Photo Source - FAO
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Thanks to the work of virologists like Dr. Robert Webster, we’ve known for decades that wild birds (most notably waterfowl) are the natural hosts of influenza A viruses - and that if you trace their lineage back far enough - all human, swine, and equine influenza A viruses are likely of avian origin.
Influenza A subtypes are categorized by two proteins they carry on their surface; their HA (hemagglutinin) and NA (neuraminidase). Each of these subtypes can have many `clades’ (branches on the family tree), and within each clade there can be many minor variants.
If you count the recently discovered `bat flu’ viruses, there are now 18 known HA proteins, and 11 known NAs (see PLoS Pathogens: New World Bats Harbor Diverse Flu Strains) – but to date, among birds - only HA types 1-16 and NA types 1-9 have been detected – making a total of 144 different avian subtypes possible.
Not all of these possible subtypes have actually been detected in the wild, but then, influenza is a constantly moving target, and subtypes may appear, and then disappear, over time.
Our understanding of the prevalence, and biodiversity, of avian influenza viruses in birds has grown in recent years, but the sudden emergence of H7N9 in China a year ago, and the surprise eruption of H5N8 in Korean poultry in January, show that there is still much more to learn.
This week, an international group of researchers (hailing from the United States, Canada, Sweden & Australia) published an open access paper in PloS One providing perhaps the most detailed review of the biodiversity of influenza A viruses in wild birds to date. Among their findings:
- Among wild birds, 112 subtypes were identified
- 49 (44%) of the 112 subtypes were also found in domestic birds
- Five subtypes were found in domestic birds, but not in the wild
- Globally, 79% (89/112) of wild bird subtypes were found in Mallards
- The top five wild host species for subtype richness (n) were: Mallard - Anas platyrhynchos (89), Ruddy Turnstone - Arenaria interpres (45), Northern Pintail - Anas acuta (43), Northern Shoveler - Anas clypeata (35), and Blue-winged Teal - Anas discors (33).
- 61% of all subtypes were found in > 1 order of birds, and 66% were detected on > 1 continent
Below you’ll find a link, and some excerpts, but by all means you’ll want to read the paper in its entirety.
Research Article
Sampling Strategies and Biodiversity of Influenza A Subtypes in Wild Birds
Sarah H. Olson, Jane Parmley, Catherine Soos, Martin Gilbert, Neus Latorre-Margalef, Jeffrey S. Hall, Phillip M. Hansbro, Frederick Leighton, Vincent Munster, Damien Joly
Published: March 05, 2014 DOI: 10.1371/journal.pone.0090826
Abstract
Wild aquatic birds are recognized as the natural reservoir of avian influenza A viruses (AIV), but across high and low pathogenic AIV strains, scientists have yet to rigorously identify most competent hosts for the various subtypes. We examined 11,870 GenBank records to provide a baseline inventory and insight into patterns of global AIV subtype diversity and richness. Further, we conducted an extensive literature review and communicated directly with scientists to accumulate data from 50 non-overlapping studies and over 250,000 birds to assess the status of historic sampling effort. We then built virus subtype sample-based accumulation curves to better estimate sample size targets that capture a specific percentage of virus subtype richness at seven sampling locations. Our study identifies a sampling methodology that will detect an estimated 75% of circulating virus subtypes from a targeted bird population and outlines future surveillance and research priorities that are needed to explore the influence of host and virus biodiversity on emergence and transmission.
Figure 1 - Subtypes found in Anseriformes (green), Charadriiformes (purple), Procellariiformes (blue), more than one order (gray), and occurrence in domestic birds (***)
While this study is not without its limitations (including geographic sampling bias, and a tendency for GenBank submissions to focus more on HPAI viruses), this study provides a number of interesting findings. From the author’s Observations and findings.
We found that some subtypes appear to be limited to certain bird orders or flyways, which suggest the presence of a limited degree of subtype specificity to host or geographic region, but may also reflect sampling biases within GenBank. Fifty-six percent (5/9) of H9 subtypes were only found in Charadriiformes, of which four, H9N4, H9N5, H9N6, and H9N7, were only detected in Delaware Bay shorebirds. Fifty percent (8/16) of N3 subtypes were only found in Anseriformes. Australia alone had 75% (3/4) of known H15 subtypes; the other H15 subtypes have not been observed to date. We also identified H8, H13, and H15 subtypes where four or more combinations with NA subtypes had not been observed. Noticeably, N7 lacked eight combinations with HA subtypes.
And finally, some excerpts from a press release from the Wildlife Conservation Society, which participated in this research.
Birds of all feathers and global flu diversity
PUBLIC RELEASE DATE:
6-Mar-2014
A group of international scientists have completed the first global inventory of flu strains in birds by reviewing more than 50 published studies and genetic data, providing new insight into the drivers of viral diversity and the emergence of disease that can ultimately impact human health and livelihoods.
The research, published in the journal PLOS ONE and performed as part of the USAID PREDICT project, identified over 116 avian flu strains in wild birds. This is roughly twice the number that were found in domestic birds, and more than ten times the number found in humans. Additionally, an analysis of studies that sampled more than 5,000 birds suggested some regions may have more viral diversity than others.
<SNIP>
"This snapshot of the world of flu virus diversity in birds is the outcome of many years of ecology and evolution, as viewed through the lens of surveillance methods utilized by scientists from around the world," said study lead and Wildlife Conservation Society (WCS) Associate Director of Wildlife Epidemiology, Dr. Sarah Olson.
Understanding the natural diversity of viruses is critically important to identifying health risks. But authorities face a challenge, both in focusing efforts in the right places, and adequately financing surveillance to describe global flu diversity. To address this, the authors introduced a new method, which borrows on approaches used by ecologists, to estimate the diversity of flu viruses in a particular location. With this approach, health authorities can design surveillance programs to detect a given percentage of flu virus diversity.
The scientists also looked at patterns of flu diversity in different bird hosts. Mallards carry the highest number of strains at 89 and ruddy turnstones were second with 45. The more a strain was shared across wild bird types, the more likely it was to be found in domestic birds, a risk factor for spillover events. They also noted that some strains could be specific to certain bird types. For example, gulls and shorebirds (Charadriiformes) carried ten strains that have not been identified in any other bird order.
According to Dr. Olson, "This inventory isn't about blaming wild birds, but it allows us to map what we know, and informs our understanding of what drives viral diversity and the emergence of rare viral strains that can infect people. Given that flu viruses can jump from domestic poultry to people, ongoing efforts at improving biosecurity at poultry farms and markets remain key to outbreak prevention."
