Discussion
This paper describes the global AIV subtype diversity and distribution
in water. It was evidenced that wild bird habitats host the highest
subtype diversity reported in water samples. Wild birds of aquatic
environments such as the Anseriformes and Charadriiformes constitute the
major natural AIV reservoir. At least 105 wild bird species of 26
different families host LPAI, and almost all the AIV subtypes have been
detected in wild aquatic bird reservoirs (Olsen et al., 2006). Wild
waterfowl greatly contribute to the geographical spread of AIV subtypes
between wetlands through migratory movements associated with high bird
densities and increased contact rates among bird species (van Dijk et
al., 2018).
Globally, a total of 112 AIV subtypes have been identified in wild birds
of which 49 have been found in domestic birds (Olson et al., 2014). Only
in China, twelve subtypes of HA (H1-H12) and eight subtypes of NA
(N4-N9) of 21 different combinations have been identified in wild birds
(Tang et al., 2020). In our analysis, we evidenced that 21 subtypes were
reported from water samples, of which eleven were detected in wild bird
habitats, mainly from Asian countries. Large parts of East Asia and all
Southeast Asia comprise the East Asian-Australasian Flyway. This flyway
supports the greatest diversity and highest number of migratory birds
worldwide (Tang et al., 2020). Likewise, a large number of wild aquatic
birds with a great potential to serve as carriers of AIV migrate to
overwintering habitats in Asia annually (Deng et al., 2013; Khalil et
al., 2020; Nakagawa et al., 2018). Nevertheless, it is well-known that
geographical variations on existing surveillance efforts can also
potentially influence the AIV detection and its spatial distribution
(Berger et al., 2018).
The Izumi plain and the Dongting Lake are recognized as prominent
overwintering sites in Japan and China, respectively (Nakagawa et al.,
2018; Zhang et al., 2011). These stopover areas for several tens of
thousands of migratory birds represented the wild bird habitats with the
highest number of HA sequences and the greatest subtype diversity,
mainly the Izumi plain; wherein, six different subtypes (H3N8, H4N6,
H4N8, H5N6, H5N8, and H6N2) were reported in water samples. Moreover, in
our phylogenetic tree, most of the viruses from the Izumi plain were
related to viruses from poultry farms of the Dongting Lake region in
China and from turkey barns in the United States, as well as from
Chinese live bird markets. Previous phylogenetic analyses of AIV strains
isolated from the Izumi plain have revealed genetic reassortments
between AIV from East Asian, European, African, and North American
countries (Khalil et al., 2020, 2021; Nakagawa et al., 2018; Okuya et
al., 2015). This trans-hemispheric genetic flow of AIV highlights the
wild-domestic bird interfaces as relevant areas for influenza A virus
surveillance (Prosser et al., 2013).
The Izumi plain and the Dongting Lake are also well-known for free-range
farming and mixing between chickens and domestic aquatic fowl (Khalil et
al., 2020). In our analyses, all the HA sequences from the subtypes
H3N2, H3N8, H4N9, H11N2, and H12N7 isolated in water samples from
poultry farms in China were close to aquatic environments. Domestic
farming in Southern Asia commonly occurs with a lack of biosecurity
measures and close contact among wild waterfowls and domestic fowls that
facilitates multiple genetic reassortments (Deng et al., 2013; Zhang et
al., 2011). This type of farming is widespread in low-income countries
where the majority of poultry is raised under extensive conditions by
family-based smallholder farms (Gilbert et al., 2015). Therefore,
regions such as Eastern Europe, Central America, and sub-Saharan Africa
also pose a high potential for AIV interspecies transmission; however,
several high-risk areas have inadequate influenza A virus surveillance
(Berger et al., 2018).
Likewise, live bird markets where different domestic and wild bird
species often share the same water, food, and housing also represent an
opportunity for interspecies transmission and viral genetic
diversification (Zhang et al., 2011). In our analyses, most of the HA
sequences were detected in water samples from live bird markets, mainly
from H9N2 and H5N1 subtypes in Asia (China and Bangladesh). For more
than a decade, Asian countries have undertaken numerous efforts to
rapidly detect and track AIVs mainly for LPAI H9N2 and HPAI H5N1 through
annual surveillance programs in poultry-related environments such as
live poultry markets, poultry farms, slaughterhouses, and wild bird
habitats (Rimi et al., 2019; Zhang et al., 2019). These efforts provide
valuable information to inform decision-making and implement risk
mitigation strategies. Unfortunately, other countries and regions do not
have the same level of surveillance or do not share that data publicly,
which hampers the possibility to better understand AIV transmission
dynamics locally and globally (Chan et al., 2010).
The H5N1 virus continues to pose an important public health threat in
East and Southeast Asian countries and has become endemic in domestic
poultry in these countries (Rimi et al., 2019). Although HPAI H5N1 has
also caused many outbreaks with severe illness in poultry from Europe
and Africa (Chowdhury et al., 2019), in our analyses HPAI H5N1 viruses
were only reported in water samples from Asian countries. Similarly, in
our study LPAI H9N2 viruses were isolated solely in water samples from
Asia. Nevertheless, LPAI H9N2 avian influenza viruses have widespread in
domestic poultry worldwide (Peacock et al., 2019).
Multiple AIV subtypes have been detected from poultry and wild birds in
Africa, Australia, Europe, and America (Alexander, 2007; Araujo et al.,
2018; Brown, 2010; Grillo et al., 2015; Hansbro et al., 2010;
Jiménez-Bluhm et al., 2018; Senne, 2007). However, our global analysis
of AIV evidenced a lack of sequences isolated from environmental water
in Africa, Oceania, and South America, as well as, in Europe. Data on
influenza in tropical countries remain scarce compared with temperate
countries (Moura, 2010). Likewise, according to Moura (2010), the
emergence of AIV strains in Asia may occur and be detected approximately
6 to 9 months earlier than in Oceania, North America, and Europe, and 12
to 18 months earlier than in South America.
It is also recognized that the prevalence and distribution of avian
influenza in most tropical countries are mostly unknown as a result of
the lack of a rigorous surveillance system (Yazdanbakhsh & Kremsner,
2009). Since the H1N1 pandemic, it has been highlighted a considerable
number of shortcomings on global epidemiological surveillance. The
absence of routine AIV monitoring has resulted in substantial
information gaps in large areas of the world, mainly from less-resourced
countries (Briand et al., 2011).
Environmental sampling has been effectively used for AIV surveillance
since the 1970s. Nevertheless, the methods and protocols are not
completely standardized, as well as, an international guideline about
data management is absent (Hood et al., 2020). This was one of the most
noticeable limitations in our analyses since several AIV no specified
the type of environment sampled (i.e., feces, water, air, mud, or
surface swabs), and thus, those HA sequences were excluded. Likewise, we
only analyzed the sequences with complete subtypes reported in the four
recognized electronic databases. In the case of Europe, there were
reported 83 sequences of H1 genes from ice and water in high-latitude
lakes visited by large numbers of migratory birds in Siberia.
Nevertheless, those sequences did not meet the inclusion criteria. We
also found several geographical regions with missing subtype data.
Therefore, the AIV subtypes described in this work may not be the exact
reflection of the global subtype diversity, but it highlights the
potential value of using this information to better understand AIV local
and global transmission dynamics. Our work also highlights the need to
improve surveillance efforts in many regions as well as to advance
towards more unified data collection and sharing standards to improve
influenza A virus surveillance and better prevent future potential
pandemics.
In conclusion, this descriptive and phylogenetic analysis of AIVs
isolated in water samples from sites at high risk for influenza
outbreaks, such as live bird markets, poultry farms, and wild bird
habitats is valuable to provide an overview and baseline information of
the current data on global AIV diversity and distribution since 2003.
However, this study highlights the need to continuing generating,
expanding, and sharing precise and detailed environmental data from
surveillance systems to allow a better understanding of the ecology and
epidemiology of AIV, especially from low- and middle-income countries.