The Pigeon circovirus (PiCV) which contains a circular single stranded DNA (approximately 2 kb) belongs to the genus Circovirus and the family Circoviridae. PiCV infections in pigeons (Columba livia) have been reported worldwide. Nowadays, pigeon racing is becoming increasingly popular and considered to be a national sport in China, and even, the greatest competitions of racing pigeons are stake place in China. However, there is no epidemiologic data on PiCV infections among racing pigeons in China. To trace the prevalence, genetic variation and evolution of PiCV in sick and healthy racing pigeons, 622 samples were collected from 11 provinces or municipalities of China from 2016 to 2019. Samples were tested by polymerase chain reaction. The results showed that the positive rate of PiCV was 19.3% (120/622) at the sample level; 59.0% (23/39) at the club level, suggesting that the virus was prevalent in Chinese racing pigeons. A sequence analysis revealed that the cap genes of the PiCV strains identified in our study display high genetic diversity and shared nucleotide homologies of 71.9%–100% and amino acid homologies of 71.7%–100%. 28 and 37 unique amino acid substitutions were observed among the cap proteins and rep proteins of our PiCV strains, respectively. Furthermore, two initiation codons (GTG and ATT) of cap gene were newly found. A cap-gene-based phylogenetic analysis showed that the strains in this study could be further divided into six groups (A, B, C, E, G, H and I) and some of our strains are closely related to worldwide strains from different types of pigeons. A large number of recombination events (31 events) were also detected in the PiCV genomes from Chinese racing pigeons. These findings suggest that PiCV strains circulating in China exhibits higher genetic diversity.

Bovine leptospirosis is a bacterial disease that affects bovine herds, causing economic losses due to reproductive problems, which require expensive treatments. The main source of transmission for cattle is still uncertain, but it has been described that small wild mammals can play an important role in the transmission cycle by being maintenance hosts for the pathogenic species of the bacterium and spreading it through urine. In this study, we characterize possible risk areas for bovine leptospirosis in the state of Veracruz, Mexico; based on the geographical distribution of small wild hosts of Leptospira sp. reported in Mexico in addition with climatic, geographic, land use and human activities variables, and validated risk map with bovine seroprevalence data. We used a generalized linear regression model to understand the association between the appearance of bovine leptospirosis seroprevalences and the favorability of wild hosts of Leptospira sp. as well as environmental variables. The parameterized model explains 13.58% of the variance. The seroprevalence in cattle showed a negative relationship with elevation, geographic length and human population density, and a positive relationship with environmental favorability for the bats reservoirs and favorability for at least one rodent and opossum reservoir. The variation in seroprevalence is mainly explained by a longitudinal gradient (10.4% of the variance) and the favourability for bats (3.0% of the variance). Describing the possible risks of seroprevalence in an important and neglected livestock geographical region, we contribute to the selection of areas of strategies for diagnosis and prevention of this relevant disease.

Peste des petits ruminants (PPR) is a viral transboundary disease of small ruminants that causes significant damage to agriculture. The disease has not been previously registered in the Republic of Kazakhstan (RK). This paper presents an assessment of the susceptibility of the RK territory to the spread of this disease in case of its importation from infected countries. Ordinary Least Squares (OLS) and Geographically Weighted Regression (GWR) models trained on the PPR outbreaks in China were used to rank municipal districts of the RK in terms of the risk of PPR spread. Spatial density of outbreaks was used as a risk indicator while a number of socio-economic, landscape and climatic indicators were considered as explanatory variables. The Exploratory Regression tool was used to reveal a best combination of independent variables based on specified thresholds of R-squared, variables’ multicollinearity and residuals’ normality and autocorrelation. The small ruminants’ density, the maximum green vegetation fraction, the annual mean temperature, the road length and density as well as the cattle density were the most significant factors. Both OLS and GWR demonstrated nearly similar model performance providing a global adjusted R-squared of 0.61. Applied to the RK, the models show the greatest risk of PPR spread in the south-eastern and northern regions of the country, especially within Almaty, Zhambyl, Turkistan, West Kazakhstan and East Kazakhstan regions. As part of the study, a country-wise survey was carried out to collect data on the distribution of livestock population the RK, which resulted in compiling a complete geo-database of small ruminants’ holdings in the country. The research results can be used to form a national strategy for the prevention of the importation and spread of PPR in Kazakhstan through targeted monitoring in high-risk areas.

The 2018 outbreak of myxomatosis in the Iberian hare (Lepus granatensis), has been hypothesized to originate from a species jump of the rabbit-associated myxoma virus (MYXV), after natural recombination with an unknown poxvirus. Iberian hares were long considered resistant to myxomatosis as no prior outbreaks were reported. To provide insights into the emergence of this recombinant virus (ha-MYXV), we investigated serum samples from 451 Iberian hares (88 live captured, 313 hunted and 50 found dead) collected over two time periods, 1994-1999 and 2017-2019, using a rabbit commercial indirect ELISA after validation, and tested different tissues or sera by a qPCR targeting M0005L/R gene conserved in MYXV and ha-MYXV. The cut-off of ELISA Relative Index 10 = 6.1 yielded an estimated positive predictive value of 96.4% (CI95% 82.6-98.0%), by comparison with qPCR positive and negative reference hares. Overall, antibodies were detected in 12.6% (57/451) of the hares tested, of which 40.3% (23/57) were also qPCR positive. Antibodies were found in apparently healthy hares sampled in 1994-1999 (n=10, none MYXV-DNA positive), and in 2017-2019 (n=28, of which 14% were MYXV-DNA positive). For the Iberian hares hunted or live trapped, seroprevalence was significantly higher in 2017-2019 (13.0%, CI95% 9.2-18.2%) than in 1994-1999 (5.4%, CI95% 3.0-9.6%) (p=0.005), and significantly higher in 2019 (p=0.007), being lower during the winter (p<0.001). While our molecular and serological results show that Iberian hares have been in contact with MYXV or an antigenically similar virus at least since 1994, they also show an increase in seroprevalence in 2018-2019. The more remote contact of hares with MYXV may have occurred with strains that circulated in wild rabbit, or unnoticed strains circulating in Iberian hare populations. This work clearly confirms the circulation of MYXV in the Iberian hare ate least 20 years before the severe virus outbreaks observed in 2018.

Peste des petits ruminants (PPR) is a contagious disease affecting small ruminants. It has been targeted by the global community for eradication within the next 10 years. Implementing eradication requires significant financial efforts, human resources, coordination among actors, and individual commitments. The objective of this study is to estimate the cost of PPR at household level, thereby providing economic information about the potential benefits for small ruminant keepers of PPR control and management strategies. Fifteen Sub-Saharan countries are included in this study, for which publicly available household level data assembled by FAO were used. We built a bioeconomic model to estimate the impact of PPR for a standardized theoretical area where each household raises an average herd comprising either 6 goats or 3 sheep and their offspring. We then used the outputs of the model to estimate the income loss due to PPR at household level. We constructed different income scenarios to account for the variability of small ruminant income in total annual income. The household income losses ranged from 0.6 to 44.8 percent of the total annual income. The percentages vary depending on the income scenario and on the gross annual economic impact of PPR on small ruminant production, which ranges from 25 to 80 percent based on the results of the bioeconomic model. Regardless of the income scenario, households in lower income quintiles are relatively more affected by PPR than households in upper quintiles. As expected, the more small ruminant production contributes to household income the greater the impact. We provide here estimates that may help, from a policy perspective, identifying the most relevant strategies and tailoring them at regional level to mitigate PPR impacts.

HPAI is endemic across parts of Indonesia, but the mechanisms of viral persistence in the poultry production system have not been well investigated. This mixed methods research conducted in Purbalingga District, Java characterised poultry populations and trade and contact networks and performed risk-based sampling for the active detection of HPAI virus in live bird markets, collector yards, backyard poultry, nomadic ducks and commercial farms. Approximately 60% of households kept birds, about half of which contributed towards household income. Traders tended to use multiple collector yards and live bird markets, and poultry might be presented at multiple markets before sale. Only the commercial farm sector implemented biosecurity practices and vaccination. Samples were screened for avian influenza virus (AIV) and positive samples were tested for the H5 and H9 sub-types. H5 virus was detected in all enterprise types, although there were few positive results in commercial farms, the backyard sector and nomadic duck flocks. The highest numbers of AIV, H5 and H9 viruses were found in the live bird markets and collector yards. The odds of detection of H5 in live bird markets and collector yards were similar; however, these were 3½ to 4 times higher than in backyard birds and nomadic ducks and 25 to 30 times higher than in commercial poultry. This suggests that transmission of infection in backyard poultry and duck production was likely to be driven more strongly by the value chain than by direct or indirect contacts at source. We could not determine whether the value chain concentrates or amplifies virus along its length, or whether AIV persists and actively circulates in live bird markets and collector yards. H5 and H9 viruses were detected year-round and were co-circulating in the different enterprise types, although no inference can be drawn regarding interactions between these HPAI and LPAI viruses.

Porcine Deltacoronavirus is a newly emergent enteric pathogen affecting swine farms worldwide. It has been detected in several countries in Europe, Asia and North America. Yet, it has not been reported in South America. In November 2019, an enteric disease outbreak in a pig farm located in San Martin, Peru was reported along with submission of three intestinal samples from pigs who succumbed to the disease. Samples were processed for molecular detection by qRT-PCR, viral isolation and further sequencing analysis. A taqman-based RT-PCR was performed to differentiate among the most relevant swine enteric coronaviruses described to date. All samples were positives to Porcine Deltacoronavirus with a cycle threshold (Ct) between 9-14, revealing a high viral load, while tested negatives to Porcine Epidemic diarrhea and Transmissible Gastroenteritis viruses. Following detection, viral isolation was performed using PK-15 and Vero cell lines. After 5 days of inoculation, no cytopathic effect was observed. A second blind passage allowed the observation of cytopathic effect on PK-15 cells, while it remained absent in Vero cells. One sample was processed for whole genome sequencing (NGS). In short, raw reads were imported into CLC genomics and assembled de novo. Out of 479k reads generated from the sample, 436k assembled into a 25501 bp contig which was 99.5% identical to a reference Porcine Deltacoronavirus strain from US within the North American phylogroup. Yet, there are relevant differences at the nucleotide and amino acid levels compared to previously described Porcine Deltacoronavirus strains. Altogether, our findings represent the first report of Porcine Deltacoronavirus in South America, its genomic characterization, which provides information of its evolutionary origin. Thus, this study offers new insights into the molecular epidemiology of Porcine Deltacoronavirus infections in the swine industry.

Borna disease virus (BoDV) can cause neurological disease in several vertebrate species, especially in horses and sheep. The recent cases of fatal encephalitis caused by BoDV in humans have raised concern regarding the zoonotic character of this virus. BoDV infection in horses is endemic in Central Europe, whereas in Spain the disease is regarded as an exotic disease in horses and serological investigations in these animals have never been performed. The aim of this study was to investigate the exposure to BoDV in breeding and sport horses in Spain and to determine risk factors for the transmission of the virus. Serum samples from 495 horses (260 sport horses and 235 Spanish Purebred breeding horses) were tested by an Indirect Fluorescence Antibody Test (IFAT). From the SP breeding horses we examined factors putatively associated with seropositivity to BoDV. A total of 164 horses (33.1%; 95% CI 29.0-37.3) showed antibodies against BoDV. Factors associated with BoDV seropositivity in the SP breeding horses were climate, age and the time of the year when the horses were sampled. This is the first report on the presence of BoDV antibodies in apparently asymptomatic breeding and sport horses in Spain. Our results demonstrate the need for BoDV surveillance in horses and possible reservoir hosts in this country, and suggests that BoDV should be included in the differential diagnosis of equine and human cases of encephalitis.

Background: The corona virus disease 2019 (COVID-19) outbreak originating in Wuhan, Hubei province, China, coincided with chunyun, the period of mass migration for the annual Spring Festival. To contain its spread, China adopted unprecedented nationwide interventions on January 23 2020. These policies included large-scale quarantine, strict controls on travel and extensive monitoring of suspected cases. However, it is unknown whether these policies have had an impact on the epidemic. We sought to show how these control measures impacted the containment of the epidemic. Methods: Web of Science database was searched on February 26, 2020 for Corona virus (COVID-19) publications published between 1997 to 2020. It was performed on the same day in order to avoid the possible bias came from update on the database because the metrics are changing over time. All publication types were considered; however publications as errata were excluded. Analysis parameters include year of publication, publication type, patterns of international collaboration, research institutions, journals, impact factor, h-index, language, and times cited. Results: A total of 12612Corona virus (COVID-19) research publications were published across the world. The Corona virus (COVID-19) associated publications were originated from 25 countries/territories, indicating the international spread of Corona virus (COVID-19) research. The USA was the largest contributor, with 4524 articles published over 32 years, followed by Peoples R China(2667 articles). The total number of citations for these publications has already achieved 8,015, with an average of 9.01 citations per each publication. The h-index for Corona virus (COVID-19) -associated publications was 48. The USA also have the highest h-index (32), followed by KSA (26) and UK (22). Netherland produced the greatest proportion of publications with international research collaboration (72.7 %) followed by the UK (71 %) and Germany (69.1 %) out of the total number of publications for each country.