H7N9 avian influenza has broken out in Chinese poultry 10 times since 2013 and impacted the industry severely. Although the epidemic is currently under control, there is still a latent threat. Epidemiological surveillance data for non-human H7N9 avian influenza from April 2013 to April 2020 were used to analyse the regional distribution and spatial correlations of positivity rates in different months and years and before and after comprehensive immunisation. In addition, positivity rate monitoring data were disaggregated into a low-frequency and a high-frequency trend sequence by wavelet packet decomposition (WPD). The particle swarm optimisation algorithm was adopted to optimise the least squares support-vector machine (LS-SVM) model parameters to predict the low-frequency trend sequence, and the autoregressive integrated moving average (ARIMA) model was used to predict the high-frequency one. Ultimately, an LS-SVM-ARIMA combined model based on WPD was constructed. The virus positivity rate was the highest in late spring and early summer, and overall it fell significantly after comprehensive immunisation. Except for the year 2015 and the single month of December from 2013 to 2020, there was no significant spatiotemporal clustering in cumulative non-human H7N9 avian influenza virus detections. Compared with the ARIMA and LS-SVM models, the LS-SVM-ARIMA combined model based on WPD had the highest prediction accuracy. The mean absolute and root mean square errors were 2.4% and 2.0%, respectively. Low error measures prove the validity of this new prediction method and the combined model could be used for inference of future H7N9 avian influenza virus cases. Live poultry markets should be closed in late spring and early summer, and comprehensive H7N9 immunisation continued.

Integrons are mobile DNA elements that allow for acquisition and dissemination of antibiotic-resistance genes among pig farm-derived bacteria. Limited information is available on integrons of Staphylococcus aureus from pig farms. The aim of this study was to characterise and investigate the prevalence of class 1 and 2 integrons in multi-drug resistant (MDR) S. aureus isolates from pig farms. A total of 724 swabs were collected from 12 pig farms in Chongqing, China, and examined by conventional microbial and molecular methods. In total, 68 isolates were S. aureus, 57 of which were methicillin resistant (MRSA). All 68 isolates were MDR strains and carried integrons, of which 88.2% (60/68) harboured both class 1 and 2. In addition, 85.3% (58/68) of the class 2 integron-positive isolates carried the β-lactam resistance gene (blaTEM₋₁), and 66.7% (40/60) of the class 1 integron–positive isolates carried the aadA1c, aadA1 or dfrA1 gene for respective streptomycin and spectinomycin or trimethoprim resistance. Class 1 and 2 integrons are common among the pig farm-derived S. aureus isolates. On account of their significance for public health, the prevalence of the integrons and their associated resistance genes in pig farm-derived S. aureus isolates should be paid special attention.

A significant threat to public health is presented by antibiotic-resistant strains of bacteria, selective pressure on which results from antibiotic use. Colistin is an antibiotic commonly used in veterinary medicine, but also one of last resort in human medicine. Since the 2015 discovery in China of the mcr-1 gene encoding colistin resistance in Enterobacteriaceae, other countries have noted its presence. This study was to find the mcr-1 gene prevalence in E. coli isolated from poultry slaughtered in Poland. Cloacal swabs were taken from December 2017 to October 2018 from broiler chickens in three regions. The samples (n = 158) were grouped as flocks treated with colistin sulphate (n = 87) and those not treated (n = 71). Resistance to antimicrobials commonly used in poultry was evaluated by minimum inhibitory concentration. The presence of the mcr-1 gene was confirmed by PCR. Isolates containing the mcr-1 gene were yielded by 11.27% of the samples from not treated flocks and 19.54% of those from treated flocks, but no statistically significant difference in the prevalence of the gene was seen between the groups. The results clearly preclude intensification of selective pressure for colistin resistance due to colistin sulphate treatment because they show that the avian gastrointestinal tract was already inhabited by colistin-resistant E. coli by the time the chickens came to the poultry house.

Porcine circovirus type 3 (PCV3) is a newly discovered porcine circovirus. The molecular characteristics and genetic evolution of PCV3 in Xinjiang province, China still being unclear, the aim of the study was their elucidation. A total of 393 clinical samples were collected from pigs on commercial farms in nine different regions of Xinjiang and phylogenetic analysis based on full-length Cap genes was performed. The prevalence at farm level was 100%, while in all the tested samples it was 22.39%. Nine PCV3 strains were detected in Xinjiang province and they shared 98.9–99.3% nucleotide and 97.5–100.0% Cap gene amino acid sequence identities with other epidemic strains from China and abroad. Compared with other epidemic strains of PCV3, there were 26 base mutation sites in the Cap gene in the nine Xinjiang strains, resulting in the mutation of amino acids at positions 20, 24, 75, 77, 108, 111 and 206. Phylogenetic analysis showed that these strains can be divided into two different genetic groups, to the first of which five strains affiliated and divided between subgroups 1.1 and 1.2, and to the second of which the other four strains affiliated and similarly divided between subgroups 2.1 and 2.2. PCV3 circulates widely among commercial pig farms in Xinjiang province, China, and displays obvious genetic diversity. The results provide epidemiological information useful for the prevention and control of PCV3 infection in the pig industry.

Since 2007, African swine fever (ASF) has posed a serious threat to the European swine industry. In Poland, the numbers of reported outbreaks in pigs and affected areas grow every year. In 2018, the disease was noted in Western Europe, in Belgium specifically, where several hundred infected wild boars have been detected so far. In 2018, the virus unexpectedly emerged in pig holdings in eastern China, northern Mongolia, Vietnam, and Cambodia, causing worldwide concern about its further spread. Since there is still no vaccine available, the only approach to control the disease is biosecurity. Identification of potential sources of the virus is extremely important in light of its phenomenal survivability. The review summarises the current knowledge about ASFV survivability and resistance to environmental conditions, and discusses the role of indirect contact in spreading the disease.

Introduction: A real-time RT-PCR method for identification and quantification of porcine epidemic diarrhoea virus (PEDV) strains in China was developed.Material and Methods: Based on the conserved sequence of the PEDV nucleocapsid (N) gene, a primer pair and probe were designed to establish a TaqMan-MGB real-time RT-PCR assay for quantitative detection of the virus. The sequence was cloned into the pMD18-T vector and a series of diluted recombinant plasmids were used to generate a standard curve with an R2 value of 0.999.Results: The developed quantitative PCR assay detected viral titres as low as 0.1 TCID₅₀ with high specificity and no cross-reaction with other porcine viruses (PoRV, TGEV, PRRSV, or CSFV). The intra-batch and inter-batch coefficients of variation were both less than 1%, which indicated good reproducibility. Thirty clinical diarrhoea samples obtained from pigs in Shanghai and Fujian were analysed using this quantitative PCR assay. Out of these samples, 93.3% were found to be PEDV positive.Conclusion: This approach is suitable for clinical sample identification and pathogenesis studies.

Porcine circovirus 4 (PCV4) was first discovered in 2019 in a herd of pigs with porcine respiratory disease, dermatitis and nephropathy syndrome in Hunan Province, China. It has subsequently been detected in other provinces and in South Korea. In consideration of the potential of the virus to cause an epidemic, rapid, sensitive, and specific detection of PCV4 is needed, as is the facilitation of further epidemiological research through elucidation of the whole genome of PCV4. This study had those two aims. Fifty-five blood samples, two pig tissue samples, nine saliva swabs and one semen sample which all originated from Sichuan province pig farms were analysed. The virus’ genome of 1,770 bp was synthesised artificially based on a Chinese reference strain and primers and probes for the ORF2 gene were designed. Then, the amplified target fragment was cloned into the pMD19-T vector and a series of diluted recombinant plasmids were used to generate a standard curve. An optimised real-time TaqMan PCR method was established. The results of this study showed that the established method is specific for PCV4 but not for other viruses, and has amplification efficiency of 99.6%, a regression squared value (R²) of 1.000 and a detection limit of 2.2×10 DNA copies. This method was shown to be analytically specific and sensitive with a low intra- and inter-assay coefficient of variation (<1.67 %). Of a total of 67 clinical samples tested using the established method, three were shown to be positive (4%). This study confirms the existence of PCV4 in Sichuan and provides a promising alternative tool for rapid detection of PCV4.

Fasciola hepatica is a trematode infecting ruminants worldwide and occasionally affecting other animal species, including humans. It causes significant economic losses. Geographic distribution and patterns of infection must be considered before control and management measures are developed for this parasite. DNA molecular markers are useful for the identification of flukes and elucidation of their genetic evolution. Therefore, the population structure of F. hepatica was studied using this method in sheep in Xinjiang, China. The molecular characteristics, genetic relationships within the population and dispersal patterns of F. hepatica isolates were analysed based on the cox1 and nad1 genes. The population structure of F. hepatica from three regions of Xinjiang was explored and a neutrality test was conducted. The cox1 and nad1 genes have 21 and 42 variable sites, respectively, which can be classified into 34 and 33 haplotypes. Median-joining network and phylogenetic tree analyses showed that there was no significant variation in F. hepatica isolates between the three geographical regions. Analysis of variance revealed that the genetic variation of F. hepatica was mainly present within the populations. The neutrality test indicated that the populations were relatively stable but the Hami population may have undergone short-term expansion. This study revealed for the first time the molecular characteristics, genetic diversity and dispersal patterns of F. hepatica isolates from sheep in Xinjiang, thus providing new insights into the genetic variation and haplotype diversity of F. hepatica from indigenous sheep.

In May 2020, an outbreak of rabbit haemorrhagic disease 2 (RHD2) caused by the rabbit haemorrhagic disease virus 2 (RHDV2, GI.2) occurred in Sichuan, China. The acute onset and short disease course resulted in rabbit mortality as high as 42.86%. Currently, basic research on the aetiology and genetic characteristics of GI.2 is lacking in China.

Derzsy’s disease and Muscovy duck parvovirus disease have become common diseases in waterfowl culture in the world and their potential to cause harm has risen. The causative agents are goose parvovirus (GPV) and Muscovy duck parvovirus (MDPV), which can provoke similar clinical symptoms and high mortality and morbidity rates. In recent years, duck short beak and dwarfism syndrome has been prevalent in the Cherry Valley duck population in eastern China. It is characterised by the physical signs for which it is named. Although the mortality rate is low, it causes stunting and weight loss, which have caused serious economic losses to the waterfowl industry. The virus that causes this disease was named novel goose parvovirus (NGPV). This article summarises the latest research on the genetic relationships of the three parvoviruses, and reviews the aetiology, epidemiology, and necropsy characteristics in infected ducks, in order to facilitate further study.