Advanced and accurate forecasting of COVID-19 cases plays a crucial role in planning and supplying resources effectively. Artificial Intelligence (AI) techniques have proved its capability in time series forecasting of the non-linear problems. In the present study, the relationship between weather factor and COVID-19 cases was assessed and also developed a forecasting model using long short term memory (LSTM), a deep learning model. The study found that the specific humidity has a strong positive correlation, whereas there is a negative correlation with maximum temperature and positive correlation with minimum temperature was observed in various geographic locations of India. The weather data and COVID-19 confirmed cases data (1st April-30th June 2020) was used to optimize univariate and multivariate LSTM time series forecast models. The optimized models were utilized to forecast the COVID-19 cases for the period 1st July 2020 to 31st July 2020 with 1 to 14 days of lead time. The results showed that the univariate LSTM model was reasonably good for the short term (1day lead) forecast of COVID-19 cases (relative error < 20%). Moreover, the multivariate LSTM model improved the medium-range forecast skill (1-7days) after including the weather factors. The study observed that the specific humidity played a crucial role in improving the forecast skill majorly in the West and northwest region of India. Similarly, the temperature played a significant role in model enhancement in the Southern and Eastern regions of India.

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.

Avian pathogenic E. coli (APEC) are generally considered to be the reservoir for human extraintestinal pathogenic E. coli (ExPEC): they share similar genetic characteristics and pathogenicity with no or minimal host specificity. In this study, we successfully isolated and identified an E. coli strain as the culprit responsible for serious colibacillosis outbreaks in intensive chicken farms in China in 2016. We investigated its phylogenetic classification (A, B1, B2, C, D, E, and F) by PCR analysis; its virulence and host range using challenge experiments with different animals; and its virulence factors, drug resistance genes, sequence type (ST), and related biological information through high-throughput sequencing. This isolate was found to belong to ST95, group B2, and serotype O18. The E. coli strain shows strong virulence in chickens with a minimum lethal dose (MLD) of 3 × 103 CFU/chicken and a strong virulence in mice with an MLD of 3 × 102 CFU/mouse and in rabbits with an MLD of 3 × 103 CFU/rabbit. Whole-genome sequencing showed that it consists of six types of prevalent resistance genes, 33 antibiotic efflux genes, and nine recognized virulent factors. The detailed data are available from GenBank (SRR13005645) for further study.

The larva of Taeniidae species can infect a wide range of mammals, causing major public health and food safety hazards worldwide. The Qinghai-Tibet Plateau (QTP), a biodiversity hotspot, is home to many species of rodents, which act as the critical intermediate hosts of many Taeniidae species. In this study, we identified two new larvae of Taenia spp., named as T. caixuepengi and T. tianguangfui, collected from the plateau pika (Ochotona curzoniae) and the Qinghai vole (Neodon fuscus), respectively in QTP, and their mitochondrial genomes were sequenced and annotated. Phylogenetic trees based on the mitochondrial genome showed that T. caixuepengi has the closest genetic relationship with T. pisiformis, while T. tianguangfui was contained in a monophyletic group with T. crassiceps, T. twitchelli and T. martis. Biogeographic scenarios analysis based on split time speculated that the speciation of T. caixuepengi (~5.49 Mya) is due to host switching caused by the evolution of its intermediate host. Although the reason for T. tianguangfui (~13.11 Mya) speciation is not clear, the analysis suggests that it should be infective to a variety of other rodents following the evolutionary divergence time of its intermediate host and the range of intermediate hosts of its genetically close species. This study confirms the species diversity of Taeniidae in the QTP, and speculates that the uplift of the QTP has not only a profound impact on the biodiversity of plants and animals, but also that of parasites.

In the present study, the highly pathogenic bovine Deltapapillomavirus (δPV) was investigated by liquid biopsy in blood samples of 168 clinically normal goats using both droplet digital PCR (ddPCR) and quantitative real time PCR (qPCR). Overall, ddPCR detected BPV E5 DNA in ~61.3% of the blood samples examined, while real time qPCR revealed the virus in ~10.7% of the same samples. Moreover, ddPCR showed BPV E5 DNA in ~78.8% of blood samples from goats that were in close contact with cattle and in 20% of blood samples from goats living in closed pens without any contact with cattle. In addition, ddPCR revealed a single BPV genotype in ~59.2% and multiple genotypes in ~40.8% of goats harboring BPV DNA, while real time qPCR detected single genotypes in ~17% and multiple genotypes in ~1%. Of the BPV co-infections detected by ddPCR, 28 (~67%) involved two genotypes, eight (~19%) three genotypes, and six (~14%) four genotypes. In contrast, real time qPCR revealed BPV co-infection by two genotypes in only one sample and failed to detect co-infection by three or four genotypes. BPV2 and BPV13 were the most prevalent viruses responsible for single and multiple co-infections, respectively. The present study showed that the ddPCR technique has much higher sensitivity and specificity in the detection of these viruses, and suggested that animal husbandry practices contribute to cross-species transmission of BPVs.

Pigeon aviadenovirus A and Pigeon circovirus are both viruses that can cause disease in pigeons. This study reports the identification of a natural co-infection of Pigeon aviadenovirus A and Pigeon circovirus in a breeding pigeon flock in central Anatolia, Turkey. Both viruses were isolated from pooled internal organs of pigeons using primary chicken embryo kidney cell cultures (CEKC) and specific pathogen free (SPF) embryonated chicken eggs. Both viruses were identified by PCR amplification followed by Sanger sequencing, while histopathological examination showed degenerated hepatocytes with basophilic intranuclear viral inclusions. The viruses have similar transmission characteristics and common clinical manifestations, but it is possible that coinfection may exacerabate disease. This is the first report of its kind in Turkey and is important for the protection against disease in pigeons.

Objective: To investigate the causes of early COVID-19 complicated with platelets(PLT) abnormality, and to analyze the possible mechanisms. Methods: The case datum of early COVID-19 complicated with PLT increase or decrease was collected. (125-350) ×109/L defined as the normal level of PLT(Group C), <125×109/L was defined as the PLT decrease group (Group A), >350×109/L defined as the PLT increase group (Group B) . The data were analyzed after collected. Results: Our statistical results showed that the incidence of COVID-19 combined PLT decreased was about 11.94% and the incidence of combined PLT increased was about 9.33% at admission. Compared with Group B and C, Group A showed a significant decrease in white blood cell, neutrophil and CD4 (P<0.05). The lymphocyte in Group A and C decreased significantly, but not find in Group B (P<0.05). Compared with Group A and C, IL-4 was increased in Group B, but lymphocyte decline was not significant (P>0.05). Conclusion: PLT abnormalities occur in all patients with different types of COVID-19. It may be related to the severity of inflammation and infection, immune regulation and megakaryocyte function, etc.

Astroviruses (AstVs) are major causative agents of gastroenteritis in children and had been detected worldwide. Recently, the novel neurotropic AstV associated with encephalitis and meningitis has been found in different species including human, bovine and ovine. However, little is known about the prevalence of neurotropic AstVs in water buffalo of China. In this study, we examined fecal samples from water buffalo in the Guangxi province of China and found different lineages of Water Buffalo Astrovirus (BufAstV) infections. In addition, we confirmed that the BufAstV infection of the brain tissues of a dead calf by immunohistochemistry technology in this study. Based on the 3’RACE and next-generation sequencing technologies, 2 full-length genomes (BufAstV-NNA-14 and BufAstV-NNA-12) and 2 ORF2 genes (BufAstV-NND-s2 and BufAstV-NNA-17) of AstVs from this source were sequenced. Phylogenetic analysis of the ORF2 indicated 3 major lineages of BufAstVs including a novel neurotropic BufAstV, a BufAstV which is related to Bovine Astrovirus (BoAstV) and a classical BufAstV. Moreover, the occurrence of genomic recombination between BufAstV and BoAstV strains have been identified. This is the first report to found a BufAstV infected in brain of water buffalo in China and details of the epidemiology, genetic diversity and possible interspecies transmission of BoAstV and BufAstV in water buffalo from the Guangxi province of China are described. KEYWORDS: astrovirus, water buffalo, bovine, neurotropic, genetic diversity, Guangxi province

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.

Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a newly identified swine enteropathogenic coronavirus that causes watery diarrhea in neonatal piglets, leading to significant economic losses to the swine industry. Currently there are no suitable serological method to assess the infection of SADV-CoV and effectiveness of vaccines, making an urgent need to exploit effect enzyme-linked immunosorbent assay (ELISA) to compensate for this deficiency. In this study, an indirect ELISA (S-iELISA) based on recombinant spike (S) protein expressed in Baculovirus was developed and evaluated. The reaction conditions of S-iELISA were optimized and cut-off value determined as 0.3711 by analyzing OD450nm values of 40 SADS-CoV-negative sera confirmed by immunoinfluscent assay (IFA) and Western Blot. The coefficients of variation of 6 positive sera within and between runs of S-iELISA were both less than 10% and cross-reactivity assays demonstrated that S-iELISA was non-cross-reactive with other swine viruses’ sera. Furthermore, the overall coincidence rate between IFA and S-iELISA was 97.3% based on testing 111 clinical serum samples. Virus neutralization test with 7 different OD450nm value sera showed that the OD450nm values tested by S-iELISA are positive correlated with virus neutralization. Finally, a total of 300 pig field serum samples were tested by S-iELISA and commercial kits of other swine enteroviruses showed that the IgG-positive for SADS-CoV, TGEV, PDCoV and PEDV were 81.7%, 54%, 65.3%, 6%, respectively. The results suggest this S-iELISA is specific, sensitive, repeatable and can be applied for vaccines evaluation and detection the SADS-CoV infection in swine industry.

Since the first report from Cherry Valley ducks on a commercial duck farm in China (2008), duck astrovirus type 1(DAstV-1) -associated duck viral hepatitis (DVH) have been detected in several commercial duck flocks. In the literature, no outbreak of DAstV-1 have been report in China since 2012. Here, the isolation, cultivation and characterization of DAstV-1 isolate are described. One DAstV-1 strain, designated as DAstV-SDZZ, was isolated from a diseased duckling. The isolated astrovirus grew well in the LMH cell line. To determine the entire genomic of the DAstV-SDZZ isolate, next-generation sequencing (NGS) technique was conducted on Illumina HiSeq platform. Complete genome sequence analysis revealed that DAstV-SDZZ isolate was 91.6%-98.7% homology with others DAstV-1 deposited in Genbank. Similar clinical symptoms were successful reproduced by experimental infection study using the DAstV-SDZZ isolate. DAstV-SDZZ is the first DAstV-1 strain whose experimental infection study has been conducted. The present works are likely to provide new insights into the pathogenicity and evolution of DAstV-1 in ducks.

Seneca Valley virus (SVV) strain (SVA/GD/China/2018) was first isolated from a buffalo farm in Guangdong, China, using seven mammalian cell lines. A genetic analysis revealed that SVA/GD/China/2018 had a high nucleotide similarity with the porcine-origin SVV strains, revealing potential cross-species transmission of SVV from pigs to buffaloes.

Pseudorabies virus (PRV) causes Aujeszky’s disease or pseudorabies (PR), which is characterized by fatal encephalitis in newborn piglets, respiratory infection in growing and fattening pigs, and reproductive failures in pregnant sows. It establishes a lifelong latent infection in the peripheral nervous system followed by subsequent intermittent shedding of infectious virus. Since 2011, highly virulent PRV strains that are genetically different from the classic PRV strains surfaced in pig herds in China. Availability of a highly sensitive and specific polymerase chain reaction (PCR)-based diagnostic assay for rapid differential detection of PRV variants is critical to prevent huge economic losses to the U.S. and Canadian pork industries if these strains enter North America and cause an outbreak. Here we describe the development and evaluation of a single-tube triplex real-time-PCR assay for differential detection of variant strains of PRV. The assay targets the intergenic region between the US2 and US6 genes in the PRV genome, is highly sensitive and specific, and it did not detect other non-target viruses, including related herpesviruses. The clinical specificity and sensitivity of the assay was evaluated using whole blood, serum, tissue and swab samples collected from known negative and experimentally inoculated pigs with either classical (Bristol) or variant (JS-2012 and HeN1) PRV strains. The targeted genomic region of this assay is also deleted in commonly used PRV gE-deleted marker vaccines, and therefore, the triplex assay did not detect viral DNA extracted from two commercial vaccine strains Bartha K-61 and Bucharest. This single-tube triplex assay can be used for routine diagnostics and epidemiological studies for detection and differentiation of classical strains from variant strains of PRV, and as a differentiation of infected and vaccinated animals (DIVA) assay when PRV gE- deletion mutant marker vaccines are used.

Rabbit hemorrhagic disease virus 2 (RHDV2) is a newly emerging Lagovirus belonging to the family Caliciviridae. After its first discovery in 2010 in France, this highly pathogenic virus rapidly spread to neighboring countries and has become the dominant strain, replacing the classical RHDV1 strains. RHDV2 was first reported in North America in 2016 in Mont-Joli, Quebec, Canada and it was reported again in 2018 and 2019 on Vancouver, Island and the southeast mainland of British Columbia (BC). The whole genome sequence of the RHDV2 Quebec isolate resembled the RHDV-N11 isolate from Navarra, Spain identified in 2011 with 97% identity. The epidemiological investigation involved three hobby farms and one personal residence. In December and February 2018, high mortality was reported in first a private feral rabbit refuge and then, a large colony of feral rabbits on the Vancouver Island University Campus, Nanaimo, BC. The virus responsible showed only 93% identity to the Quebec RHDV2 isolate at the nucleotide level. Additional cases of RHDV2 on Vancouver Island and on the BC mainland affecting feral, captive domestic and commercial rabbits were reported subsequently. Vaccination was recommended to control the outbreak and an inactivated bivalent vaccine was made available to the private veterinary practices. In June 2019 an isolated RHDV2 outbreak was reported in an apartment building in Vancouver, BC. This virus showed only 97% identity to the RHDV2 isolate responsible for the BC outbreak in 2018 at the nucleotide level suggesting that it was an independent incursion. In October 2020, there are reports of partial recovery of the feral population in Nanaimo and to date there are no confirmed deaths of native rabbit species in BC.

Lumpy skin disease (LSD) is an emerging viral disease, particularly of cattle and water buffalo. The disease is caused by lumpy skin disease virus (LSDV), a member of the genus Capripoxvirus of family Poxviridae which is manifested by characteristic skin nodules, pyrexia, lachrymation, nasal discharge, and swelling of superficial lymph nodes. Lumpy skin disease causes huge economic losses to the livestock farmers due to significant milk loss, damage of the hides, and reproductive problems such as abortion and infertility in affected animals. Initially, LSD was confined to Africa but later spread to Asia and Europe, particularly after 2012. This article describes the spatial and temporal patterns of LSD outbreaks that occurred from 2005-Mid-September, 2020 using the publicly available outbreak data from the World Animal Health Information System (WAHIS) of the World Organization for Animal Health (OIE). There were 3118 LSD outbreaks reported in the last 15 years with 2265 (72.6%) from Europe, 462 from Asia (14.8%), and 391(12.5%) outbreaks from Africa. 3070 (98.46%) of the total outbreaks during the study period occurred since 2012, with the highest month-wise outbreaks observed in July (778) and seasonally in the summer season (1873) which corresponds with the vector season. Since 2012, around 3 (2.78) new countries per year are being affected by LSD. The current situation of LSD spread demands for globally coordinated efforts to control this transboundary disease. Effective surveillance for early detection, vector control measures, vaccination, and regulation of animal movement is necessary to curb down the further spread of LSD.

Advanced and accurate forecasting of COVID-19 cases play a crucial role in management of hospital facility, policy decision, logistic support, and economy of the country. Artificial Intelligence (AI) techniques have proved its capability in time series forecasting of the non-linear problems. The present study assessed the relationship between weather parameters and COVID-19 cases and found the specific humidity have strong positive association, maximum temperature have negative and minimum temperature have positive association in most of the states in India. Further, we have developed a weather integrated LSTM (long short term memory) models for advanced (1-14 days) forecasting of the COVID-19 cases over different states in India. To achieve the goal we have utilized the humidity and temperature time series data along with the COVID-19 confirmed cases data (1st April-30th June 2020) to optimise the LSTM model in univariate and multivariate modes. The optimised models are utilized to forecast the COVID-19 cases for the period 1st July, 2020 to 31st July 2020 with 1 to 14days lead time. The results shows that the univariate LSTM model (past COVID-19 input) have reasonably good skill (Relative Error < 20%) in short range forecast (1day lead) for most of the selected states, whereas the skill is degraded with the medium and long range forecast. The major finding of the current study is that the medium range (1-7days) forecasting skill is enhanced in some of the states with the weather integrated multivariate LSTM models. The states (Maharashtra, Gujarat, Rajasthan, Madhya Pradesh, Haryana, and Punjab) located in West and North West India region, humidity play a key role in enhancement of medium range forecasting skill of the LSTM model. It is also observed that the states located in high humid regions (Kerala, Tamil Nadu, and West Bengal) temperature plays a key role in model enhancement.

We isolated avian, swine, human influenza viruses, and one hybrid influenza virus from minks in China. The H5N1 hybrid virus had pandemic potential because its seven genomic segments were from H1N1 human influenza virus and its HA gene was from H5N6 highly pathogenic avian influenza virus carrying multiple mammalian-adaptive mutations.

Tetracycline resistance is still considered one of the most abundant antibiotic resistances among pathogenic and commensal microorganisms. The aim of this study was to evaluate the prevalence of tet genes encoding tetracycline resistance in broiler chickens in Tunisia, by PCR. Individual cloacal swabs from 195 broiler chickens were collected at two slaughterhouses in the governorate of Ben Arous (Grand Tunis, Tunisia). Chickens were from 7 farms and belonged to 13 lots consisting of 15 animals randomly selected. Individual whole genomic DNA was extracted and tested for 14 tet genes. All the lots examined were positive for at least 9 tet genes, with an average number of 11 tet genes per lot. Of the 195 animals tested, 194 (99%) were positive for one or more tet genes. Tet(L), tet(M) and tet(O) genes were found in 98% of the samples, followed by tet(A) in 90.2%, tet(K) in 88.7% and tet(Q) in 80%. These results confirm the antimicrobial resistance impact in the Tunisian’s poultry sector and suggest the urgent need to establish a robust national antimicrobial resistance monitoring plan.

Tracing the globally circulating SARS-CoV-2 mutants is essential for the outbreak alerts and far-reaching epidemiological surveillance. The available technique to identify the phylogenetic clades through high-throughput sequencing is costly, time-consuming, and labor-intensive that hinders viral genotyping in low-income countries. Here, we propose a rapid, simple, and cost-effective amplification-refractory mutation system (ARMS)-based multiplex reverse-transcriptase PCR assay to identify six distinct phylogenetic clades: S, L, V, G, GH, and GR. This approach is applied on 24 COVID-19 positive samples as confirmed by CDC approved real-time PCR assay for SARS-CoV-2. Our multiplex PCR is designed in a mutually exclusive way to identify V-S and G-GH-GR clade variants separately. The pentaplex assay included all five variants and the quadruplex comprised of the triplex variants alongside either V or S clade mutations that created two separate subsets. The procedure was optimized in the primer concentration (0.2-0.6 µM) and annealing temperature (56-60°C) of PCR using a 3-5 ng/µl cDNA template synthesized upon random- and oligo(dT)-primer based reverse transcription. The different primer concentrations for the triplex and quadruplex adjusted to different strengths ensured an even amplification with a maximum resolution of all targeted amplicons. The targeted Sanger sequencing further confirmed the presence of the clade-featured mutations with another set of our designed primers. This multiplex ARMS-PCR assay is a sample, cost-effective, and convenient that can successfully discriminate against the circulating phylogenetic clades of SARS-CoV-2.

Since late 2011, pseudorabies virus (PRV; Suid herpesvirus 1) infection was widely prevalent in vaccinated swine farms in China, and caused tremendous economic losses in the swine industry. To understand the epidemic and biological characteristics of the virus, a total of 1,174 tissue samples were collected from Bartha-K61-immunized swine farms in Henan province of China between 2012 and 2019, and PRV strains were isolated and the complete sequences of gE and gC genes were amplified by PCR. The detection rate of PRV was 15.25% (179/1174), which varied from 6.61% to 25.00% between 2012 and 2019. And 16 PRV isolates were obtained, and could cause clinical symptoms and death in mice. The phylogenetic trees based on the sequences of gE and gC genes showed that the 16 PRV strains in this study at these two phylogenetic trees all clustered to a relatively independent branch altogether with the Chinese variant PRV strains (after 2012), and sequence analysis of the isolates revealed that gE and gC both contained amino acid insertions, substitutions or deletions compared with European-American PRV strains and early Chinese PRV strains (before 2012). In addition, it was the first report that eight strains (8/16) in this study harbored a unique amino acid substitution at site 280 (F to L) of gC gene. In the protection assay, the emulsion containing inactivated PRV NY isolate could provide complete protection against variant NY, and the titer of neutralizing antibodies was 1:82. This study might enrich our understanding of the evolution of variant PRVs as well as pave the way for finding a model virus to develop a novel vaccine based on PRV variants.

Cryptosporidium parvum is a major zoonotic pathogen responsible for outbreaks of severe diarrhea in humans and calves. Almost all investigations of cryptosporidiosis outbreaks caused by C. parvum have focused on its IIa subtype family in industrialized nations. From December 2018 to April 2019, approximately 200 neonatal calves on a large cattle farm in Hebei Province, China presented watery diarrhea and over 40 died. To investigate the cause of the outbreak, 179 and 223 fecal specimens were collected during and after the diarrhea outbreak from the farm, including 40 and 56 from neonatal calves, respectively. Among them, 18 fecal specimens from ill calves during the peak of the outbreak were analyzed for four common enteric pathogens using enzymatic immunoassay (EIA), 75 additional specimens from neonatal calves were tested for rotavirus by EIA, and all specimens were analyzed for Cryptosporidium spp. using PCR and sequencing techniques. Of the initial 18 specimens from sick calves, ten were positive for C. parvum, five for rotavirus, and one for coronavirus. The overall prevalence of rotavirus in neonatal calves was 20.0% (15/75), with no significant differences during (21.6% or 8/37) and after (18.4% or 7/38) the outbreak. In contrast, the prevalence of C. parvum was significantly higher during the outbreak (60.0%, 24/40) than after the outbreak (30.4%, 17/56). C. parvum infection was associated with the occurrence of watery diarrhea in neonatal calves (odds ratio = 11.19), while no association was observed between C. bovis infection and diarrhea. All C. parvum isolates were identified as subtype IIdA20G1. Older animals were infected with C. bovis, C. ryanae, C. occultus, and C. andersoni. This is one of the few reports of outbreaks of severe diarrhea caused by C. parvum IId subtypes in calves. More attention should be directed toward preventing the dissemination of C. parvum in China.

African swine fever (ASF) has spread across many countries in Europe since the introduction into Georgia in 2007. We report here on the first cases of ASF in wild boar detected in Germany close to the border with Poland. In addition to the constant risk of ASF virus (ASFV) spread through human activities, movements of infected wild boar also represent a route of introduction. Since ASF emerged in Western Poland in November 2019, surveillance efforts, in particular examination of wild boar found dead, were intensified in the regions of Germany bordering with Poland. The first case of ASF in wild boar in Germany was therefore detected by passive surveillance and confirmed on 10th September 2020. By 24th September 2020, 32 cases were recorded. Testing of samples from tissues of carcasses in different stages of decomposition yielded cycle threshold values from 18 to 36 in the OIE-recommended PCR which were comparable between the regional and national reference laboratory. Blood swabs yielded reliable results, indicating that the method is suitable also under outbreak conditions. Phylogenetic analysis of the ASFV whole-genome sequence generated from material of the first carcass detected in Germany, revealed that it groups with ASFV genotype II including all sequences from Eastern Europe, Asia and Belgium. However, some genetic markers including a 14 bp tandem repeat duplication in the O174L gene were confirmed that have so far been detected only in sequences from Poland (including Western Poland). Epidemiological investigations that include estimated postmortem intervals of wild boar carcasses of infected animals suggest that ASFV had been introduced into Germany in the first half of July 2020 or even earlier.

Avian influenza (AI) has a worldwide distribution and affects domestic and wild birds, thus causing great economic losses to the poultry industry. This study was carried out to detect avian influenza H5 antigen and antibodies in some wild birds in Zaria and its environs, Nigeria. A total of 136 wild birds, comprising 20 Laughing doves (Spilolepia senegalensis), 22 Speckled pigeons (Columba guinea), 25 Cattle egrets (Bubulcus ibis), 25 Senegalese parrots (Poicephalus senegalus), 21 Mallards (Anas platyrhynchos) and 23 Geese (Anseranserini) were used for the study. Some of the birds (Laughing doves, Speckled pigeons, Cattle egrets and Senegalese parrots) were captured around poultry houses, while others (Mallards and Geese) were sampled from live bird markets (LBMs). Blood samples, oropharyngeal and cloacal swabs were collected from each bird. Sera were tested for avian influenza virus (AIV) H5 antibody using enzyme linked immunosorbent assay (ELISA). Pooled oropharyngeal and cloacal swabs of each bird species (8-10 samples) were tested for AIV antigen using one-step reverse transcriptase polymerase chain reaction (RT-PCR). Results revealed overall prevalence of 6.62 % and 3.85 % for AIV antibody and antigen respectively. Based on species, AIV antibody was detected in Laughing dove (10 %), Speckled pigeon (13.64 %) and Mallard (19.05 %). Also, AIV antigen was detected in Senegalese parrot (20 %). In conclusion, AIV antibody and antigen were detected in wild birds in Zaria. Thus, these species of birds could play significant roles in the spread of this virus to chickens. Therefore, measures to limit the interactions of these wild birds with chickens should be implemented to minimize the spread of AI.

Porcine circovirus 4 (PCV4), a novel and unclassified member of the genus Circovirus, was first reported in China in 2019. Aimed at providing more evidence about the active circulation of PCV4, this study screened 335 pooled internal organs and detected the virus (i) at the rates of 3.28%, (ii) from both clinical healthy and clinical sick pigs of various age groups, and (iii) in six out of nice provinces of Korea. The complete genomic sequence of a Korean PCV4 strain (E115) was 1,770 nucleotides in length and had 98.5% to 98.9% identity to three PCV4 strains available at GenBank up to date. Utilizing a set of bioinformatic programs, it was revealed that the Korean PCV4 strain contained several genomic features of (i) a palindrome stem-loop structure with conserved nonanucleotide, (ii) packed overlapping ORFs oriented in different directions, and (iii) two intergenic regions in between genes encoding putative replication- associated protein (Rep) and capsid (Cap) proteins. This study also predicted the presence of essential elements known so far for the replication of circoviruses, for example, the origin of DNA replication, endonuclease and helicase domains of Rep, the nuclear localization signal on the putative Cap protein. Finally, based on the phylogeny inferred from sequences of the putative Rep protein, it was suggested that PCV4 belong to genus Circovirus of family Circoviridae and losely related to three previous known porcine circoviruses of PCV1, PCV2 and PCV3.