Emerging Infectious Diseases

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)--the virus that causes coronavirus disease (COVID-19)--has been detected in domestic dogs and cats, raising concerns of transmission from, to, or between these animals. There is currently no indication that feline- or canine-to-human transmission can occur, though there is rising evidence of the reverse. To explore the extent of animal-related transmission, we aggregated 17 case reports on confirmed SARS-CoV-2 infections in animals as of 15 May 2020. All but two animals fully recovered and had only mild respiratory or digestive symptoms. Using data from probable cat-to-cat transmission in Wuhan, China, we estimated the basic reproduction number R0 under this scenario at 1.09 (95% confidence interval: 1.05, 1.13). This value is much lower than the R0 reported for humans and close to one, indicating that the sustained transmission between cats is unlikely to occur. Our results support the view that the pet owners and other persons with COVID-19 in close contact with animals should be cautious of the way they interact with them.

Many studies have identified antibiotic resistant (ABR) Escherichia coli on meat. Appropriate hand hygiene and cooking practices should minimise the risk of gastrointestinal colonisation with ABR E. coli found on meat, and the subsequent chance of causing resistant opportunistic extraintestinal infection. There are large gaps in our understanding of the prevalence, origins and zoonotic potential of ABR E. coli found on meat, however, and particularly for meat reared in extensive farming systems. Wales is a devolved nation within the United Kingdom having large populations of extensively-reared sheep and beef cattle. To help address knowledge gaps around ABR E. coli on extensively reared meat, therefore, beef mince and lamb loin/leg steaks/chops were purchased from 50 (beef) and 46 (lamb) independent butchers across Wales. Following enrichment culture, 200 g meat samples were found to be positive for E. coli resistant to amoxicillin (31% positivity), streptomycin (28%), spectinomycin (29%), amoxicillin-clavulanate (11%), 3rd generation cephalosporins (2%) and fluoroquinolones (5%). Phylogenetic analysis confirmed that Welsh lamb meat ABR E. coli isolates (n=79) are more closely related to those found in faecal samples collected around sheep (n=352) than around beef cattle (n=361) on Welsh farms. This suggests that faecal contamination at or around slaughter is their primary origin. We found no closely related meat/infection clones (<20 SNPs distant and the same antibiotic resistance genes) when comparing ABR E. coli from Welsh meat (n=92) and those causing extraintestinal infections in people (n=2387) in an English region bordering Wales. We conclude, therefore, that the wider zoonotic implications of finding ABR E coli on beef and lamb meat sold at independent butchers in Wales are small.

Animal to human transmission of SARS-CoV-2 has not previously been reported in a zoo setting. A vaccinated African lion with physical limitations requiring hand feeding tested positive for SARS-CoV-2 after development of respiratory signs. Zoo employees were screened, monitored prospectively for development of symptoms, then re-screened as indicated, with confirmation by RT-PCR and whole-genome virus sequencing when possible. Trace-back investigation narrowed the source of infection to one of five people. Three exposed employees subsequently developed symptoms, two with viral genomes identical to the lions. Forward contact tracing investigation confirmed probable lion-to-human transmission. Close contact with large cats is a risk factor for bidirectional zoonotic SARS-CoV-2 transmission that should be considered when occupational health and biosecurity practices at zoos are designed and implemented. SARS-CoV-2 rapid testing and detection methods in big cats and other susceptible animals should be developed and validated to facilitate timely implementation of One Health investigations.

From 2003 to 25 February 2023, the avian influenza (H5N1) virus was confirmed in 59 human infections, including 39 deaths ([~]66% case-fatality rate) reported in 13 of 25 provinces in Cambodia. We aimed to assess current knowledge, attitude, and practice toward changes in poultry handling behaviors, poultry consumption, and poultry mortality reporting among rural villagers in areas affected by Avian influenza (H5N1) in Cambodia. A cross-section survey was conducted in August 2023. There were 208 participants residing in Prey Veng province who were invited to be interviewed face-to-face. Descriptive statistics were performed using STATA V17. The participants average age was 55 years old (SD=13.3 years), 78.4% were female, 59% had completed primary school, 56.7% were farmers, 68.3% raised chickens in their backyards, and 10.2% raised ducks, 23% of participants cooked sick or dead birds for their families, 32% knowing information about avian influenza virus was a lower proportion from healthcare providers, 10.6% from village health support groups were, and 2% from village animal health workers were only, 49% have been reported poultry illness and deaths to local authorities. The avian influenza epidemic in Cambodia is a genuine threat to animals and a possible concern to humans. To prevent and control this, we strongly advise everyone who works with poultry or wild game birds always to be prepared to follow appropriate hygiene standards and to cook poultry meat properly.

The 2021 discovery of a divergent lineage (B.1.641) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in white-tailed deer (Odocoileus virginianus) from Ontario raised concerns that deer were a potential reservoir. To assess whether white-tailed deer continued to be infected with B.1.641 and to test for spillover into other species, we established a surveillance program in Ontario by sampling wildlife via existing monitoring programs and through active surveillance of captive and wild animals. Between 2022 to 2024, we tested 2,839 animals, identifying one active SARS-CoV-2 infection (a likely spillover of a recombinant XBB.2.3.11.3 lineage), but no cases of B.1.641. Overall, 93 animals (6.8%) tested positive for SARS-CoV-2 antibodies, including 89 white-tailed deer, two Virginia opossums (Didelphis virginiana), one American mink (Neogale vison), and one river otter (Lontra canadensis). In Southwestern Ontario, where B.1.641 was originally detected, 15.2% of deer samples were seropositive. Generalized Linear Models demonstrated that seropositive deer were more likely to be found in areas with a higher fall deer harvest and human population density, and closer to previous B.1.641 cases. Our data suggest that deer-associated B.1.641 may have caused a relatively localized epizootic without forming a stable reservoir. This study underscores the importance of One Health-focused surveillance.

SARS-CoV-2 is believed to have emerged from an animal reservoir; however, the frequency of and risk factors for inter-species transmission remain unclear. We carried out a community-based study of pets in households with one or more confirmed SARS-CoV-2 infection in humans. Among 119 dogs and 57 cats with completed surveys, clinical signs consistent with SARS-CoV-2 were reported in 20 dogs (21%) and 19 cats (39%). Out of 81 dogs and 32 cats sampled for testing, 40% of dogs and 43% of cats were seropositive, and 5% of dogs and 8% of cats were PCR positive; this discordance may be due to delays in sampling. Respondents commonly reported close human-animal contact and willingness to take measures to prevent transmission to their pets. Reported preventative measures showed a slightly protective trend for both illness and seropositivity in pets, while sharing of beds and bowls had slight harmful effects.

Control of the COVID-19 pandemic requires a detailed understanding of prevalence of SARS-CoV-2 virus in the population. Case-based surveillance is necessarily biased towards symptomatic individuals and sensitive to varying patterns of reporting in space and time. The real-time assessment of community transmission antigen study (REACT-1) is designed to overcome these limitations by obtaining prevalence data based on a nose and throat swab RT-PCR test among a representative community-based sample in England, including asymptomatic individuals. Here, we describe results comparing rounds 1 and 2 carried out during May and mid June / early July 2020 respectively across 315 lower tier local authority areas. In round 1 we found 159 positive samples from 120,620 tested swabs while round 2 there were 123 positive samples from 159,199 tested swabs, indicating a downwards trend in prevalence from 0.13% (95% CI, 0.11%, 0.15%) to 0.077% (0.065%, 0.092%), a halving time of 38 (28, 58) days, and an R of 0.89 (0.86, 0.93). The proportion of swab-positive participants who were asymptomatic at the time of sampling increased from 69% (61%, 76%) in round 1 to 81% (73%, 87%) in round 2. Although health care and care home workers were infected far more frequently than other workers in round 1, the odds were markedly reduced in round 2. Age patterns of infection changed between rounds, with a reduction by a factor of five in prevalence in 18 to 24 year olds. Our data were suggestive of increased risk of infection in Black and Asian (mainly South Asian) ethnicities. Using regional and detailed case location data, we detected increased infection intensity in and near London. Under multiple sensitivity analyses, our results were robust to the possibility of false positives. At the end of the initial lockdown in England, we found continued decline in prevalence and a shift in the pattern of infection by age and occupation. Community-based sampling, including asymptomatic individuals, is necessary to fully understand the nature of ongoing transmission.

Highly pathogenic avian influenza (HPAI) H5N1 has caused the deaths of more than 100 million birds since 2021, and human cases since 1997 have been associated with significant morbidity and mortality. Given the recent detection of HPAI H5N1 in dairy cattle and H5N1 RNA detections in pasteurized retail milk in the United States, we established the Pan-Canadian Milk (PCM) Network. Through our network of collaborators from across Canada, retail milk is being procured longitudinally and sent to a central laboratory for testing for the presence of influenza A virus RNA. To date (05 July 2024), we have tested 92 retail milk samples from all ten Canadian provinces (NL, NS, PEI, NB, QC, ON, MB, SK, AB, and BC) and all have tested negative for influenza A virus RNA. Testing is ongoing and these results will be updated on rolling basis as additional data becomes available. Despite no known HPAI infections of dairy cattle in Canada to date, H5N1 poses a significant threat to the health of both humans and other animals. Routine surveillance of retail milk on a national scale will allow for monitoring of infected dairy cattle on an ongoing basis in a cost-effective, standardized, scalable and easily accessible manner. Our network and testing will act as an early detection system to help inform containment and mitigation activities if positive samples are identified.

Crimean-Congo Hemorrhagic Fever (CCHF) is a potential high-threat zoonotic disease caused by the Crimean-Congo hemorrhagic fever virus (CCHFV). Transmission of CCHFV occurs primarily through bites of infected Hyalomma ticks or via direct contact with the blood or tissues of infected animals or humans. This study presents a cross-sectional assessment of CCHFV seroprevalence and risk factors associated with occupational and environmental exposures among cattle and swine agricultural workers. Nine provinces across the Democratic Republic of the Congo (DRC) were selected and collection took place from June 2023 to July 2024. Five herds per species in each province were randomly visited, and at each facility or herd, up to 20 animals were chosen for serum sampling and attached tick collection. In five provinces, farm workers present on the day of collection were enrolled. Detection of anti-CCHFV Immunoglobulin G (IgG) antibodies was assessed via an in-house nucleoprotein-based enzyme-linked immunosorbent assay (ELISA). Among the 1,118 cattle surveyed across nine provinces 57.0% (95%CI: 54.1-59.9%) were seroreactive. Cattle from two provinces in the southeast, Tanganyika and Lualaba, had 94.6% (95%CI: 89.9-99.2%) and 90.7% (95%CI: 84.9-96.5%) reactivity, respectively. Among the 1,020 swine surveyed 13.4% (95%CI: 11.1-15.2%) were seroreactive. Among the 180 agricultural workers surveyed, 12.8% (95%CI: 7.9-17.6%) (23) were seroreactive for CCHF antibodies. This serologic survey indicated that CCHFV is circulating in the DRC and the southeast provinces are particularly at risk for spillover and morbidity among humans. Though no human cases have been reported since 2008, surveillance for CCHF should be considered among veterinary professional and healthcare workers.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infects wildlife. Recent studies highlighted that variants of concern (VOC) may expand into novel animal reservoirs with the potential for reverse zoonosis. North American white-tailed deer are the only deer species in which SARS-CoV-2 has been documented, raising the question whether further reservoir species exist as new VOC emerge. Here, we report the first cases of deer SARS-CoV-2 seropositivity in Eurasia, in a city population of fallow deer in Dublin, Ireland. Deer were seronegative in 2020 (circulating variant in humans: Alpha), one animal was seropositive in 2021 (Delta variant), and 57% of animals tested in 2022 were seropositive (Omicron variant). Ex vivo, a clinical isolate of Omicron BA.1 infected fallow deer precision cut lung slice type-2 pneumocytes, also a major target of infection in human lungs. Our findings suggest a change in host tropism as new variants emerged in the human reservoir, highlighting the importance of continued wildlife disease monitoring and limiting human-wildlife contacts. Teaser: This study is the first report of SARS-CoV-2 seropositivity in fallow deer, highlighting expansion of viral variants into new host reservoirs.

Law Enforcement Officers (LEOs), firefighters, and other first responders are at increased risk of SARS-CoV-2 infection compared to healthcare personnel but have relatively low COVID-19 vaccine uptake. Resistance to COVID-19 vaccine mandates among first responders has the potential to disrupt essential public services and threaten public health and safety. Using data from the HEROES-RECOVER prospective cohorts, we report on the increased illness burden of COVID-19 among unvaccinated first responders. From January to September 2021, first responders contributed to weekly active surveillance for COVID-19-like illness (CLI). Self-collected respiratory specimens collected weekly, irrespective of symptoms, and at the onset CLI were tested by Reverse Transcription Polymerase Chain Reaction (RT-PCR) assay for SARS-CoV-2. Among 1415 first responders, 17% were LEOs, 68% firefighters, and 15% had other first responder occupations. Unvaccinated (41%) compared to fully vaccinated (59%) first responders were less likely to believe COVID-19 vaccines are very or extremely effective (17% versus 54%) or very or extremely safe (15% versus 54%). From January through September 2021, among unvaccinated LEOs, the incidence of COVID-19 was 11.9 per 1,000 person-weeks (95%CI=7.0-20.1) compared to only 0.6 (95%CI=0.2-2.5) among vaccinated LEOs. Incidence of COVID-19 was also higher among unvaccinated firefighters (9.0 per 1,000 person-weeks; 95%CI=6.4-12.7) compared to those vaccinated (1.8 per 1,000; 95%CI=1.1-2.8). Once they had laboratory-confirmed COVID-19, unvaccinated first responders were sick for a mean{+/-}SD of 14.7{+/-}21.7 days and missed a mean of 38.0{+/-}46.0 hours of work. These findings suggest that state and local governments with large numbers of unvaccinated first responders may face major disruptions in their workforce due to COVID-19 illness.

This study reports the sequence analysis of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) from infected individuals within the Greater Geelong region, Victoria, Australia. All but one individual had recently returned from travelling abroad, and all had clinical signs consistent with SARS-CoV-2 infection. SARS-CoV-2 belonging to three lineages were detected and represent separate introductions of the virus into the region. Sequence data were consistent with the recent travel history of each case. Full virus genome sequencing can play an important role in supporting local epidemiological tracing and monitoring for community transmission. Quality of the SARS-CoV-2 sequences obtained was highly dependent on appropriate sample collection and handling.

A Central Texas resident found an engorging Ornithodoros turicata tick attached to their leg while at home. The tick was submitted for testing, which confirmed that it was infected with a Borrelia species. Spirochetes were successfully cultured and whole genome sequencing confirmed that the species was Borrelia turicatae. The tick submitter reported being hospitalized and was recovering from Bells Palsy. Searching the Texas National Electronic Disease Surveillance System indicated that the individual had an undiagnosed febrile illness that spanned three weeks prior to finding the tick attached on them. These findings indicated possible recurrent tick exposure in a domestic environment.

During the ongoing western equine encephalitis virus (WEEV) outbreak in South America, we described three fatal cases in horses from Rio Grande do Sul, Brazil. We sequenced WEEV strains and identified a novel lineage causing these cases. Continued surveillance and horse immunization are needed to mitigate the WEEV burden.

After the end of the first epidemic episode of SARS-CoV-2 infections, as cases began to rise again during the summer of 2020, we at IHU Mediterranee Infection in Marseille, France, intensified the genomic surveillance of SARS-CoV-2, and described the first viral variants. In this study, we compared the incidence curves of SARS-CoV-2-associated deaths in different countries and reported the classification of SARS-CoV-2 variants detected in our institute, as well as the kinetics and sources of the infections. We used mortality collected from a COVID-19 data repository for 221 countries. Viral variants were defined based on [&ge;]5 hallmark mutations shared by [&ge;]30 genomes. SARS-CoV-2 genotype was determined for 24,181 patients using next-generation genome and gene sequencing (in 47% and 11% of cases, respectively) or variant-specific qPCR (in 42% of cases). Sixteen variants were identified by analysing viral genomes from 9,788 SARS-CoV-2-diagnosed patients. Our data show that since the first SARS-CoV-2 epidemic episode in Marseille, importation through travel from abroad was documented for seven of the new variants. In addition, for the B.1.160 variant of Pangolin classification (a.k.a. Marseille-4), we suspect transmission from mink farms. In conclusion, we observed that the successive epidemic peaks of SARS-CoV-2 infections are not linked to rebounds of viral genotypes that are already present but to newly-introduced variants. We thus suggest that border control is the best mean of combating this type of introduction, and that intensive control of mink farms is also necessary to prevent the emergence of new variants generated in this animal reservoir.

SARS-CoV-2 originated in animals and is now easily transmitted between people. Sporadic detection of natural cases in animals alongside successful experimental infections of pets, such as cats, ferrets and dogs, raises questions about the susceptibility of animals under natural conditions of pet ownership. Here we report a large-scale study to assess SARS-CoV-2 infection in 817 companion animals living in northern Italy, sampled at a time of frequent human infection. No animals tested PCR positive. However, 3.4% of dogs and 3.9% of cats had measurable SARS-CoV-2 neutralizing antibody titers, with dogs from COVID-19 positive households being significantly more likely to test positive than those from COVID-19 negative households. Understanding risk factors associated with this and their potential to infect other species requires urgent investigation. One Sentence SummarySARS-CoV-2 antibodies in pets from Italy.

The ongoing national mpox outbreak in the Democratic Republic of the Congo has resulted in more >30,000 suspected cases in the country from January 2023 to August 2024. While these historic case totals have been driven by primarily by zoonosis, the emergence of Clade Ib monkeypox virus (MPXV), which is connected to more sustained human-to-human transmission, has been associated with increasing public health impacts in eastern DRC. First identified in South Kivu province, Clade Ib MPXV has been identified in multiple non-endemic East African countries for the first time. In DRC, there have been concerns over broader Clade Ib expansion in the country that could further complicate containment and mitigation responses. Here, we report the first introductions of Clade Ib into North Kivu province, including within internal displacement camps, with suspected close contact transmission that includes non-intimate contacts and children. These findings demonstrate that mpox case investigations and community messaging campaigns should include considerations for non-sexual contact-mediated transmission of Clade Ib that includes children <15 years.

Shigella is a highly infectious bacterial pathogen spread via the fecal-oral route. Person to person spread during sexual contact among men who have sex with men (MSM) has been widely reported (1, 2). From January 2017 through May 2019, 74 culture confirmed multidrug resistant (MDR) shigellosis infections were reported in the Portland, Oregon area. Infections were caused by three divergent Shigella sonnei strains. To prevent additional illness and characterize the epidemiology of MDR shigellosis, a multifaceted investigation was conducted including expanded questionnaires, whole genome sequencing (WGS), antimicrobial susceptibility testing (AST), medical chart review, and sex partner notification. Among the 68 cases for which interviews were completed, 66 (97%) were among MSM. Patients reported having multiple sex partners (90%) and meeting on mobile dating or hook-up applications (63%). Forty percent reported methamphetamine use. Prevention and control challenges included low awareness of shigellosis among MSM and healthcare providers, inappropriate antimicrobial therapy, treatment failures, and limited sex partner elicitation. Results highlight the need for interventions to increase MSM and provider awareness of MDR Shigella spread through sexual contact to reduce shigellosis morbidity, limit ongoing transmission, and prevent future outbreaks. SummaryO_ST_ABSWhat is already known about this topic?C_ST_ABSMultidrug resistant (MDR) shigellosis among men who have sex with men (MSM) has been widely reported. Risk factors for specific MDR strains are of concern. What is added by this report?Between 2017 and 2019, three diverse MDR Shigella sonnei strains began co-circulating among sexually active MSM in the Portland, Oregon area. Patients reported multiple sex partners, use of mobile applications to meet partners, methamphetamine use, and housing insecurity. MDR shigellosis commonly resulted in hospitalization, treatment failure, and prolonged morbidity. What are the implications for public health practice?Interventions to increase MSM and provider awareness of MDR Shigella spread through sexual contact are necessary. To reduce morbidity and limit transmission, sexual health education should be provided to all adult patients with Shigella, and healthcare providers should order culture with antimicrobial susceptibility testing to inform antimicrobial therapy.

The US broiler production system processes over 9.3 billion chickens annually through a highly integrated pyramid structure where two primary breeding companies supply genetic stock to approximately 40 major integrators operating nationwide. To provide a quantitative, system-wide estimate of contamination origins, I analyzed whole genome sequences from Salmonella and Campylobacter isolates collected from over 800 processing facilities as part of the USDAs Food Safety Inspection Service (FSIS) verification sampling (2019-2024). Single-linkage clustering identified isolates sharing common origins ([&le;]2, 4, or 8 SNPs genome-wide), which were categorized by facility, company, and geographical distributions to infer contamination sources. Among the isolates analyzed, geographically dispersed multi-company clusters implying a primary breeder origin accounted for 78% of Campylobacter, 77% of non-Enteritidis Salmonella, and 96% of Salmonella Enteritidis isolates. Geographic spread analysis revealed that Enteritidis isolates matched a random distribution model consistent with contamination originating from the highest levels of the breeding pyramid. Campylobacter showed regional clustering implying sources at lower levels of the breeding pyramid. Cluster persistence exceeded multiple production cycles (median >4 years for Campylobacter, >4.5 years for 75% of Enteritidis isolates), indicating stable contamination reservoirs upstream of processing. These results demonstrate that the primary breeders are a major source of broiler contamination and suggest that upstream interventions targeting breeding stock, in particular for Enteritidis, may represent an efficient strategy for further reducing clinical cases of foodborne illness.

SARS-CoV-2 variants of concern (VOC) have spread throughout the world. In Mexico, VOC B.1.351 has been detected on one occasion and B.1.1.7 several times. We detected lineages B.1.351 and B.1.1.7 in patients who traveled to USA and B.1.1.7 in a patient with no travel history. Article summary lineIntroduction of B.1.351 and B.1.1.7 S ARS-CoV-2 variants in Monterrey, Mexico.