Role of domestic ducks in the maintenance and spread of avian influenza viruses in Indonesia, The

2012 Summer.Includes bibliographical references.Wild waterfowl and aquatic birds serve as the natural reservoir host for influenza A viruses. As the reservoir, wild waterfowl play an important role in the persistence and transmission of influenza viruses among bird populations and to other mammalian species. In many Asian countries, domestic ducks are raised for meat and egg production. Some of these domestic ducks are ranged on rice paddies or post-harvest rice fields. The ducks provide service to the rice fields by fertilizing the field with feces and aerating the field by swimming and walking through the ground cover. Additionally, the ducks serve as a form of insect control through their natural grazing behaviors. The role that domestic ducks play in the ecology of influenza viruses is poorly understood. Highly pathogenic avian influenza H5N1 virus (HPAI H5N1) originated in Guangdong Province, China in 1996, which was followed by global dissemination of the virus that began in 2003. This virus is unprecedented in geographical spread, economic consequences and public health significance. At the present time, HPAI H5N1 virus is endemic six countries, including Indonesia. Indonesia has experienced the highest incidence of human infections with HPAI H5N1 virus and one of the highest case fatality rates. Control of the virus in Indonesia has proven extremely challenging, due to its diverse and complex poultry and domestic duck production systems. HPAI H5N1 virus is highly virulent in chickens and turkeys and causes severe systemic disease. Outbreaks of HPAI H5N1 in poultry populations are accompanied by high mortality. In contrast, HPAI H5N1 virus is typically nonpathogenic or mildly pathogenic in ducks and mortality in duck flocks during outbreaks of the virus is absent or limited. This allows ducks to serve as silent carriers of the virus, as they may shed large quantities of virus without displaying clinical signs of illness allowing infected ducks to evade detection by flock owners or government livestock officials. Domestic duck production is common in Southeast Asia. Indonesia has a large domestic duck population, estimated at more than 34 million ducks. Because HPAI H5N1 induces only mild disease in domestic ducks, outbreaks of the virus are difficult to detect and are rarely reported by domestic duck flock owners. Thus, domestic duck flocks have been left out of many government HPAI H5N1 surveillance and control programs. While a number of studies have demonstrated that the presence of domestic ducks in a country or at a specific location may be a risk factor for the presence of HPAI H5N1 virus, few studies have been conducted evaluating the role that domestic ducks play in the ecology of HPAI H5N1 virus. The objectives of the studies described in this dissertation were to elucidate the role of domestic ducks in the maintenance and spread of avian influenza viruses, particularly HPAI H5N1 virus, by evaluating domestic duck flock characteristics and behaviors, estimating the prevalence and incidence of avian influenza viruses in these flocks and characterizing HPAI H5N1 viruses detected in the field. To meet the objectives, two studies were conducted in West Java, Indonesia. The first study was a cross-sectional study aimed at characterizing domestic duck flocks and estimating the point prevalence and seroprevalence of avian influenza viruses, particularly HPAI H5N1 virus. This study was followed by a 7 month longitudinal study, aimed at estimating the incidence of avian influenza viruses, particularly HPAI H5N1 virus, in domestic duck flocks and evaluating flock illness and mortality during avian influenza virus outbreaks. A subset of samples from each of the studies was transported to the United States for virus characterization. The findings of the studies conducted demonstrate that domestic duck flocks are raised in complex production systems, are highly mobile, have significant contact with wild and domestic birds and mammals, are frequently ill and are provided with little formal veterinary care. The prevalence and incidence of avian influenza virus, including HPAI H5N1 virus, are high in domestic duck flocks in Indonesia. Clinical signs of illness and increased mortality did not correlate with the presence of avian influenza virus in the flock. Interestingly, there was also no correlation between increased flock mortality and the presence of HPAI H5N1 virus in the flock, demonstrating that domestic duck flocks can be asymptomatically infected with HPAI H5N1 virus while shedding high quantities of virus. Characterization of some of the viruses isolated from domestic duck flocks demonstrated that the flocks can be infected with more than one avian influenza virus at one time, as demonstrated by one flock that was positive for HPAI H5N1, as well as H3 and H7 avian influenza viruses. These situations are concerning, as domestic duck flocks may serve as mixing vessels for avian influenza viruses and co-infections in these flocks may result in the emergence of novel influenza viruses that may have capabilities for human-to-human transmission. It is likely that domestic ducks play an important role in the maintenance and spread of avian influenza viruses, including HPAI H5N1 virus. A number of domestic duck flock practices, including extensive flock movement, frequent introduction and sale of ducks, free-ranging of ducks in areas where they have contact with wild birds and animals and continual contact of duck flocks with other duck and poultry flocks, increasingly adds to the difficulty of control of HPAI H5N1 virus within this production system and makes eradication of the virus within a country extremely challenging

LIMITED ANTIBODY EVIDENCE OF EXPOSURE TO MYCOBACTERIUM BOVIS IN FERAL SWINE (\u3ci\u3eSUS SCROFA\u3c/i\u3e) IN THE USA

Bovine tuberculosis is a chronic disease of cattle (Bos taurus) caused by the bacterium Mycobacterium bovis. Efforts have been made in the US to eradicate the disease in cattle, but spillover into wildlife and subsequent spillback have impeded progress in some states. In particular, infection in white-tailed deer (Odocoileus virginianus) has been followed by infection in cattle in some Midwestern states. Infection has also been documented in feral swine (Sus scrofa) on the Hawaiian island of Molokai and in various European countries, but no large-scale survey of antibody exposure to the bacteria has been conducted in feral swine in the US. We tested 488 sera from feral swine collected near previously documented outbreaks of bovine tuberculosis in cattle and captive cervids, in addition to 2,237 feral swine sera collected across the US from 1 October 2013 to 30 September 2014. While all but one of the samples were antibody negative, the results are important for establishing baseline negative data since feral swine are capable reservoirs and could be implicated in future outbreaks of the disease

SARS‑CoV‑2 entry into and evolution within a skilled nursing facility

SARS-CoV-2 belongs to the family Coronaviridae which includes multiple human pathogens that have an outsized impact on aging populations. As a novel human pathogen, SARS-CoV-2 is undergoing continuous adaptation to this new host species and there is evidence of this throughout the scientific and public literature. However, most investigations of SARS-CoV-2 evolution have focused on largescale collections of data across diverse populations and/or living environments. Here we investigate SARS-CoV-2 evolution in epidemiologically linked individuals within a single outbreak at a skilled nursing facility beginning with initial introduction of the pathogen. The data demonstrate that SARSCoV- 2 was introduced to the facility multiple times without establishing an interfacility transmission chain, followed by a single introduction that infected many individuals within a week. This largescale introduction by a single genotype then persisted in the facility. SARS-CoV-2 sequences were investigated at both the consensus and intra-host variation levels. Understanding the variability in SARS-CoV-2 during transmission chains will assist in understanding the spread of this disease and can ultimately inform best practices for mitigation strategies

Diffusion of influenza viruses among migratory birds with a focus on the Southwest United States

The Southwest United States, including Arizona and New Mexico, has a diverse climate and is home to many different avian species. We sequenced the hemagglutinin (HA) gene of twenty influenza specimens for the years 2007–2009. This included four from Arizona, and sixteen from New Mexico. We analyzed the sequences and determined the following HA subtypes: H3, H4, H6, H8, and H11. For each subtype, we combined our virus sequences with those from a public database, and inferred phylogeographic models of influenza diffusion. Statistical phylogeography indicated that overall evolutionary diffusion of avian influenza viruses is geographically structured (p \u3c 0.05). In addition, we found that diffusion to the Southwest was often from nearby states including California. For H3, H4 and H6, the intra-flyway gene flow rates were significantly (p \u3c 0.001) higher than those of inter-flyway. Such rate difference was also observed in H8 and H11, yet, without statistical significance (p = 0.132, p = 0.190, respectively). Excluding any one flyway from the calculation generated similar results, suggesting that such barrier effect on gene flow rates is not exclusively produced by any single flyway. We also calculated the Bayes factor test for the significant non-zero rates between states and identified significant routes both within and across flyways. Such inter-flyway spread of influenza was probably the result of birds from four flyways co-mingling on breeding grounds in northern regions or marshaling on staging areas post breeding in Canada or Alaska, before moving south each fall. This study provides an initial analysis of evolutionary diffusion of avian influenza virus to and from the Southwest United States. However, more sequences from this region need to be generated to determine the role of host migration and other factors on influenza diffusion

LIMITED ANTIBODY EVIDENCE OF EXPOSURE TO MYCOBACTERIUM BOVIS IN FERAL SWINE (\u3ci\u3eSUS SCROFA\u3c/i\u3e) IN THE USA

Bovine tuberculosis is a chronic disease of cattle (Bos taurus) caused by the bacterium Mycobacterium bovis. Efforts have been made in the US to eradicate the disease in cattle, but spillover into wildlife and subsequent spillback have impeded progress in some states. In particular, infection in white-tailed deer (Odocoileus virginianus) has been followed by infection in cattle in some Midwestern states. Infection has also been documented in feral swine (Sus scrofa) on the Hawaiian island of Molokai and in various European countries, but no large-scale survey of antibody exposure to the bacteria has been conducted in feral swine in the US. We tested 488 sera from feral swine collected near previously documented outbreaks of bovine tuberculosis in cattle and captive cervids, in addition to 2,237 feral swine sera collected across the US from 1 October 2013 to 30 September 2014. While all but one of the samples were antibody negative, the results are important for establishing baseline negative data since feral swine are capable reservoirs and could be implicated in future outbreaks of the disease

Influenza Exposure In United States Feral Swine Populations

Swine play an important role in the disease ecology of influenza. Having cellular receptors in common with birds and humans, swine provide opportunities for mixed infections and potential for genetic re-assortment between avian, human, and porcine influenza. Feral swine populations are rapidly expanding in both numbers and range and are increasingly coming into contact with waterfowl, humans, and agricultural operations. In this study, over 875 feral swine were sampled from six states across the United States for serologic evidence of exposure to influenza. In Oklahoma, Florida, and Missouri, USA, no seropositive feral swine were detected. Seropositive swine were detected in California, Mississippi, and Texas, USA. Antibody prevalences in these states were 1%in Mississippi, 5%in California, and 14.4%in Texas. All seropositive swine were exposed to H3N2 subtype, the predominant subtype currently circulating in domestic swine. The only exceptions were in San Saba County, Texas, where of the 15 seropositive samples, four were positive for H1N1 and seven for both H1N1 and H3N2. In Texas, there was large geographical and temporal variation in antibody prevalence and no obvious connection to domestic swine operations. No evidence of exposure to avian influenza in feral swine was uncovered. From these results it is apparent that influenza in feral swine poses a risk primarily to swine production operations. However, because feral swine share habitat with waterfowl, prey on and scavenge dead and dying birds, are highly mobile, and are increasingly coming into contact with humans, the potential for these animals to become infected with avian or human influenza in addition to swine influenza is a distinct possibility

Giardia and Cryptosporidium in resident wildlife species in Arctic Alaska

Giardia and Cryptosporidium are zoonotic protozoan parasites that can infect humans and other taxa, including wildlife, often causing gastrointestinal illness. Both have been identified as One Health priorities in the Arctic, where climate change is expected to influence the distribution of many wildlife and zoonotic diseases, but little is known about their prevalence in local wildlife. To help fill information gaps, we collected fecal samples from four wildlife species that occur seasonally on the northern Alaska coastline or in nearshore marine waters—Arctic fox (Vulpes lagopus), polar bear (Ursus maritimus), Pacific walrus (Odobenus rosmarus divergens), and caribou (Rangifer tarandus)—and used immunofluorescence assays to screen for Giardia cysts and Cryptosporidium oocysts. We detected Giardia cysts in 18.3% and Cryptosporidium oocysts in 16.5% of Arctic foxes (n = 109), suggesting that foxes may be potentially important hosts in this region. We also detected Giardia cysts in a single polar bear (12.5%; n = 8), which to our knowledge represents the first such report for this species. Neither parasite was detected in walruses or caribou

Limited antibody evidence of exposure to Mycobacterium bovis in feral swine (Sus scrofa) in the USA

Bovine tuberculosis is a chronic disease of cattle (Bos taurus) caused by the bacterium Mycobacterium bovis. Efforts have been made in the US to eradicate the disease in cattle, but spillover into wildlife and subsequent spillback have impeded progress in some states. In particular, infection in white-tailed deer (Odocoileus virginianus) has been followed by infection in cattle in some Midwestern states. Infection has also been documented in feral swine (Sus scrofa) on the Hawaiian island of Molokai and in various European countries, but no large-scale survey of antibody exposure to the bacteria has been conducted in feral swine in the US. We tested 488 sera from feral swine collected near previously documented outbreaks of bovine tuberculosis in cattle and captive cervids, in addition to 2,237 feral swine sera collected across the US from 1 October 2013 to 30 September 2014. While all but one of the samples were antibody negative, the results are important for establishing baseline negative data since feral swine are capable reservoirs and could be implicated in future outbreaks of the disease.Peer Reviewe

Domestic sheep show average Coxiella burnetii seropositivity generations after a sheep-associated human Q fever outbreak and lack detectable shedding by placental, vaginal, and fecal routes.

Coxiella burnetii is a globally distributed zoonotic bacterial pathogen that causes abortions in ruminant livestock. In humans, an influenza-like illness results with the potential for hospitalization, chronic infection, abortion, and fatal endocarditis. Ruminant livestock, particularly small ruminants, are hypothesized to be the primary transmission source to humans. A recent Netherlands outbreak from 2007-2010 traced to dairy goats resulted in over 4,100 human cases with estimated costs of more than 300 million euros. Smaller human Q fever outbreaks of small ruminant origin have occurred in the United States, and characterizing shedding is important to understand the risk of future outbreaks. In this study, we assessed bacterial shedding and seroprevalence in 100 sheep from an Idaho location associated with a 1984 human Q fever outbreak. We observed 5% seropositivity, which was not significantly different from the national average of 2.7% for the U.S. (P>0.05). Furthermore, C. burnetii was not detected by quantitative PCR from placentas, vaginal swabs, or fecal samples. Specifically, a three-target quantitative PCR of placenta identified 0.0% shedding (exact 95% confidence interval: 0.0%-2.9%). While presence of seropositive individuals demonstrates some historical C. burnetii exposure, the placental sample confidence interval suggests 2016 shedding events were rare or absent. The location maintained the flock with little or no depopulation in 1984 and without C. burnetii vaccination during or since 1984. It is not clear how a zero-shedding rate was achieved in these sheep beyond natural immunity, and more work is required to discover and assess possible factors that may contribute towards achieving zero-shedding status. We provide the first U.S. sheep placental C. burnetii shedding update in over 60 years and demonstrate potential for C. burnetii shedding to reach undetectable levels after an outbreak event even in the absence of targeted interventions, such as vaccination