Mapping the risk of avian influenza in wild birds in the US
BMC Infectious Diseases
Trevon L Fuller 0
Sassan S Saatchi 0 2
Emily E Curd 0 1
Erin Toffelmier 0
Henri A Thomassen 0
Wolfgang Buermann 0 6
David F DeSante 5
Mark P Nott 5
James F Saracco 5
CJ Ralph 4
John D Alexander 3
John P Pollinger 0
Thomas B Smith 0 1
0 Center for Tropical Research, Institute of the Environment, University of California , Los Angeles, La Kretz Hall, Suite 300, Box 951496, Los Angeles, CA 90095-1496 , USA
1 Department of Ecology and Evolutionary Biology, University of California, Los Angeles , 621 Charles E. Young Drive South, Los Angeles, CA 90095-1606 , USA
2 Radar Science Technical Group, Radar Science & Engineering Section, Jet Propulsion Laboratory, California Institute of Technology , 4800 Oak Grove Drive, Pasadena, CA 91109-8099 , USA
3 Klamath Bird Observatory , P.O. Box 758, Ashland, OR 97520 , USA
4 U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station, Redwood Sciences Laboratory , 1700 Bayview Drive, Arcata, CA 95521 , USA
5 The Institute for Bird Populations , P.O. Box 1346, Point Reyes Station, CA 94956-1346 , USA
6 Department of Atmospheric and Oceanic Sciences, University of California, Los Angeles , Los Angeles, CA 90095-1565 , USA
Background: Avian influenza virus (AIV) is an important public health issue because pandemic influenza viruses in people have contained genes from viruses that infect birds. The H5 and H7 AIV subtypes have periodically mutated from low pathogenicity to high pathogenicity form. Analysis of the geographic distribution of AIV can identify areas where reassortment events might occur and how high pathogenicity influenza might travel if it enters wild bird populations in the US. Modelling the number of AIV cases is important because the rate of co-infection with multiple AIV subtypes increases with the number of cases and co-infection is the source of reassortment events that give rise to new strains of influenza, which occurred before the 1968 pandemic. Aquatic birds in the orders Anseriformes and Charadriiformes have been recognized as reservoirs of AIV since the 1970s. However, little is known about influenza prevalence in terrestrial birds in the order Passeriformes. Since passerines share the same habitat as poultry, they may be more effective transmitters of the disease to humans than aquatic birds. We analyze 152 passerine species including the American Robin (Turdus migratorius) and Swainson's Thrush (Catharus ustulatus). Methods: We formulate a regression model to predict AIV cases throughout the US at the county scale as a function of 12 environmental variables, sampling effort, and proximity to other counties with influenza outbreaks. Our analysis did not distinguish between types of influenza, including low or highly pathogenic forms. Results: Analysis of 13,046 cloacal samples collected from 225 bird species in 41 US states between 2005 and 2008 indicates that the average prevalence of influenza in passerines is greater than the prevalence in eight other avian orders. Our regression model identifies the Great Plains and the Pacific Northwest as high-risk areas for AIV. Highly significant predictors of AIV include the amount of harvested cropland and the first day of the year when a county is snow free. Conclusions: Although the prevalence of influenza in waterfowl has long been appreciated, we show that 22 species of song birds and perching birds (order Passeriformes) are influenza reservoirs in the contiguous US.
There is a strong link between influenza in birds and
human health because influenza epidemics in human
populations occur when viruses that typically inhabit the
avian gastrointestinal tract mutate or reassort, enabling
them to cross the species barrier to infect people [
Mutations arise in avian influenza virus (hereafter "AIV")
due to the high error rate of influenza RNA polymerase
and the large population size and short generation time of
the virus [
]. Reassortment is the exchange of RNA
segments between distinct influenza viruses. When human
influenza viruses and AIV reassort, they produce
offspring virions that represent a mixture of the parental
types' RNA and are infectious to humans in some cases
]. For example, in 1968, one million people died in an
influenza pandemic that resulted from the reassortment
of an influenza virus from Ukrainian ducks and a virus
that had circulated in people since 1957 [
Today, outbreaks of H5N1 influenza in Africa, Asia,
Europe, and the Middle East further illustrate the human
health implications of influenza in birds. (Influenza
viruses are classified into "HA" and "NA" subtypes based
on surface proteins.) People contract H5N1 by handling
infected poultry or wild birds after which the virus binds
to receptors in the pulmonary alveoli, causing pneumonia
and death due to respiratory failure [
]. Since July
2003, there have been 436 human cases of H5N1 in the
Eastern hemisphere with a 60% mortality rate [
75% of these cases, the infected people had contact with
]. However, H5N1 has also evolved limited
person-to-person transmission within human families
]. Public health authorities are concerned that the
evolution of wider human-to-human transmission could
result in a H5N1 pandemic that could cause up to 142
million deaths at a cost of $US 4.4 trillion [
ongoing human pandemic of H1N1 influenza, which has
caused over 296,000 human cases and at least 15,921
deaths since mid-February 2009, contains genes from
avian, human, and swine influenza viruses .
To date, influenza viruses have been isolated from 105
species of wild birds representing 26 families [
birds, the H5 and H7 AIV subtypes have periodically
mutated from a low pathogenicity form (hereafter
"LPAI"), which is typically asymptomatic in wild birds, to
a highly pathogenic form (hereafter "HPAI") that causes
mortality rates of up to 100% in chickens [
analysis did not distinguish between influenza subtypes
or differentiate LPAI from HPAI.) HPAI also differs from
LPAI in that the former has more amino acids adjacent to
the hemagglutinin cleavage site, which allows it to
replicate in a broader range of tissues [for details, see [
Aside from poultry, no HPAI H5N1 has been detected to
date in the US, though six LPAI H5N1 viruses have been
detected in North America since 2004 [
]. AIV mutated
from LP to HP form in poultry in the US in the 1920s, in
1984, and in 2004 [
]. Although none of these US
outbreaks resulted in the infection of humans with HPAI,
it is plausible that HPAI could reassort or mutate to
become transmissible to people. As few as five amino acid
changes can transform the HP influenza virus into an
airborne form that is infectious to mammals [
]. In the
event of an HPAI epizootic in migratory birds in the US,
these species could spread HPAI across the country along
migratory routes because ducks infected with HP H5
remain healthy enough to migrate [
]. Indeed, HPAI
has already been detected in wild birds in Chad, China,
Nigeria, and South Africa [
We analyze the geographic distribution of AIV in wild
birds in the US with the goal of inferring where
reassortment events might occur and how HPAI might travel if it
enters wild bird populations. Our method for detecting
the influenza virus in samples from passerines does not
determine whether the virus is LPAI or HPAI (see below).
However, 67% of our samples are from non-passerines
and are known to be LPAI. Thus, this study assumes that
most of our AIV-positive samples are LPAI. We model
the geographic distribution of AIV to provide insights
about how HPAI might spread if it is introduced to the
US in the future. Since we cannot guarantee that the
passerine samples are LPAI, when referring to samples that
tested positive for influenza virus, we will use the term
"AIV" rather than "LPAI". As noted in the Discussion, the
characterization of the subtype and pathogenicity of AIVs
isolated from passerines in the US remains an important
area for future research.
Although the monitoring of HPAI viruses is important,
another critical issue in AIV biosafety is the detection of
H5 and H7 LPAI viruses. LPAI H7 has been transmitted
directly to humans in the US in 1976, 2002, and 2003
]. These cases resulted in conjunctivitis, fever, and
upper-respiratory tract symptoms of influenza-like
illness, but no fatalities. LPAI H5 and H7 can mutate to
HPAI relatively easily given the right environment (for
example, poultry sheds). We refer the interested reader to
Verdugo et al. , who have developed a model for
detecting H5 and H7 LPAI in poultry and predicting
when they will evolve to HPAI.
The aims of this research are to measure the prevalence
of AIV in different species of wild birds in the US and to
prioritize geographical regions for future influenza
surveillance. Although aquatic birds in the orders
Anseriformes and Charadriiformes have been recognized as
reservoirs of AIV since the 1970s, much less is known
about AIV prevalence in terrestrial birds in the order
]. Examples of Anseriformes (ducks)
that have high prevalence of influenza in the US include
the Mallard (Anas platyrhynchos) and the Northern
Pintail (Anas acuta) [
]. Shorebirds of the order
Charadriiformes in which high influenza prevalence has been
detected in the US include the Ruddy Turnstone
(Arenaria interpres) and the Red Knot (Calidris canutus)
]. Recent work detected high prevalence of
influenza in passerines in China, including the Eurasian Tree
Sparrow (Passer montanus) [
]. The present study is
necessary in order to test the hypothesis that passerines
are important reservoirs of AIV in the US. Further
motivation for our study comes from the fact that public
health agencies have limited funding to test wild birds for
AIV. Thus, it is crucial that the establishment of
surveillance sites should be as efficient as possible. For example,
the number of sites that are monitored should be small
but the sites should be located in counties that are most
likely to have birds with AIV. We aim to test the
hypothesis that environmental variables can be used to predict
AIV cases in wild birds. Next, based on the relationship
between AIV and environmental predictors, we attempt
to identify the US counties most likely to be influenza
hotspots for wild birds.
Our study makes the following contributions. First,
guidelines formulated by the World Health Organization
recognize the importance of epidemiological modelling
using tools such as GIS for the control of AIV [
Nevertheless, most previous work on the geographic
distribution of AIV has analyzed Asia and Africa [e.g. [
To date, studies of AIV in wild birds in the US have
focused on Alaska [
]. However, there may be
overlooked hotspots of AIV in the contiguous US [
We contribute the first predictions about AIV cases in the
contiguous US at the county scale. Second, we analyze
new passerine samples from the Atlantic, Mississippi, and
Pacific Flyways supplemented with existing samples from
online databases to provide the first comprehensive
assessment of AIV prevalence in US passerines. The main
finding reported in this article is that the prevalence of
influenza in passerines is greater than the prevalence in
eight other avian orders. The implication of this finding
for human health is that, along with poultry and
waterfowl, passerines in the US are a potential vector for the
transmission of AIV to people [
Influenza samples from wild birds
The data set comprised 13,046 samples from 136 counties
or parishes in 41 US states (Figure 1, Additional file 1,
Table S1, and Additional file 2, Table S1). The new
samples included in this analysis comprise cloacal swabs
collected from December 2005 to 2008 primarily during the
Spring breeding season at banding stations that are part
of the Monitoring Avian Productivity and Survival
(MAPS) program, during the Fall as part of the Landbird
Monitoring Network of the Americas (LaMNA), and
during the Winter as part of the Monitoring Avian Winter
Survival (MAWS) program in collaboration with UCLA's
Center for Tropical Research [
]. Since it is routine
for the samples collected by the banding network to be
stored at room temperature for prolonged periods, we
utilized 100% ethanol as a storage medium. Viral RNA
was extracted using a commercial magnetic bead kit
(Ambion MagMAX viral RNA isolation kit). The vRNA
was then converted to cDNA in a real-time reverse
transcription PCR reaction using an Ambion AgPath-ID
onestep PCR kit and run on a 7900 HT Fast Real-Time PCR
System. PCR primers targeted a conserved region of the
Matrix 1 gene: 5-GAR ATC GCG CAG ARA CTT GA-3
and 5-CAC TGG GCA CGG TGA GC-3 are forward and
reverse primers, respectively. For analysis of the
sensitivity of the MagMAX and AgPath-ID kits, see . We
used High Resolution Melt Analysis to identify putative
positives based on melt temperature and then confirmed
amplicon length (143 bp) on a 3% agarose gel. Viral cDNA
was purified using a Zymoclean DNA gel recovery kit.
We used the same PCR primers in BigDye Terminator
sequencing reactions and then products were run on an
Applied Biosystems 3730 system. Chromatograms were
visualized in Geneious and then confirmed as AIV
through a BLAST search of the NCBI database. The field
and laboratory methods utilized in this study were
approved by an Institutional Review Board at the
University of California, Los Angeles. AIV-positive samples have
been deposited in GenBank under Accession Numbers
HM355888 to HM355917.
Since our samples were cloacal swabs with no
measurable volume, we could not estimate the viral load of
influenza in passerines defined as the number of copies of the
virus per unit of body fluid. We can nevertheless infer
that our copy number is very low based on cycle of
threshold (Ct) values, which is the cycle at which the
samples began to amplify. Since the Ct values were fairly
high, we estimate that our copy number is uniformly low
across the passerine samples. (Ct values >35 are typically
interpreted as indicating the absence of influenza in
We investigated the association between AIV cases in
wild birds in the contiguous US and 12 predictor
variables, which measured agricultural and commercial
activity as well as climate (Table 1). The predictor
variables are all publicly available. First, we analyzed
measures of agricultural activity because rice crop production
is correlated with H5N1 outbreaks in Southeast Asia [
We included the amount of harvested cropland in the
county in units of hectares, the mean size of farms in the
county, and the % of the county in cropland [
]. We also
examined the % of family-owned farms in the county
because the use of employees who were not family
members was significant for explaining AIV outbreaks in
Virginia in 2002 [
]. In addition, we analyzed the density of
roads in each county that connect major population
centers and the human population density (as a surrogate
measure of trade activity) because proximity to trade
routes such as highways has been hypothesized to explain
the spread of H5N1 from Asia to Europe in 2005 and
proximity to roads was found to be a significant variable
for explaining outbreaks of HPAI H5N1 in poultry in
Romania in 2005 [
]. The density of poultry in the
county was included in the analysis to test the hypothesis
that poultry spread AIV to wild birds .
We incorporated total annual precipitation and
minimum temperature data interpolated from weather
stations using the Parameter-elevation Relationships on
Independent Slopes Model (PRISM) method, which
accounts for physiographic features such as terrain
barriers that result in rain shadows and is considered the most
accurate representation of US climate patterns [
Previous work has posited a relationship between
temperature and influenza cases. For example, the 1918 pandemic
coincided with an unusually hot winter in eastern North
America and north central Asia caused by one of the
strongest El Niño/Southern Oscillation (ENSO) events of
the twentieth century [
]. We hypothesized that
precipitation and minimum temperature might affect influenza
prevalence in wild birds because AIV can be transmitted
to birds in a moist environment and cold weather affects
bird dispersal [
], which may influence the spread of the
]. (For these and the following meteorological
variables, we used the average value of the variable from
2006 to 2008 because our AIV samples came from
December 2005 to 2008). Finally, we examined: (i) a
binary variable set to one if the majority of the land in the
county was ever covered by snow/ice and set to zero
otherwise, (ii) the day of the year when the majority of the
land in the county was first covered by snow/ice, and (iii)
the day of the year when the majority of the land in the
county was first free of snow/ice, all of which were
inferred from satellite radar . We included these
variables related to freeze and thaw date because the timing
of spring migration depends on the first day of thaw and
fall migration depends on the first day of freeze. These
variables may indirectly explain AIV spread by affecting
bird dispersal [
]. Variables were iteratively removed
from the spatial regression model via backward
elimination until only variables with a t-statistic in the 95th
percentile remained [
]. Forward selection gave the same
Spatial regression model
The statistical model represents the number of AIV cases
per county as a Poisson-distributed random variable,
which is appropriate for analyzing disease cases in which
some geographic units have many cases but most units
have few or no cases [
]. In the model, the number of
Calculated as the average minimum temperature
of all of the 800 m pixels in the county
http://www.fao.org/geonetwork/srv/en/ The data were aggregated to the county scale
resources.get?id=12720&fname=glbpo25cor.zip and the total number of poultry was divided by
&access=private the area of the county
Calculated as the number roads in each county
that connect major population centers
Calculated as the first day of the year when more
than half of the county was not frozen
Calculated as the average precipitation of all of
the 800 m pixels in the county
Calculated from freeze and thaw date
Calculated as the first day of the year when more
than half of the county was frozen
The total human population was divided by the
area of the county
Harvested cropland (ha)
Human population density
Mean farm size (ha)
Minimum temperature (°C)
Percent family owned farms
Percent of county in cropland
Thaw date (°C)
Total annual precipitation (mm)
AIV cases per county depends on the environmental
variables as well as spatial proximity to other counties with
AIV cases. In particular, we utilized a spatial regression
model to account for autocorrelation in AIV cases among
counties that are close together geographically. Failure to
address autocorrelation results in underestimation of the
degrees of freedom of the data, which decreases the
standard errors of the parameter estimates in a regression
]. Thus, ignoring autocorrelation may lead to
the erroneous conclusion that a variable is significant for
explaining AIV cases when the variable is in fact
non-significant. The model incorporates spatial autocorrelation
by constructing a semivariogram and also accounts for
differences in sampling effort among counties [
the model was fitted to the 136 counties for which we had
AIV samples, we predicted the number of AIV cases in
the other 2973 US counties by applying the model to the
unsampled counties. We utilized a generalized linear
mixed model, which is a form of kriging with a
semivariogram, rather than a conditional autoregressive model
because the latter cannot readily be extended to
nonGaussian data [
]. The Poisson distribution provided a
better fit to our data on flu cases than the Gaussian
distribution (see Additional file 3). The accuracy of the spatial
regression was assessed using two measures. First, we
calculated the generalized chi-squared statistic. If a
regression model is accurate, then the generalized chi-squared
statistic divided by the degrees of freedom of the data
should be close to one [
]. The model provided a
good fit to the data insofar as the generalized chi-squared
statistic divided by the degrees of freedom was 0.9.
Collinearity among the regressors was also acceptably low
(variance inflation factors <1.75) . Second, we used a
leave-one-out procedure that fitted the model to the data
from 135 counties and then measured the model's
accuracy on the remaining county. When the procedure was
repeated 136 times, the root mean squared error (r.m.s.e.)
was 6.33 AIV cases per county. This r.m.s.e. is acceptable
based on the rule of thumb that the r.m.s.e. should be no
greater than one-quarter of the range [
]. (For our data
set, the range was 76.) Further details of the statistical
model can be found in Additional file 3.
Among the eight avian orders analyzed here,
Passeriformes had the largest number of species in which AIV
was detected (22 species) followed by ducks (order
Anseriformes, 16 species) and shorebirds (order
Charadriiformes, 1 species). We tested 4,341 samples from
passerine birds, of which 0.89% were AIV-positive (Figure
2). Table 2 lists the top five species in terms of
AIV-prevalence for each avian order.
Influenza prevalence in Passeriformes
We evaluated the hypothesis that AIV was equally
prevalent among 11 avian orders by testing the null hypothesis
Two orders (Charadriiformes and Falconiformes) had only one AIV-positive species. For orders in which influenza was detected in at least five
species, the top five species in terms of prevalence are listed below.
that AIV prevalence was the same among the orders. The
null hypothesis was rejected, indicating that AIV is more
common in some orders than in others (Kruskal-Wallis
KW = 124, df = 10, p < 0.0001). Next, we ranked the
orders based on AIV prevalence. The number of
passerine species that tested positive for AIV (n = 22) was
greater than the number of positive species detected in
ten other orders, including waterfowl. However, our
sampling was also biased towards passerines. To address this,
we calculated fraction of AIV-positive samples from each
order. This corrects for the fact that we had more samples
from some orders than from others. The fraction of
samples from passerines that tested positive for AIV was
greater than the prevalence in eight other orders of birds
in the contiguous US (Figure 2). We note, however, that
for some of these eight orders the number of species and
samples represented in our database is small.
Nevertheless, AIV prevalence in Passeriformes was greater than in
Falconiformes, an order in which we tested four species
and 270 samples, and Piciformes, and order in which we
tested 14 species and 105 samples.
Environmental predictors of influenza prevalence in the sampled counties
For the remainder of the analysis, we pooled the samples
from all 11 orders so as to increase the geographic region
represented by data. Significant predictors of the number
of AIV cases per county in wild birds were thaw date, the
% of harvested cropland in the county, and minimum
temperature (Table 3). We interpret each of these
variables in turn beginning with thaw date. Freeze/thaw
dynamics have previously been hypothesized to explain
the prevalence of AIV in ducks in Europe (Andrew
Dobson, Princeton University, personal communication,
2009). We posit that thaw date affects influenza in wild
birds in the US according to the following mechanism.
Waterfowl have large populations with high annual
turnover rates, so that a large fraction of the population is
immunologically naïve each year [
]. In particular,
hatchlings are susceptible to infection from adults via
fecal-oral transmission at breeding grounds, which have
densities of up to 210 birds/m2 [
]. At these sites,
adults shed the virus into the water in feces and the young
are infected by ingesting the water . Prevalence of AIV
in gulls in the US is typically highest in spring and in
]. The sign of the coefficient for thaw date is
negative, indicating that if the thaw date occurs later in
the year, then the number of cases of AIV is predicted to
decrease [Table 3, for details see [
]]. We conjecture that
thaw date explains AIV cases because if a site thaws
earlier, then waterfowl can occupy the site sooner, and there
are more opportunities for adults to infect juveniles than
if the site were to become free of snow and ice later in the
year. In our data set, the prevalence of influenza among
hatchling year birds is significantly greater than in
second-year or adult birds (x12 = 64.87, one-sided p = 4 ×
1016). That finding is compatible with the hypothesis that a
high fraction of hatchlings are infected by adults at the
The amount of harvested cropland per county was very
highly significant for explaining AIV cases. This result is
consistent with previous analyses that showed a
significant effect of agricultural production on AIV cases in
Southeast Asia [
]. We hypothesize that agricultural
activity results in increased AIV prevalence because it
reduces the amount of natural habitat available to avian
migrants. For example, the conversion of wetlands to
farms may create bottlenecks at stopover sites along
migratory corridors, concentrating waterfowl into high
densities, such as the congregations of Teal and Snow
Geese at Kesterson National Wildlife Refuge in
California's Central Valley during migration. The resulting
crowding and intermingling of different species is
thought to increase the probability that a bird will be
infected with influenza .
Minimum temperature also emerged as significant for
explaining AIV cases. The sign of the coefficient that
represents the effect of minimum temperature was estimated
to be negative, meaning that if temperature increases,
then the number of AIV cases is predicted to decrease
(Table 3). This finding is compatible with the ecology of
AIV, which is known to survive longer outside the host in
cold conditions [
]. During the 1984 Pennsylvania
outbreak of H5N2, the virus survived in barns for as long as
105 days during cool weather . In addition, winters
are long and cold at Qinghai Lake, China, which was the
site of an outbreak of HPAI in wild birds in 2005 [
has also been conjectured that cold snaps explain the
spread of HPAI by wild birds in Europe insofar as cold
weather events prompt the dispersal of infected birds,
resulting in the spread of the virus [
example, in 2006, mute swans that typically winter on the
Black Sea became infected when bad weather forced
them to leave. This led to the discovery of infected mute
swans in Azerbaijan, Georgia, Iran, Kazakhstan, and 20
European countries . Additionally, frost is one of the
stress factors associated with dead wild birds infected
with HPAI [
Influenza predictions for the unsampled counties
The analysis at the county scale identifies the Mississippi
River basin as a hotspot for AIV cases in the contiguous
US (Figure 3(a)), which may be because wetlands in the
basin with shallow pools of water are conducive to the
transmission of the virus [
]. The Pacific Northwest is
also classified as a hotspot, though this may be due in
part to the fact that many of our samples of passerines
came from this region (Figure 1(b), Additional file 4,
Figure S1). At the state scale, Minnesota is predicted to have
the most cases of AIV in the contiguous US (Figure 4).
This is not surprising since AIV is known to have been
introduced to turkey farms in Minnesota by wild birds
135 times since 1968 [
]. At the county scale, there is a
pronounced north-to-south gradient in the predicted
number of AIV cases in the contiguous US (Figure 3(a)).
This finding is compatible with the theory that the virus
persists better in the colder environments of the northern
US than the warmer environment of southern US states.
Finally, the model predicts a large number of AIV cases in
the Corn Belt of the Central US (Figure 3(a)). This area is
Percent harvested cropland per county: Range: 0-100
known to be a major migratory flyway for ducks and also
has intensive agricultural production [
], which is a
significant risk factor for AIV according to our model. If we
reformulate the regression model to estimate the
probability of AIV occurrence rather than estimating the
number of cases of AIV, the spatial pattern of AIV in the
contiguous US remains qualitatively similar (Additional
file 5, Figure S1).
Implications for influenza surveillance and control in wild birds
Although the role of ducks and wading birds as influenza
reservoirs has long been appreciated, our analysis shows
that land birds constitute an important natural host of the
influenza virus in the US. Analysis of 225 avian species
indicates that influenza prevalence is higher in passerines
than in eight other orders of birds in the contiguous US.
Thus, the implication of this study for surveillance is that
passerines should be monitored as a potential vector for
transmitting AIV to humans, in addition to water birds
and domesticated birds.
Since vaccinating against or stamping out AIV in all
wild birds would be impossible, it is important to
prioritize populations for such management activities [
model predicts that the risk of AIV outbreaks in wild
birds is highest in California, the Great Plains,
Minnesota, Texas, and Washington (Figures 3 and 4). The Plains
region is predicted to have the highest number of AIV
cases due to its significant agricultural production and
cold winter temperatures, which allow AIV to persist
outside the host in environmental reservoirs (Figure 4). Our
prediction that there will be an AIV hotspot in the Pacific
Northwest is driven by our samples from passerine birds
because almost all of the positive samples from
Passeriformes came from this region. The Passeriformes with
the highest AIV-prevalence was the Golden-crowned
Kinglet (Regulus satrapa), but this result should be
interpreted cautiously since we had few samples for this
species (Table 2, Additional file 2, Table S1). The passerine
bird that showed the highest prevalence among the
species for which we had a large number of samples was
Swainson's Thrush (Catharus ustulatus). Swainson's
Thrush is a Neotropical migrant whose breeding sites
include remote areas of the Pacific Northwest that are
isolated from human settlements or farms [
]. The fact
that we detected high AIV-prevalence in Swainson's
Thrush supports the hypothesis that passerines birds
constitute a reservoir of AIV even without the spillover of
influenza from domestic birds to wild birds at farms in
the breeding range. However, further work is needed to
investigate the possible exposure of Swainson's Thrush to
poultry in its winter range.
Conversely, the Mississippi Flyway in the Plains region
had only one AIV-positive sample each from song birds
and shorebirds, so our prediction of an AIV hotspot in
this part of the country is determined primarily by
influenza-positive ducks (Anseriformes). The Anseriformes
species with the highest AIV prevalence was the Mute
Swan (Cygnus olor), which had 100% prevalence in our
data set (Table 1). However, this prevalence may not be
representative of natural populations insofar as our
sample size for this species was small. Among the
well-sampled Anseriformes species, AIV-prevalence was high in
the Mallard (Anas platyrhynchos) and the Green-winged
Teal (Anas carolinensis) (Additional file 2, Table S1). This
result is compatible with previous studies that have
detected high prevalence in both of these duck species
[reviewed in [
In addition to estimating the mean number of AIV
cases in wild birds per county, we predict the standard
error of the number of cases (Figure 3(b)). If the standard
error for a particular county is large, then there is a great
deal of uncertainty about AIV cases in the county. To
reduce this uncertainty, counties with large standard
errors, such as those in central Washington and central
Montana, can be targeted for increased surveillance.
Human health implications of influenza in wild birds
Previous spatial models have predicted the occurrence
and non-occurrence of AIV [
]. The novel
contribution of our model is the prediction of the number of cases
of influenza in wild birds. Understanding the number of
AIV cases in a county, rather than the occurrence or
nonoccurrence of the virus, is important because the rate of
co-infection with multiple influenza viruses increases
with the number of AIV cases . Co-infection is the
source of reassortment events that give rise to new
pandemic strains of AIV; indeed, such an event preceded the
1918 influenza pandemic that killed 50-100 million
]. Since the number of AIV cases is
predicted to be highest in the Great Plains and the Pacific
Northwest, we predict that these two geographical
regions will also have a concomitantly higher risk of
coinfection and reassortment. Thus, the threat to human
health due to the evolution of HPAI through
reassortment is greatest in those two parts of the country. As a
consequence, implementing biosecurity practices for the
control of HPAI is especially crucial in those two areas
Efforts undertaken by US health departments to plan
for AIV since 2005 are thought to have facilitated the
response of federal, state, and local agencies to the novel
H1N1 epidemic during the Spring of 2009 [
modelling the distribution of AIV in the US and
allocating health care resources based on the predictions of such
models may contribute to an improved technological
infrastructure for responding to future epizootics and
epidemics of influenza as well as other public health
Shortcomings of the analysis and areas for future research
Among the limitations of the analysis is that we did not
construct separate models for AIV in different species of
wild birds. However, this shortcoming may not be severe
because H5 AIV does not show species-specific
differences in North America [
]. Moreover, like our
analysis, epidemiological models often analyze the distribution
of the pathogen rather than that of the host species [e.g.
]. Another limitation of the analysis is that our viral
storage and detection methodology does not permit the
characterization of the HA or NA subtype of a sample
that tests positive for influenza. This is a shortcoming
because it may be more important to map the
distribution of subtypes that are highly virulent in mammals such
as H5 or H7. Our models are based on the detection of
influenza A through matrix gene detection rather than
the analysis of the H5 and H7 subtypes. Thus, if these two
subtypes have unique geographic distributions because
they are only transmitted by particular species of wild
birds, then our modelling approach might fail to capture
this. However, wild birds in the US exhibit a high rate of
turnover in serotypes according to a roughly 2-year cycle
]. Thus, modelling the geographic
distributions of the H5 or H7 subtypes would require detailed
annual surveys. Although such surveys have been
conducted for Delaware Bay [
], such data are not available
for sites that represent broad geographic sampling of the
In the Eastern hemisphere, cases of H5N1 AIV in
people typically increase in cooler months [
]. We found that
cool temperatures are also a good predictor of AIV cases
in wild birds. Influenza dynamics in wild birds in the US
appear to depend on climatic variables rather than a fixed
annual cycle because the relationship between AIV cases
and day of the year is weak (Pearson's = 0.17). A
hypothesis that emerges from this study is that H5N1 may be
more prevalent in humans during cool months because
both the prevalence of the virus in birds and the rate of
avian-to-human transmission are higher in cool weather.
Future field studies could assess the evidence in support
of this hypothesis by testing for influenza in birds and
people simultaneously in the same geographic region
during cool weather. If the hypothesis is not confirmed, a
possible alternative explanation for the increase in human
cases of influenza during cool weather is that people
spend more time indoors during the cool winter months
and thus have greater exposure to infected individuals [
The recent H1N1 pandemic has demonstrated the
public health significance of reassortment events between
avian and swine influenza viruses. Such reassortment
might be expected to be more frequent in geographic
regions where (i) swine production is intensive and (ii)
there is also high prevalence of influenza in wild birds.
Regions that score high for both (i) and (ii) could have a
greater likelihood of influenza reassortment events in
livestock or wildlife hosts of the influenza virus. For
example, results indicate that the Mississippi Flyway in
the central US has significant swine production along
with a significant number of cases of AIV in ducks
(Additional file 6, Figure S1). However, the risk of an influenza
epidemic in humans may depend on other parameters,
such as contact rates among people, wild birds, poultry,
and swine, and the transmission efficiency of the virus.
The available data on the exposure of humans to AIV is
extremely limited and difficult to interpret due to a lack
of standardized methods for serological testing [reviewed
]]. We consider the improvement of such data an
important avenue for future work and refer the interested
reader to Moffett et al. [
] for the incorporation of
contact rates and transmission efficiencies into a model of
The main conclusion of this research is that land birds
(Passeriformes) constitute an important natural reservoir
of influenza in the contiguous US. The importance of this
finding is that since passerine species are common in
urban habitats they could readily transmit highly
pathogenic influenza to people in the event that a highly
pathogenic subtype evolves through mutation or through
reassortment in a bird that is co-infected with distinct
influenza viruses. Aquatic birds are typically referred to
as the most important avian vector of influenza.
However, since passerines occupy the same habitat as poultry
and there have already been outbreaks of HPAI in US
poultry, passerines may be more effective at transmitting
HPAI to people than aquatic birds. The geographical
regions with the highest risk of influenza in wild birds are
the Great Plains and the Pacific Northwest; the threat to
human health due to reassortment events that produce
pandemic influenza subtypes is also greatest in these two
Additional file 1 Influenza samples from wild birds used in the study.
This file provides a detailed description of the geographical study region
and lists the online databases from which we obtained samples in addition
to the samples tested at the UCLA Center for Tropical Research.
Additional file 2 Description of the samples by species. The table in
this file reports the prevalence of flu in the 225 avian species analyzed in
this study, which represent 11 orders of birds.
Additional file 3 Formulation of the spatial regression model. This file
explains how we constructed the semivariogram in the spatial regression
model, provides a mathematical formulation of the model, and explains
how we fitted the model.
Additional file 4 Geographic locations of AIV-positive samples in the
contiguous US (n = 325). This file contains a map showing the bird
banding stations where wild birds tested positive for AIV.
Additional file 5 Probability of AIV occurrence in US counties or
county equivalents. This file consists of a map constructed by modifying
the spatial model to generate probabilistic predictions about the influenza
in wild birds, which are restricted to being between zero and one, rather
than estimates of the number of influenza cases, which range from zero
cases to 76 cases per county.
Additional File 6 Hotspots of swine production and AIV cases in wild
birds in the contiguous US. This file shows the overlap between areas
with intensive swine production in the US and areas in which we predict
high prevalence of AIV in wild birds. Reassortment between avian and
swine influenza viruses may be more common in such areas.
The authors declare that they have no competing interests.
TF designed the study's analytical methods and drafted the manuscript. SS
helped design the analytic methods, including the preparation of the satellite
data described in the Methods. EC supervised the first year of laboratory
activities, helping to design laboratory techniques for influenza testing, and wrote a
FileMaker Pro database to summarize the samples. ET supervised the second
year of laboratory activities including flu testing and the cataloguing of more
than 10,000 cloacal samples. HT helped design the analytic aspects of the
study and carried out a review of the literature about flu in wild birds. WB
helped design the study's analytic strategy including the selection of the type
of remote-sensed images to be used in the spatial model and selected the
spatial scale of these images. DD designed the study's field activities including the
sampling of passerine birds as part of the MAPS bird banding network. PN
reviewed and revised a preliminary draft of the manuscript, provided guidance
about the study's analytical approach, and helped design sampling activities as
part of the MAPS network. JM supervised field activities as part of the MAWS
bird banding network and designed Figure 2 of the manuscript. CJR
supervised field activities in the LaMNA bird banding network, which provided flu
samples during the migratory period. JA helped supervised the LaMNA bird
banding stations and revised a draft of the article. JP directed laboratory
activities during both years of flu testing and helped draft the Methods section of
the manuscript. TBS helped design the analytic aspect of the study and helped
draft the manuscript. All authors read and approved the final manuscript.
This work was supported by the joint National Science Foundation-National
Institute of Health Ecology of Infectious Diseases Program (grant number
EF0430146); and by the National Institute of Allergy and Infectious Diseases
(grant number EID-1R01AI074059-01). We thank the LaMNA, MAPS, and MAWS
personnel and partners who collected the samples included in this analysis.
Thanks are due to Betty J. Reardon and Stavana Strutz for comments on an
earlier draft of this manuscript. We thank two reviewers for comments that
improved the quality of manuscript. For discussions we thank François Elvinger,
Ryan Harrigan, and Falk Huettmann. The BioHealthBase Bioinformatics
Resource Center has been wholly funded with Federal funds from the National
Institute of Allergy and Infectious Diseases, National Institutes of Health,
Department of Health and Human Services, under Contract No.
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