Genome sequences of seven Megrivirus strains from chickens in The Netherlands

We report seven chicken megrivirus genome sequences identified in chicken fecal samples from a broiler farm in The Netherlands. The sequences were determined using metagenomic sequencing and would expand our understanding of the genome diversity of megriviruses

Contribution of cats and dogs to SARS-CoV-2 transmission in households

INTRODUCTION: SARS-CoV-2 is known to jump across species. The occurrence of transmission in households between humans and companion animals has been shown, but the contribution of companion animals to the overall transmission within a household is unknown. The basic reproduction number ( R 0) is an important indicator to quantify transmission. For a pathogen with multiple host species, such as SARS-CoV-2, the basic reproduction number needs to be calculated from the partial reproduction numbers for each combination of host species. METHOD: In this study, the basic and partial reproduction numbers for SARS-CoV-2 were estimated by reanalyzing a survey of Dutch households with dogs and cats and minimally one SARS-CoV-2-infected human. RESULTS: For households with cats, a clear correlation between the number of cats and the basic reproduction number (Spearman's correlation: p 0.40, p-value: 1.4 × 10 -5) was identified, while for dogs, the correlation was smaller and not significant (Spearman's correlation: p 0.12, p-value: 0.21). Partial reproduction numbers from cats or dogs to humans were 0.3 (0.0-2.0) and 0.3 (0.0-3.5) and from humans to cats or dogs were 0.6 (0.4-0.8) and 0.6 (0.4-0.9). DISCUSSION: Thus, the estimations of within-household transmission indicated the likelihood of transmission from these companion animals to humans and vice versa, but the observational nature of this study limited the ability to establish conclusive evidence. This study's findings support the advice provided during the pandemic to COVID-19 patients to maintain distance from companion animals as a precautionary measure and given the possibility of transmission, although there is an overall relatively limited impact on the pandemic when compared to human-to-human transmission

Genome sequence of a Minacovirus strain from a farmed mink in The Netherlands

We report the genome sequence of a Minacovirus strain identified from a fecal sample from a farmed mink (Neovison vison) in The Netherlands that was tested negative for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using real-time PCR (RT-PCR). The viral genome sequence was obtained using agnostic deep sequencing

Establishing farm dust as a useful viral metagenomic surveillance matrix

Farm animals may harbor viral pathogens, some with zoonotic potential which can possibly cause severe clinical outcomes in animals and humans. Documenting the viral content of dust may provide information on the potential sources and movement of viruses. Here, we describe a dust sequencing strategy that provides detailed viral sequence characterization from farm dust samples and use this method to document the virus communities from chicken farm dust samples and paired feces collected from the same broiler farms in the Netherlands. From the sequencing data, Parvoviridae and Picornaviridae were the most frequently found virus families, detected in 85-100% of all fecal and dust samples with a large genomic diversity identified from the Picornaviridae. Sequences from the Caliciviridae and Astroviridae familes were also obtained. This study provides a unique characterization of virus communities in farmed chickens and paired farm dust samples and our sequencing methodology enabled the recovery of viral genome sequences from farm dust, providing important tracking details for virus movement between livestock animals and their farm environment. This study serves as a proof of concept supporting dust sampling to be used in viral metagenomic surveillance

Establishing farm dust as a useful viral metagenomic surveillance matrix.

Farm animals may harbor viral pathogens, some with zoonotic potential which can possibly cause severe clinical outcomes in animals and humans. Documenting the viral content of dust may provide information on the potential sources and movement of viruses. Here, we describe a dust sequencing strategy that provides detailed viral sequence characterization from farm dust samples and use this method to document the virus communities from chicken farm dust samples and paired feces collected from the same broiler farms in the Netherlands. From the sequencing data, Parvoviridae and Picornaviridae were the most frequently found virus families, detected in 85-100% of all fecal and dust samples with a large genomic diversity identified from the Picornaviridae. Sequences from the Caliciviridae and Astroviridae familes were also obtained. This study provides a unique characterization of virus communities in farmed chickens and paired farm dust samples and our sequencing methodology enabled the recovery of viral genome sequences from farm dust, providing important tracking details for virus movement between livestock animals and their farm environment. This study serves as a proof of concept supporting dust sampling to be used in viral metagenomic surveillance

Increased risk of pneumonia amongst residents living near goat farms in different livestock-dense regions in the Netherlands

BACKGROUND: Previous studies, performed between 2009-2019, in the Netherlands observed an until now still unexplained increased risk for pneumonia among residents living close to goat farms. Since data were collected in the provinces Noord-Brabant and Limburg (NB-L), an area with relatively high air pollution levels and proximity to large industrial areas in Europe, the question remains whether the results are generalizable to other regions. In this study, a different region, covering the provinces Utrecht, Gelderland, and Overijssel (UGO) with a similar density of goat farms, was included to assess whether the association between goat farm proximity and pneumonia is consistently observed across the Netherlands. METHODS: Data for this study were derived from the Electronic Health Records (EHR) of 21 rural general practices (GPs) in UGO, for 2014-2017. Multi-level analyses were used to compare annual pneumonia prevalence between UGO and data derived from rural reference practices ('control area'). Random-effects meta-analysis (per GP practice) and kernel analyses were performed to study associations of pneumonia with the distance between goat farms and patients' home addresses. RESULTS: GP diagnoses of pneumonia occurred 40% more often in UGO compared to the control area. Meta-analysis showed an association at a distance of less than 500m (~70% more pneumonia compared to >500m) and 1000m (~20% more pneumonia compared to >1000m). The kernel-analysis for three of the four individual years showed an increased risk up to a distance of one or two kilometers (2-36% more pneumonia; 10-50 avoidable cases per 100,000 inhabitants per year). CONCLUSIONS: The positive association between living in the proximity of goat farms and pneumonia in UGO is similar to the previously found association in NB-L. Therefore, we concluded that the observed associations are relevant for regions with goat farms in the entire country

Air pollution from livestock farms and the oropharyngeal microbiome of COPD patients and controls

Air pollution from livestock farms is known to affect respiratory health of patients with chronic obstructive pulmonary disease (COPD). The mechanisms behind this relationship, however, remain poorly understood. We hypothesise that air pollutants could influence respiratory health through modulation of the airway microbiome. Therefore, we studied associations between air pollution exposure and the oropharyngeal microbiota (OPM) composition of COPD patients and controls in a livestock-dense area. Oropharyngeal swabs were collected from 99 community-based (mostly mild) COPD cases and 184 controls (baseline), and after 6 and 12 weeks. Participants were non-smokers or former smokers. Annual average livestock-related outdoor air pollution at the home address was predicted using dispersion modelling. OPM composition was analysed using 16S rRNA-based sequencing in all baseline samples and 6-week and 12-week repeated samples of 20 randomly selected subjects (n = 323 samples). A random selection of negative control swabs, taken every sampling day, were also included in the downstream analysis. Both farm-emitted endotoxin and PM10 levels were associated with increased OPM richness in COPD patients (p 0.05). However, members of the genus Streptococcus were more abundant in COPD patients (Benjamini-Hochberg adjusted p < 0.01). Moderate correlation was found between ordinations of 20 subjects analysed at 0, 6, and 12 weeks (Procrustes r = 0.52 to 0.66; p < 0.05; Principal coordinate analysis of Bray-Curtis dissimilarity), indicating that the OPM is relatively stable over a 12 week period and that a single sample sufficiently represents the OPM. Air pollution from livestock farms is associated with OPM richness of COPD patients, suggesting that the OPM of COPD patients is susceptible to alterations induced by exposure to air pollutants

SARS-CoV-2 infection in dogs and cats is associated with contact to COVID-19 positive household members

Several domestic and wild animal species are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Reported (sero)prevalence in dogs and cats vary largely depending on the target population, test characteristics, geographical location and time period. This research assessed the prevalence of SARS-CoV-2-positive cats and dogs (PCR- and/or antibody positive) in two different populations. Dogs and cats living in a household with at least one confirmed COVID-19-positive person (household (HH) study; 156 dogs and 152 cats) and dogs and cats visiting a veterinary clinic (VC) (VC study; 183 dogs and 140 cats) were sampled and tested for presence of virus (PCR) and antibodies. Potential risk factors were evaluated and follow-up of PCR-positive animals was performed to determine the duration of virus shedding and to detect potential transmission between pets in the same HH. In the HH study, 18.8% (27 dogs, 31 cats) tested SARS-CoV-2 positive (PCR- and/or antibody positive), whereas in the VC study, SARS-CoV-2 prevalence was much lower (4.6%; six dogs, nine cats). SARS-CoV-2 prevalence amongst dogs and cats was significantly higher in the multi-person HHs with two or more COVID-19-positive persons compared with multi-person HHs with only one COVID-19-positive person. In both study populations, no associations could be identified between SARS-CoV-2 status of the animal and health status, age or sex. During follow-up of PCR-positive animals, no transmission to other pets in the HH was observed despite long-lasting virus shedding in cats (up to 35 days). SARS-CoV-2 infection in dogs and cats appeared to be clearly associated with reported COVID-19-positive status of the HH. Our study supports previous findings and suggests a very low risk of pet-to-human transmission within HHs, no severe clinical signs in pets and a negligible pet-to-pet transmission between HHs

Residential exposure to livestock farms and lung function in adolescence - The PIAMA birth cohort study

Background: There is a growing interest in the impact of air pollution from livestock farming on respiratory health. Studies in adults suggest adverse effects of livestock farm emissions on lung function, but so far, studies involving children and adolescents are lacking. Objectives: To study the association of residential proximity to livestock farms and modelled particulate matter ≤10 μm (PM10) from livestock farms with lung function in adolescence. Methods: We performed a cross-sectional study among 715 participants of the Dutch prospective PIAMA (Prevention and Incidence of Asthma and Mite Allergy) birth cohort study. Relationships of different indicators of residential livestock farming exposure (distance to farms, distance-weighted number of farms, cattle, pigs, poultry, horses and goats within 3 km; modelled atmospheric PM10 concentrations from livestock farms) with forced expiratory volume in 1 s (FEV1) and forced vital capacity (FVC) at age 16 were assessed by linear regression taking into account potential confounders. Associations were expressed per interquartile range increase in exposure. Results: Higher exposure to livestock farming was consistently associated with a lower FEV1, but not with FVC among participants living in less urbanized municipalities (<1500 addresses/km2, N = 402). Shorter distances of homes to livestock farms were associated with a 1.4% (0.2%; 2.7%) lower FEV1. Larger numbers of farms within 3 km and higher concentrations of PM10 from livestock farming were associated with a 1.8% (0.8%, 2.9%) and 0.9% (0.4%,1.5%) lower FEV1, respectively. Conclusions: Our findings suggest that higher exposure to livestock farming is associated with a lower FEV1 in adolescents. Replication and more research on the etiologic agents involved in these associations and the underlying mechanisms is needed

SARS-CoV-2 infection in cats and dogs in infected mink farms

Animals like mink, cats and dogs are susceptible to SARS-CoV-2 infection. In the Netherlands, 69 out of 127 mink farms were infected with SARS-CoV-2 between April and November 2020 and all mink on infected farms were culled after SARS-CoV-2 infection to prevent further spread of the virus. On some farms, (feral) cats and dogs were present. This study provides insight into the prevalence of SARS-CoV-2-positive cats and dogs in 10 infected mink farms and their possible role in transmission of the virus. Throat and rectal swabs of 101 cats (12 domestic and 89 feral cats) and 13 dogs of 10 farms were tested for SARS-CoV-2 using PCR. Serological assays were performed on serum samples from 62 adult cats and all 13 dogs. Whole Genome Sequencing was performed on one cat sample. Cat-to-mink transmission parameters were estimated using data from all 10 farms. This study shows evidence of SARS-CoV-2 infection in 12 feral cats and 2 dogs. Eleven cats (18%) and two dogs (15%) tested serologically positive. Three feral cats (3%) and one dog (8%) tested PCR-positive. The sequence generated from the cat throat swab clustered with mink sequences from the same farm. The calculated rate of mink-to-cat transmission showed that cats on average had a chance of 12% (95%CI 10%–18%) of becoming infected by mink, assuming no cat-to-cat transmission. As only feral cats were infected it is most likely that infections in cats were initiated by mink, not by humans. Whether both dogs were infected by mink or humans remains inconclusive. This study presents one of the first reports of interspecies transmission of SARS-CoV-2 that does not involve humans, namely mink-to-cat transmission, which should also be considered as a potential risk for spread of SARS-CoV-2