Evolutionary and genotypic analyses of global porcine epidemic diarrhea virus strains

Porcine epidemic diarrhea virus (PEDV), which re‐emerged in China in October 2010, has spread rapidly worldwide. Detailed analyses of the complete genomes of different PEDV strains are essential to understand the relationships among re‐emerging and historic strains worldwide. Here, we analysed the complete genomes of 409 strains from different countries, which were classified into five subgroup strains (i.e., GI‐a, GI‐b, GII‐a, GII‐b, and GII‐c). Phylogenetic study of different genes in the PEDV strains revealed that the newly discovered subgroup GII‐c exhibited inconsistent topologies between the spike gene and other genes. Furthermore, recombination analysis indicated that GII‐c viruses evolved from a recombinant virus that acquired the 5′ part of the spike gene from the GI‐a subgroup and the remaining genomic regions from the GII‐a subgroup. Molecular clock analysis showed that divergence of the GII‐c subgroup spike gene occurred in April 2010, suggesting that the subgroup originated from recombination events before the PEDV re‐emergence outbreaks. Interestingly, Ascaris suum, a large roundworm occurring in pigs, was found to be an unusual PEDV host, providing potential support for cross‐host transmission. This study has significant implications for understanding ongoing global PEDV outbreaks and will guide future efforts to develop effective preventative measures against PEDV.     

Genetic Detection and Characterization of Atypical Bovine Pestiviruses in Foetal Bovine Sera Claimed to be of Australian Origin

Summary Two European laboratories independently detected atypical bovine pestiviral nucleic acids in three commercial batches of foetal bovine serum (FBS) that was claimed by the producers to be of Australian origin. Additional batches of FBS were obtained directly from Australia to exclude possible contamination of the Australian FBS with that of South American origin during manufacturing/packaging in European countries. RT‐PCR amplification of partial 5′untranslated region and the complete N^pro gene yielded a specific band with expected size, which was confirmed by DNA sequencing. Bayesian analysis of sequence data demonstrated a closer phylogenetic relation of the newly detected atypical bovine pestiviruses to those of South American origin, which were related to the recognized bovine pestivirus species, bovine viral diarrhoea virus. Taken together, the results indicated the presence of atypical bovine pestiviruses in the Australian FBS, and most likely in Australian Continent.     

A fatal diarrhoea outbreak in farm‐raised Deinagkistrodon acutus in China is newly linked to potentially zoonotic Aeromonas hydrophila

Deinagkistrodon acutus is a venomous pit viper commonly used in traditional Chinese medicine; farming these snakes has become a major industry. In 2017, an outbreak of fatal diarrhoea among farm‐raised D. acutus in Hunan Province caused the deaths of 5,600 snakes within 3 weeks. We isolated a brand‐new sequence type of Aeromonas hydrophila (ST516) from lesions and confirmed that this bacterium was the causal agent of the outbreak. Snakes infected with the bacterium in the laboratory showed similar clinical symptoms to those of snakes in the original outbreak. We also tested bacterial virulence in Kunming mice to examine the likelihood of zoonosis. Isolates were pathogenic to mice, causing diarrhoea within 4 hr post‐challenge, which indicates that the bacterium can potentially infect mammals. Environmental analysis showed that polluted spring water likely caused the diarrhoea in snakes. This study is the first to report on a large‐scale outbreak of fatal diarrhoea in farm‐raised snakes, originating in a pathogen that can infect mammals. These results should raise awareness regarding potential anthropozoonosis among poikilotherms, mammals, and humans; appropriate prevention or control methods should be developed.     

A cluster of rotavirus enteritis in adult transplant recipients

Diarrhea following solid organ transplantation is a common side effect of some immunosuppressive agents but can also be caused by many pathogens. An outbreak of rotavirus (RV) enteritis presenting with severe diarrhea in four solid organ recipients was analyzed. The first case was diagnosed in a 6-month-old liver recipient who was prehospitalized on a pediatric ward. Within 1 month, three adult patients (two liver, one renal recipient) presented with enteritis. During diarrhea a significant rise in tacrolimus levels was observed. One patient developed toxic megacolon with ulcerative colitis. Infections were self-limiting but led to secondary infectious complications and prolonged hospitalization. This is the first reported outbreak of RV enteritis in a multiorgan transplant unit involving adult patients. Although no fingerprinting or subtyping of the virus was performed we assume the child was the primary source. In transplant recipients presenting with diarrhea RV infection should be considered.     

The racing pigeon (Columba livia domestica) industry in Victoria,Australia, and epidemiology of a novel Group A rotavirus outbreak

A novel Group A rotavirus, first identified clinically in racing, feral and fancy pigeons in Western Australia, had spread throughout Australia by March 2017. In December 2016, the putative index case of rotavirus in racing pigeons in the state of Victoria was confirmed at a regional bird sale, with rapid spread to peri‐urban Melbourne, the capital city. A survey sent to approximately 400 Victorian pigeon fanciers identified eight (of 85 respondents) with a confirmed rotavirus infection in their loft(s). If a fancier had purchased live birds, either from the regional sale or from another source, there was a 13%–38% increased likelihood of the loft subsequently being confirmed rotavirus‐positive. An increased loft‐level risk of rotavirus was also positively associated with the number of neighbouring lofts within a 5‐km radius of a home loft. It was concluded that rotavirus was primarily transmitted beyond the Victorian index case through the movement of live birds into a loft, either deliberately through bird purchase and/or inadvertently through the entry of pigeons from neighbouring lofts. As pigeon racing inherently requires consistent contact between birds from different lofts, vaccination is recommended as a primary method of rotavirus control in this unique industry.     

Drastic decline of hepatitis E virus detection in domestic pigs after the age of 6 months,Corsica, France

Suidae is an important reservoir of hepatitis E virus (HEV) and a source of transmission to humans (direct contact or via consumption of meat products). Our goal was to characterize the epidemiology of HEV infecting domestic pigs in Corsica Island, a French region hyperendemic for HEV. In Corsica, traditional extensive (or semi‐extensive) outdoor pig farming system is common. Sixteen farms were selected according to location and breeding system. Individual pig faeces samples were collected and qRT‐PCR for detecting HEV RNA was performed. Nucleic acids from HEV‐positive samples were amplified using specific ORF2 genotyping system. The genotype and subtype of the Corsican HEV sequences were determined by phylogenetic analysis. Among the 919 porcine faeces samples tested 9.2% (n = 85) were positive. The presence of viral RNA was correlated with (a) age (>6 months) Adjusted Odd Ratio (AOR) 0.25 [0.068–0.90] p = .032; 3–4 months AOR = 4.94 [2.30–10.62] p = .000043) with the logistic regression model with a random effect at the farm level. Among the 85 positive samples, 83 belonged to genotype 3c and two to genotype 3f. The highest prevalence was observed in the 3–4 months age group and older age (>6 months) was negatively related to HEV infection and this suggests that traditional breeding with a late slaughter age may limit the risk of transmission to humans. A kinetic study of pigs from birth to slaughtering would allow to ensure that the type of traditional breeding reported here is very favourable to the absence of the virus in slaughtered pigs and in pork products.     

A Review of the Current Status of Relevant Zoonotic Pathogens in Wild Swine (Sus scrofa) Populations: Changes Modulating the Risk of Transmission to Humans

Many wild swine populations in different parts of the World have experienced an unprecedented demographic explosion that may result in increased exposure of humans to wild swine zoonotic pathogens. Interactions between humans and wild swine leading to pathogen transmission could come from different ways, being hunters and game professionals the most exposed to acquiring infections from wild swine. However, increasing human settlements in semi‐natural areas, outdoor activities, socio‐economic changes and food habits may increase the rate of exposure to wild swine zoonotic pathogens and to potentially emerging pathogens from wild swine. Frequent and increasing contact rate between humans and wild swine points to an increasing chance of zoonotic pathogens arising from wild swine to be transmitted to humans. Whether this frequent contact could lead to new zoonotic pathogens emerging from wild swine to cause human epidemics or emerging disease outbreaks is difficult to predict, and assessment should be based on thorough epidemiologic surveillance. Additionally, several gaps in knowledge on wild swine global population dynamics trends and wild swine–zoonotic pathogen interactions should be addressed to correctly assess the potential role of wild swine in the emergence of diseases in humans. In this work, viruses such as hepatitis E virus, Japanese encephalitis virus, Influenza virus and Nipah virus, and bacteria such as Salmonella spp., Shiga toxin‐producing Escherichia coli, Campylobacter spp. and Leptospira spp. have been identified as the most prone to be transmitted from wild swine to humans on the basis of geographic spread in wild swine populations worldwide, pathogen circulation rates in wild swine populations, wild swine population trends in endemic areas, susceptibility of humans to infection, transmissibility from wild swine to humans and existing evidence of wild swine–human transmission events.     

Leptospira interrogans infection of southern tamanduas (Tamandua tetradactyla,Linnaeus, 1758) in Brazil

Leptospirosis is a zoonotic disease of global importance caused by an obligate aerobic spirochaete that infects a wide variety of domestic and wild animals. Natural hosts are asymptomatic or show moderate signs of the disease. Accidental hosts develop a severe, often lethal, form of the disease. All young southern tamanduas died suddenly at the zoo in the city of João Pessoa, Brazil. The animals were found dead without any noticeable clinical signs. Necropsy revealed extensive haemorrhage in the subcutaneous tissues, kidneys, lungs in addition to the presence of red fluid in the thoracic, abdominal and pericardial cavities. Histopathology of kidneys exhibited acute interstitial nephritis and tubular necrosis. Immunohistochemical staining revealed typical leptospiral wavy forms and aggregates in the lumen of several kidney tubules and lungs. Pathological and molecular investigations confirmed Leptospira interrogans infection. The adult tamanduas did not present with clinical alterations. To our knowledge, this investigation is the first study to report that leptospirosis should be considered as a possible cause of death in tamanduas. This article warns of the risks of anthropization with respect to Leptospira transmission to tamanduas, other animals and humans.     

Phylogenetic profiling for zoonotic Ehrlichia spp. from ixodid ticks in the Eastern Cape,South Africa

Ticks are obligate hematophagous parasite of vertebrate that transmit a range of pathogenic microorganisms that can cause diseases in livestock and humans. The range of tick‐borne disease causative agents infecting domestic animals and humans has recently increased. Several significant zoonotic tick‐borne diseases such as ehrlichiosis among others are on the increase worldwide. This study was designed to investigate the occurrence of zoonotic Ehrlichia spp. from samples collected from livestock in selected communities in the Eastern Cape Province, South Africa. Tick samples were manually collected from domesticated animals in selected homesteads. The ticks were morphologically identified to species and tested for Ehrlichia infection via polymerase chain reaction (PCR), using genus‐specific disulphide bond formation protein (dsbA) gene primers. This was followed by sequence analysis of amplicons and phylogeny. Of the 1,200 ticks collected, Amblyomma hebraeum was most prevalent (n = 335; 27.9%), followed by Rhipicephalus appendiculatus (n = 274; 22.8%), Rhipicephalus decoloratus; (n = 224; 18.7%) and Rhipicephalus eversti eversti (n = 200, 16.7%). Ehrlichia DNA was detected in 19/1,200 (1.6%) of the screened DNA samples. A homology search of the generated sequences revealed a high percentage of identity between 95% and 98% with other homologous dsbA gene sequences of other Ehrlichia species in GenBank. Phylogenetic analysis showed that the obtained sequences clustered unambiguously with other Ehrlichia sequences from different geographical regions of the world. We concluded that Ehrlichial pathogens are vectored by the ticks collected from domesticated animals in the study areas, thus suggesting concern for public health, as some of the recovered pathogens are zoonotic in nature and could pose serious public health risk through human exposure to tick bites.     

Prevalence and Risk Factors Associated with Leptospira spp. Infection in Technified Swine Farms in the State of Alagoas,Brazil Risk Factors Associated with Leptospira spp. in Swine Farms

The aim of this study was to determine the prevalence and to identify the risk factors associated with Leptospira spp. infection in technified pig farms in the state of Alagoas, Brazil. To compose sample for the prevalence study, 342 pigs were used (312 sows and 30 boars) proceeding from seven swine farms distributed in five districts of the state of Alagoas, Brazil. The infection’s serological diagnosis was performed by microscopic agglutination test. The risk factors analysis was performed using research questionnaires consisting of objective questions related to the breeder, the general characteristics of the property, and the productive, reproductive and sanitary management. Prevalence of 16.1% (55/342) of pigs seropositive was obtained. The associated risk factors were not performing quarantine (P = 0.003, OR = 5.43, CI = 1.79–16.41) and the use of artificial insemination (P = 0.023, OR = 3.38, CI = 1.18–9.66). A significant association of sow infection with the increased number of stillborn and mummified foetuses was found, as well as with the increased frequency of oestrus recurrence and the increased weaning‐to‐oestrus interval of seropositive sows. One might state that Leptospira spp. infection is disseminated in technified pig farms in the State of Alagoas, favouring reproductive failures and the impairment of zootechnical performance in these properties. The risk factors identified in this study are facilitators in the infecting agent dissemination and should be adjusted to control the disease in the herds studied.     

A G3P[13] porcine group A rotavirus emerging in China is a reassortant and a natural recombinant in the VP4 gene

Group A rotaviruses (RVA s) are a major cause of serious intestinal disease in piglets. In this study, a novel pig strain was identified in a stool sample from China. The strain was designated RVA /Pig/China/LNCY /2016/G3P[13] and had a G3‐P[13]‐I5‐R1‐C1‐M1‐A8‐N1‐T1‐E1‐H1 genome. The viral protein 7 (VP 7) and non‐structural protein 4 (NSP 4) genes of RVA /Pig/China/LNCY /2016/G3P[13] were closely related to cogent genes of human RVA s, suggesting that a reassortment between pig and human strains had occurred. Recombination analysis showed that RVA /Pig/China/LNCY /2016/G3P[13] is a natural recombinant strain between the P[23] and P[7] RVA strains, and crossover points for recombination were found at nucleotides (nt) 456 and 804 of the VP 4 gene. Elucidating the biological characteristics of porcine rotavirus (PoRV ) will be helpful for further analyses of the epidemic characteristics of this virus. The results of this study provide valuable information for RVA recombination and evolution and will facilitate future investigations into the molecular pathogenesis of RVA s.     

A viral metagenomic analysis reveals rich viral abundance and diversity in mosquitoes from pig farms

Mosquitoes harbour a diversity of viruses and are responsible for several mosquito‐borne viral diseases of humans and animals, thereby leading to major public health concerns, and significant economic losses across the globe. Viral metagenomics offers a great opportunity for bulk analysis of viral genomes retrieved directly from environmental samples. In this study, we performed a viral metagenomic analysis of five pools of mosquitoes belonging to Aedes, Anopheles and Culex species, collected from different pig farms in the vicinity of Shanghai, China, to explore the viral community carried by mosquitoes. The resulting metagenomic data revealed that viral community in the mosquitoes was highly diverse and varied in abundance among pig farms, which comprised of more than 48 viral taxonomic families, specific to vertebrates, invertebrates, plants, fungi, bacteria and protozoa. In addition, a considerable number of viral reads were related to viruses that are not classified by host. The read sequences related to animal viruses included parvoviruses, anelloviruses, circoviruses, flavivirus, rhabdovirus and seadornaviruses, which might be taken up by mosquitoes from viremic animal hosts during blood feeding. Notably, sample G1 contained the most abundant sequence related to Banna virus, which is of public health interest because it causes encephalitis in humans. Furthermore, non‐classified viruses also shared considerable virus sequences in all the samples, presumably belonging to unexplored virus category. Overall, the present study provides a comprehensive knowledge of diverse viral populations carried by mosquitoes at pig farms, which is a potential source of diseases for mammals including humans and animals. These viral metagenomic data are valuable for assessment of emerging and re‐emerging viral epidemics.     

Evaluation of bovine viral diarrhoea virus control strategies in dairy herds in Hokkaido,Japan, using stochastic modelling

Bovine viral diarrhoea virus (BVDV ) infection in cattle can result in growth retardation, reduced milk production, reproductive disorders and death. Persistently infected animals are the primary source of infection. In Hokkaido, Japan, all cattle entering shared pastures in summer are vaccinated before movement for disease control. Additionally, these cattle may be tested for BVDV and culled if positive. However, the effectiveness of this control strategy aiming to reduce the number of BVDV ‐infected animals has not been assessed. The aim of this study was to evaluate the effectiveness of various test‐and‐cull and/or vaccination strategies on BVDV control in dairy farms in two districts of Hokkaido, Nemuro and Hiyama. A stochastic model was developed to compare the different control strategies over a 10‐year period. The model was individual‐based and simulated disease dynamics both within and between herds. Parameters included in the model were obtained from the literature, the Hokkaido government and the Japanese Ministry of Agriculture, Forestry and Fisheries. Nine different scenarios were compared as follows: no control, test‐and‐cull strategies based on antigen testing of either calves or only cattle entering common pastures, vaccination of all adult cattle or only cattle entering shared pastures and combinations thereof. The results indicate that current strategies for BVDV control in Hokkaido slightly reduced the number of BVDV ‐infected animals; however, alternative strategies such as testing all calves and culling any positives or vaccinating all susceptible adult animals dramatically reduced those. To our knowledge, this is the first report regarding the comparison of the effectiveness between the current strategies in Hokkaido and the alternative strategies for BVDV control measures.     

Absence of Hepatitis E virus circulation in wild rabbits (Oryctolagus cuniculus) and Iberian hares (Lepus granatensis) in Mediterranean ecosystems in Spain

In recent decades, cases of autochthonous hepatitis E (HE) have sharply increased in European countries where foodborne transmission is considered the main route of HE virus (HEV) transmission. Although rabbits are considered the main reservoir of the zoonotic HEV‐3ra subtype, information on the role of wild lagomorphs in the epidemiology of HEV remains scarce. The aim of this study therefore was to assess the circulation of HEV in European wild rabbits (Oryctolagus cuniculus) and Iberian hares (Lepus granatensis), the most important lagomorph species in Spanish Mediterranean ecosystems. Liver samples from 372 wild rabbits and 78 Iberian hares were analysed using a broad‐spectrum RT‐PCR that detects HEV genotypes 1–8. None of the 450 lagomorphs tested were positive for HEV infection. To the best of our knowledge, this is the first study to assess HEV circulation in wild rabbits in Spain and the first to evaluate HEV infection in Iberian hares. Our results indicate absence of HEV circulation in wild rabbits and Iberian hares in southern Spain during the study period, which suggests that the risk of transmission of HEV from wild lagomorphs to other species, including humans, is low.     

Estimating the between‐farm transmission rates for highly pathogenic avian influenza subtype H5N1 epidemics in Bangladesh between 2007 and 2013

Highly Pathogenic Avian Influenza (HPAI ) is classified by the World Organization for Animal Health as one of the notifiable diseases. Its occurrence is associated with severe socio‐economic impacts and is also zoonotic. Bangladesh HPAI epidemic data for the period between 2007 and 2013 were obtained and split into epidemic waves based on the time lag between outbreaks. By assuming the number of newly infected farms to be binomially distributed, we fit a Generalized Linear Model to the data to estimate between‐farm transmission rates (β). These parameters are then used together with the calculated infectious periods to estimate the respective basic reproduction numbers (R ₀). The change in β and R ₀ with time during the course of each epidemic wave was explored. Finally, sensitivity analyses of the effects of reducing the delay in detecting infection on a farm as well as extended infectiousness of a farm beyond the day of culling were assessed. The point estimates obtained for β ranged from 0.08 (95% CI : 0.06–0.10) to 0.11 (95% CI : 0.08–0.20) per infectious farm per day while R ₀ ranged from 0.85 (95% CI : 0.77–1.02) to 0.96 (95% CI : 0.72–1.20). Sensitivity analyses reveal that the estimates are quite robust to changes in the assumptions about the day in reporting infection and extended infectiousness. In the analysis allowing for time‐varying transmission parameters, the rising and declining phases observed in the epidemic data were synchronized with the moments when R ₀ was greater and less than one, respectively. From an epidemiological perspective, the consistency of these estimates and their magnitude (R ₀ ≈ 1) indicate that the effectiveness of the deployed control measures was largely invariant between epidemic waves and the trend of the time‐varying R ₀ supports the hypothesis of sustained farm‐to‐farm transmission that is possibly initiated by a few unique introductions.     

Molecular detection and phylogenetic analysis of hepatitis E virus strains circulating in wild boars in south‐central Italy

Hepatitis E virus (HEV) is a zoonotic pathogen with a worldwide distribution, and infects several mammalian species, including pigs and wild boars, which are recognized as its natural reservoirs. The virus causes a usually self‐limiting liver disease with a mortality rate generally below 1%, although mortality rates of 15%–25% have been recorded in pregnant woman. Chronic infections can also occur. The prevalence of HEV has been extensively studied in wild boars and pigs in northern Italy, where intensive pig herds are predominantly located. In contrast, few data have been collected in south‐central Italy, where small pig herds are surrounded by large regional parks populated with heterogeneous wild fauna. In this study, 291 liver samples from wild boars caught in south‐central Italy were analysed with the molecular detection of viral RNA. Our results confirm the circulation of HEV in these animals, with a mean prevalence of 13.7% (40 of 291). A nucleotide sequence analysis showed that the HEV strains were highly conserved within the same geographic areas. The wild boar HEV strains belonged to the HEV‐3c subtype, which is frequently described in wild boars, and to an uncommon undefined subtype (HEV‐3j‐like).The viral prevalence detected is concerning because it could represent a potential risk to hunters, meat workers and consumers of wild boar liver and derivative products. The hypothesized inter‐species transmission of HEV to pigs and the possibility that the virus maintains its virulence in the environment and the meat chain also present potential risks to human health, and warrant further investigations in the near future.     

Genetic analysis of post‐epizootic amphibian chytrid strains in Bolivia: Adding a piece to the puzzle

The evolutionary history and dispersal pattern of Batrachochytrium dendrobatidis (Bd), an emergent fungal pathogen responsible for the decline and extinctions of many species of amphibians worldwide, is still not well understood. In South America, the tropical Andes are known as an important site for amphibian diversification, but also for being a place where hosts are at greater risk of chytridiomycosis. In an attempt to understand the history and the geographic pattern of Bd‐associated amphibian declines in Bolivia, we isolated Bd from hosts at two locations that differ in their chronology of Bd prevalence and host survival outcome, the cloud forests of the Amazonian slopes of the Andes and Lake Titicaca in the altiplano. We genotyped Bd from both locations and sequenced the genome from the cloud forest isolate and then compared them to reference sequences of other Bd strains across the world. We found that the Bolivian chytrid isolates were nearly genotypically identical and that they belong to the global panzootic lineage (Bd‐GPL). The Bolivian Bd strain grouped with other tropical New World strains but was closest to those from the Brazilian Atlantic Forest. Our results extend the presence of Bd‐GPL to the central Andes in South America and report this hypervirulent strain at Lago Titicaca, where Bd has been detected since 1863, without evidence of amphibian declines. These findings suggest a more complex evolutionary history for this pathogen in Bolivia and may point to the existence of an old lineage of Bd that has since been extirpated following the arrival of the panzootic Bd‐GPL or that the timing of Bd‐GPL emergence is earlier than generally acknowledged.     

Global knowledge gaps in the prevention and control of bovine viral diarrhoea (BVD) virus

The significant economic impacts of bovine viral diarrhoea (BVD) virus have prompted many countries worldwide to embark on regional or national BVD eradication programmes. Unlike other infectious diseases, BVD control is highly feasible in cattle production systems because the pathogenesis is well understood and there are effective tools to break the disease transmission cycle at the farm and industry levels. Coordinated control approaches typically involve directly testing populations for virus or serological screening of cattle herds to identify those with recent exposure to BVD, testing individual animals within affected herds to identify and eliminate persistently infected (PI) cattle, and implementing biosecurity measures such as double‐fencing shared farm boundaries, vaccinating susceptible breeding cattle, improving visitor and equipment hygiene practices, and maintaining closed herds to prevent further disease transmission. As highlighted by the recent DISCONTOOLS review conducted by a panel of internationally recognized experts, knowledge gaps in the control measures are primarily centred around the practical application of existing tools rather than the need for creation of new tools. Further research is required to: (a) determine the most cost effective and socially acceptable means of applying BVD control measures in different cattle production systems; (b) identify the most effective ways to build widespread support for implementing BVD control measures from the bottom‐up through farmer engagement and from the top‐down through national policy; and (c) to develop strategies to prevent the reintroduction of BVD into disease‐free regions by managing the risks associated with the movements of animals, personnel and equipment. Stronger collaboration between epidemiologists, economists and social scientists will be essential for progressing efforts to eradicate BVD from more countries worldwide.     

Risk Factors and Spatial Distribution of Canine Coccidioidomycosis in California, 2005–2013

Given the predisposition of dogs to coccidioidomycosis, identification of high‐risk regions for coccidioidomycosis in dogs may improve early recognition of emerging human disease. We sought to identify risk factors for canine coccidioidomycosis and to produce a risk map for coccidioidomycosis occurrence. Forty‐one dogs seen at the Veterinary Medical Teaching Hospital at the University of California, Davis, between 2005 and 2013 with coccidioidomycosis were identified together with a control population of 79 dogs. Owners were surveyed about potential risk factors including younger age, digging behaviour, and travel to Arizona or the California central valley. Risk factors were analysed using logistic regression analysis. Outcomes were used to generate a risk map for coccidioidomycosis in California. There was a significant correlation between the reported rate of coccidioidomycosis in humans and our risk map for canine coccidioidomycosis in California, supporting the idea of dogs as sentinels for emerging geographic areas for coccidioidomycosis in humans.