Geology topics
Publications and source records attributed to Hon S. Ip.
In August 2020, outbreaks of coronavirus disease were confirmed on mink farms in Utah, USA. We surveyed mammals captured on and around farms for evidence of infection or exposure. Free-ranging mink, presumed domestic escapees, exhibited high antibody titers, suggesting a potential severe acute respiratory syndrome coronavirus 2 transmission pathway to native wildlife.
Rabbit hemorrhagic disease, a notifiable foreign animal disease in the US, was reported for the first time in wild native North American lagomorphs in April 2020 in the southwestern US. Affected species included the desert cottontail ( Sylvilagus audubonii ), mountain cottontail ( Sylvilagus nuttallii ), black-tailed jackrabbit ( Lepus californicus ), and antelope jackrabbit ( Lepus alleni ). Desert cottontails ( n =7) and black-tailed jackrabbits ( n =7) collected in April and May 2020 were necropsied at the US Geological Survey National Wildlife Health Center and tested positive for Lagovirus europaeus GI.2, also known as rabbit hemorrhagic disease virus 2 (GI.2/RHDV2/b), by real-time PCR at the US Department of Agriculture's Foreign Animal Disease Diagnostic Laboratory. Gross and microscopic lesions were similar to those reported in European rabbits ( Oryctolagus cuniculus ) and other hare ( Lepus ) species with GI.2/RHDV2/b infection; they included epistaxis (12/13; 92%); massive hepatocellular dissociation (14/14; 100%) and necrosis or apoptosis (11/11; 100%); pulmonary congestion (12/12; 100%), edema (12/13; 92%), and hemorrhage (11/12; 92%); and acute renal tubular injury (3/8; 38%). As in previous reports, massive hepatocellular dissociation and necrosis or apoptosis were the most diagnostically distinct finding. As North American Sylvilagus and Lepus species appear to be susceptible to fatal GI.2/RHDV2/b infection, additional work is needed to understand the host range, pathogenicity, and potential population effects of GI.2/RHDV2/b in North America.
The USGS National Wildlife Health Center (NWHC) Quarterly Mortality Report provides brief summaries of epizootic mortality and morbidity events by quarter. The write-ups, highlighting epizootic events and other wildlife disease topics of interest, are published in the Wildlife Disease Association quarterly newsletter. A link is provided in this WDA newsletter to the Wildlife Health Information Sharing Partnership event reporting system (WHISPers) so readers can view associated data.
In situ hybridization (ISH) and immunohistochemistry (IHC) are essential tools to characterize SARS-CoV-2 infection and tropism in naturally and experimentally infected animals and also for diagnostic purposes. Here, we describe three RNAscope ® -based ISH assays targeting the ORF1ab, spike, and nucleocapsid genes and IHC assays targeting the spike and nucleocapsid proteins of SARS-CoV-2.
Wild birds have been shown to be significant sources of numerous types of pathogens that are relevant to humans and agriculture. The presence of large numbers of migratory birds in such a sensitive and important ecosystem as the Platte River in central Nebraska, USA, could potentially serve a significant source of bird-derived pathogens in the water/sediment and riverine environment. In 2009 and 2010, a study was completed to investigate the potential water-quality impacts of Sandhill Cranes and Snow Geese on the microbial water quality of the central Platte River during their spring migration period. Fecal material, river-bottom sediment, and water samples were collected from January through May of each year during the spring migration season of Sandhill Cranes in the Central Flyway of North America. Results indicate that several types of fecal indicator bacteria and from a range of viral, protozoan, and bacterial pathogens, Campylobacter jejuni were present in Sandhill Crane excreta, and at significantly higher frequency and densities in water and sediments when the Sandhill Cranes were present, particularly during evening roosts within the Platte River environment. Therefore, further investigation of the health significance of avian pathogens is warranted for the Platte River in Central Nebraska during migration of Sandhill Cranes and other waterfowl.
Although wild waterfowl are the main reservoir for low pathogenic avian influenza viruses (LPAIv), the environment plays a critical role for the circulation and persistence of AIv. LPAIv may persist for extended periods in cold environments, suggesting that waterfowl breeding areas in the northern hemisphere may be an important reservoir for AIv in contrast to the warmer southern wintering areas. We evaluated whether southern wetlands, with relatively small populations (thousands) of resident waterfowl, maintain AIv in the summer, prior to the arrival of millions of migratory birds. We collected water and fecal samples at ten wetlands in two regions (Yolo Bypass and Sacramento Valley) of the California Central Valley during three bi-weekly intervals beginning in late July, 2010. We detected AIv in 29/367 fecal samples (7.9%) and 12/597 water samples (2.0%) by matrix real time Reverse Transcription Polymerase Chain Reaction (rRT-PCR). We isolated two H3N8, two H2N3, and one H4N8 among rRT-PCR positive fecal samples but no live virus from water samples. Detection of AIv RNA in fecal samples was higher from wetlands in the Sacramento Valley (11.9%) than in the Yolo Bypass (0.0%), but no difference was found for water samples (2.7 vs. 1.7%, respectively). Our study showed that low densities of hosts and unfavorable environmental conditions did not prevent LPAIv circulation during summer in California wetlands. Our findings justify further investigations to understand AIv dynamics in resident waterfowl populations, compare AIv subtypes between migratory and resident waterfowl, and assess the importance of local AIv as a source of infection for migratory birds.
From September to December 2011, 162 New England harbor seals died in an outbreak of pneumonia. Sequence analysis of postmortem samples revealed the presence of an avian H3N8 influenza A virus, similar to a virus circulating in North American waterfowl since at least 2002 but with mutations that indicate recent adaption to mammalian hosts. These include a D701N mutation in the viral PB2 protein, previously reported in highly pathogenic H5N1 avian influenza viruses infecting people. Lectin staining and agglutination assays indicated the presence of the avian-preferred SAα-2,3 and mammalian SAα-2,6 receptors in seal respiratory tract, and the ability of the virus to agglutinate erythrocytes bearing either the SAα-2,3 or the SAα-2,6 receptor. The emergence of this A/harbor seal/Massachusetts/1/2011 virus may herald the appearance of an H3N8 influenza clade with potential for persistence and cross-species transmission.
Several species of wild raptors have been found in Eurasia infected with highly pathogenic avian influenza virus (HPAIV) subtype H5N1. Should HPAIV (H5N1) reach North America in migratory birds, species of raptors are at risk not only from environmental exposure, but also from consuming infected birds and carcasses. In this study we used American kestrels as a representative species of a North American raptor to examine the effects of HPAIV (H5N1) infection in terms of dose response, viral shedding, pathology, and survival. Our data showed that kestrels are highly susceptible to HPAIV (H5N1). All birds typically died or were euthanized due to severe neurologic disease within 4-5 days of inoculation and shed significant amounts of virus both orally and cloacally, regardless of dose administered. The most consistent microscopic lesions were necrosis in the brain and pancreas. This is the first experimental study of HPAIV infection in a North American raptor and highlights the potential risks to birds of prey if HPAIV (H5N1) is introduced into North America.
A real-time reverse transcription polymerase chain reaction test for the identification of the H7 subtype in North American Avian influenza viruses (AIVs) was first reported in 2002; however, recent AIV surveillance efforts in wild birds and H7 outbreaks in poultry demonstrated that the 2002 test did not detect all H7 AIVs present in North and South America. Therefore, a new test, the 2008 Pan-American H7 test, was developed by using recently available H7 nucleotide sequences. The analytical specificity of the new assay was characterized with an RNA panel composed of 19 H7 viruses from around the world and RNA from all hemagglutinin subtypes except H16. Specificity for North and South American lineage H7 viruses was observed. Assay limits of detection were determined to be between 103 and 104 gene copies per reaction with in vitro transcribed RNA, and 100.0 and 10 0.8 50% egg infectious doses per reaction. The 2008 Pan-American H7 test also was shown to perform similarly to the 2002 test with specimens from chickens experimentally exposed to A/Chicken/BritishColumbia/314514-2/04 H7N3 highly pathogenic AIV. Furthermore, the 2008 test was able to detect 100% (n = 27) of the H7 AIV isolates recovered from North American wild birds in a 2006-2007 sample set (none of which were detected by the 2002 H7 test).
American white pelicans (Pelecanus erythrorhynchos) are colonial-nesting birds and their breeding sites are concentrated in a few small areas, making this species especially vulnerable to factors that can influence productivity, such as disease, disturbance, predation, weather events and loss of nesting habitat. Nearly half of the American white pelican population breeds at four colonies in the northern plains: Chase Lake National Wildlife Refuge (NWR) in North Dakota, Bitter Lake (Waubay NWR) in South Dakota, Medicine Lake NWR in Montana, and Marsh Lake in Minnesota. Thus, sustained productivity at these colonies is crucial to the health of the entire species. During the latter half of the 2002 and 2003 breeding seasons, unusually high mortality of pelican chicks was observed at these colonies. West Nile virus (WNv) was identified as one source of these losses. In 2004-2007 we monitored three major colonies in the northern plains to assess mortality of chicks during the late breeding season. We documented severe weather events, disturbance, and WNv as factors contributing to chick mortality. Before WNv arrived in the region in 2002, chick mortality after mid-July was ???4%, and then jumped to as high as 44% in the years since WNv arrived. WNv kills older chicks that are no longer vulnerable to other common mortality factors (e.g., severe weather, gull predation) and typically would have survived to fledge; thus WNv appears to be an additive mortality factor. Persistence of lower productivity at American white pelican colonies in the northern plains might reduce the adult breeding population of this species in the region.
Water birds are considered the reservoir for avian influenza viruses. We examined this assumption by sampling and real-time reverse transcription-PCR testing of 939 Asian land birds of 153 species. Influenza A infection was found, particularly among migratory species. Surveillance programs for monitoring spread of these viruses need to be redesigned.
Wild-bird surveillance in North America for avian influenza (AI) viruses with a goal of early identification of the Asian H5N1 highly pathogenic AI virus has identified at least six low-pathogenicity H5N1 AI viruses between 2004 and 2006. The hemagglutinin (HA) and neuraminidase (NA) genes from all 6 H5N1 viruses and an additional 38 North American wild-bird-origin H5 subtype and 28 N1 subtype viruses were sequenced and compared with sequences available in GenBank by phylogenetic analysis. Both HA and NA were phylogenetically distinct from those for viruses from outside of North America and from those for viruses recovered from mammals. Four of the H5N1 AI viruses were characterized as low pathogenicity by standard in vivo pathotyping tests. One of the H5N1 viruses, A/MuteSwan/MI/451072-2/06, was shown to replicate to low titers in chickens, turkeys, and ducks. However, transmission of A/MuteSwan/MI/451072-2/06 was more efficient among ducks than among chickens or turkeys based on virus shed. The 50% chicken infectious dose for A/MuteSwan/MI/451072-2/06 and three other wild-waterfowl-origin H5 viruses were also determined and were between 10 5.3 and 107.5 50% egg infective doses. Finally, seven H5 viruses representing different phylogenetic clades were evaluated for their antigenic relatedness by hemagglutination inhibition assay, showing that the antigenic relatedness was largely associated with geographic origin. Overall, the data support the conclusion that North American H5 wild-bird-origin AI viruses are low-pathogenicity wild-bird-adapted viruses and are antigenically and genetically distinct from the highly pathogenic Asian H5N1 virus lineage. Copyright ?? 2007, American Society for Microbiology. All Rights Reserved.
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