention on these routes.

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Section: Discussionmentioning

confidence: 86%

Spread and Persistence of Influenza A Viruses in Waterfowl Hosts in the North American Mississippi Migratory Flyway

Fries

Nolting

Bowman

et al. 2015

J Virol

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“…Sequence comparisons based on 1,608 nt of the HA gene from each of the 3 duck isolates identified A/turkey/Germany/MV-R2472/2014 (H5N8) as the closest match, at 99.8% similarity. We implemented further phylogenetic analysis using Bayesian Markov chain Monte Carlo simulation in the BEAST package version 1.7 ( 9 ). The maximum clade credibility tree (Figure 1) had a similar topology to that observed for the maximum-likelihood tree.…”

Section: The Studymentioning

confidence: 99%

Genetic Characterization of Highly Pathogenic Avian Influenza (H5N8) Virus from Domestic Ducks, England, November 2014

Hanna¹,

Banks²,

Marston³

et al. 2015

Emerg. Infect. Dis.

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“…First, spatial correlation in the invasion and transmission of parasites may result in the formation of parasite lineages based on the geographic origin or overlap of host species. This has been used in the past to track how parasites evolve and move across a landscape, such as with feline immunodeficiency virus in mountain lions (Biek et al, 2006), avian influenza in North American waterfowl (Lu et al, 2014), and brucellosis in cows, elk, and bison (Kamath et al, 2016). Second, lineages may form due to adaptation to a definitive host (the host in which a parasite reaches maturity) with only weak adaptation to intermediate hosts.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic and geographic patterns of bartonella host shifts among bat species

McKee

Hayman

Kosoy

et al. 2016

Infection, Genetics and Evolution

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The influence of factors contributing to parasite diversity in individual hosts and communities are increasingly studied, but there has been less focus on the dominant processes leading to parasite diversification. Using bartonella infections in bats as a model system, we explored the influence of three processes that can contribute to bartonella diversification and lineage formation: (1) spatial correlation in the invasion and transmission of bartonella among bats (phylogeography); (2) divergent adaptation of bartonellae to bat hosts and arthropod vectors; and (3) evolutionary codivergence between bats and bartonellae. Using a combination of global fit techniques and ancestral state reconstruction, we found that codivergence appears to be the dominant process leading to diversification of bartonella in bats, with lineages of bartonellae corresponding to separate bat suborders, superfamilies, and families. Furthermore, we estimated the rates at which bartonellae shift bat hosts across taxonomic scales (suborders, superfamilies, and families) and found that transition rates decrease with increasing taxonomic distance, providing support for a mechanism that can contribute to the observed evolutionary congruence between bats and their associated bartonellae. While bartonella diversification is associated with host sympatry, the influence of this factor is minor compared to the influence of codivergence and there is a clear indication that some bartonella lineages span multiple regions, particularly between Africa and Southeast Asia. Divergent adaptation of bartonellae to bat hosts and arthropod vectors is apparent and can dilute the overall pattern of codivergence, however its importance in the formation of Bartonella lineages in bats is small relative to codivergence. We argue that exploring all three of these processes yields a more complete understanding of bat-bartonella relationships and the evolution of the genus Bartonella, generally. Application of these methods to other infectious bacteria and viruses could uncover common processes that lead to parasite diversification and the formation of host-parasite relationships.

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Determining the Phylogenetic and Phylogeographic Origin of Highly Pathogenic Avian Influenza (H7N3) in Mexico

Cited by 28 publications

References 46 publications

Spread and Persistence of Influenza A Viruses in Waterfowl Hosts in the North American Mississippi Migratory Flyway

Spread and Persistence of Influenza A Viruses in Waterfowl Hosts in the North American Mississippi Migratory Flyway

Genetic Characterization of Highly Pathogenic Avian Influenza (H5N8) Virus from Domestic Ducks, England, November 2014

Phylogenetic and geographic patterns of bartonella host shifts among bat species

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