Genetic detection and analysis of porcine norovirus in pigs farmed in north Vietnam.

Norovirus (NoV) causing gastroenteritis symptoms, which has been reported in several hosts, including humans, pigs, and rats. This study was conducted to identify porcine viral infection and to characterize NoV strains from pigs in some provinces in north Vietnam. Totally, 102 fecal samples from diarrheal pigs on farms in six cities and provinces in northern Vietnam during July 2022 to March 2023 were collected. Polymerase chain reaction was used to identify the viral genome. Positive samples were used for nucleotide sequencing of the partial RNA-dependent RNA polymerase gene sequence. Five (4.9 %) positive stool samples were detected from animals farmed in five different farms, with one positive animal identified in each farm. Genetic analysis indicated that nucleotide identity was in the range 97.77-99.62 % among the 5 NoVs in this study. Phylogenetic analysis pointed out that the five NoVs were Genotype II.19 viruses. Genetically, these strains were closely related to porcine NoV strains that were reported in China in 2009.

Duck Tembusu virus in North Vietnam: epidemiological and genetic analysis reveals novel virus strains.

Tembusu virus (TMUV) is an important infectious disease, causing economic losses in duck production. Since the first report of TMUV infection in Vietnam in 2020, the disease has persisted and affected poultry production in the country. This study conducted epidemiological and genetic characterization of the viral strains circulating in north Vietnam based on 130 pooled tissue samples collected in six provinces/cities during 2021. The TMUV genome was examined using conventional PCR. The results indicated that 21 (16.15%) samples and 9 (23.68%) farms were positive for the viral genome. The positive rate was 59.26% for ducks at ages 2-4 weeks, which was significantly higher than for ducks at ages >4 weeks and < 2 weeks. Genetic analysis of the partial envelope gene (891 bp) sequences indicated that the five Vietnamese TMUVs shared 99.55-100% nucleotide identity, while the rates were in the range 99.59-100% based on the pre-membrane gene sequences (498 bp). The five Vietnamese TMUV strains obtained formed a novel single subcluster. These strains were closely related to Chinese strains and differed from the vaccine strain, suggesting that Vietnamese TMUV strains were field viruses. It needs to be further studied on vaccine development to prevent effects of TMUV infection on poultry production across Vietnam.

Porcine Sapovirus in Northern Vietnam: Genetic Detection and Characterization Reveals Co-Circulation of Multiple Genotypes.

Porcine sapovirus (PoSaV) has been reported in many countries over the world, which may cause gastroenteritis symptoms in pigs with all ages. There has been no report on PoSaV infection in Vietnam up to now. In this study, a total of 102 samples were collected from piglets, fattening pigs, and sows with diarrhea in several cities and provinces in northern Vietnam. The PoSaV genome was examined using polymerase chain reaction (PCR). Sequencing of the partial RNA-dependent RNA polymerase (RdRp) gene sequences (324 bp) was performed. Of the 102 tested samples, 10 (9.8%) and 7/20 (35%) were detected as positive for the PoSaV RdRp gene using the PCR method at the individual and farm levels, respectively. Genetic analysis of the partial RdRp gene region of about 324 bp indicated that the nucleotide identity of the current 10 Vietnamese viral strains ranged from 61.39% to 100%. Among the 10 strains obtained, 8 belonged to genotype III and the remaining 2 strains were clustered in genotype VIII. The Vietnamese genotype III viruses formed two sub-clusters. The Vietnamese PoSaV strains were closely related to PoSaVs reported in South Korea, Venezuela, and the Netherlands. This research was the first to describe PoSaV infection in northern Vietnam during 2022-2023.

Viral RNA extraction using an automatic nucleic acid extractor with magnetic particles and genetic characterization of bovine viral diarrhea virus in Tokachi Province, Japan, in 2016-2017.

In this study, the viral genome extraction performance of automatic nucleic acid extractors and manual nucleic acid extraction kits was compared. We showed that compared with manual kits, the automatic extractors showed superior genome extraction performance using bovine viral diarrhea virus (BVDV) genome-positive cattle sera and bovine coronavirus/infectious bovine rhinotracheitis virus-spiked cattle nasal swabs. In addition, the subgenotyping of BVDV strains detected in Tokachi Province in Japan during 2016-2017 was performed. Results showed that most of these BVDV strains belonged to subgenotype 1b, while few strains belonged to subgenotypes 1a and 2a. This study showed the high applicability of automatic nucleic acid extractors in extracting multiple viral genomes and the dominant subgenotype of BVDV in Tokachi.

Epidemiological Analysis and Genetic Characterization of Parvovirus in Ducks in Northern Vietnam Reveal Evidence of Recombination.

In total, 130 tissue-pooled samples collected from ducks in some provinces/cities in north Vietnam were examined for waterfowl parvovirus genome identification. Twenty-six (20%) samples were positive for the parvovirus infection, based on polymerase chain reaction analysis. Of the 38 farms tested, 14 (36.84%) were positive for the waterfowl parvovirus genome. The rate of the parvovirus genome detection in ducks aged 2−4 weeks (37.04%) was significantly (p < 0.05) higher than that at ages <2 weeks (9.09%) and >4 weeks (16.30%). The positive rate on medium-scale farms (9.36%) was significantly (p < 0.05) lower than for small-scale (31.03%) and large-scale (29.73%) farms. The lengths of the four Vietnamese waterfowl parvovirus genomes identified were 4750 nucleotides. Among the four Vietnamese parvovirus genomes, nucleotide identities were from 99.29% to 99.87%. Phylogenetic analysis of the near-complete genomes indicated that the waterfowl circulating in northern Vietnam belonged to the novel goose parvovirus (NGPV) group. The Vietnamese NGPV group was closely related to the Chinese group. Recombination analysis suggested that the Vietnam/VNUA-26/2021 strain was generated by a recombination event. One positive selection site of the capsid protein was detected.

Genetic characterization of chicken anemia viruses newly isolated from diseased chicks in Japan in 2020.

In this study, a total of nine chicken samples obtained from two broiler flocks in Oita and Tottori prefectures in 2020 were examined for Chicken anemia virus (CAV) infection. The samples were collected from clinically suspected flocks and diseased chickens. The CAV genome was detected in all nine samples tested by real-time PCR. Phylogenetic analyses and sequence comparisons of the full-length VP1 gene sequences indicated that all the Japanese CAV strains obtained in this study formed a similar cluster of genotype III and shared high nucleotide (99.62-100%) identity. The current Japanese CAV strains were closely related to Chinese CAV strains but not related to vaccine strains. One positive selection site of VP1 was detected among the Japanese CAV strains.

Pathological and virological analysis of concurrent disease of chicken anemia virus infection and infectious bronchitis in Japanese native chicks.

A concurrent infection of chicken anemia virus (CAV) and infectious bronchitis virus (IBV) was detected in Japanese native chicks in 2017, in which a high mortality rate (97.7%) was recorded in a small flock of 130 chicks exhibiting poor growth. Histological examination revealed that the affected chicks exhibited two different pathological entities: one was severe hematopoietic and lymphocytic depletion with abnormally large cells containing intranuclear inclusion bodies of CAV, whereas the other was renal tubular necrosis due to IBV infection. Immunohistochemistry detected CAV antigens in the bone marrow, liver, and spleen as well as IBV antigens in the kidneys, trachea, and air sacs. CAV was isolated from the liver sample of the chicks, and the isolated strain was designated as CAV/Japan/HS1/17. A phylogenetic analysis of the CAV VP1 gene revealed that CAV/Japan/HS1/17 is genetically similar to Chinese strains collected from 2014 to 2016. An experimental infection was performed using CAV/Japan/HS1/17 and specific-pathogen-free chicks to determine the pathogenicity of CAV/Japan/HS1/17. The isolate caused 100% anemia and 70% mortality to chicks inoculated at one day old, 80% of chicks inoculated at seven days old also developed anemia, and 10% died from CAV infection. These results suggest that the unusually high mortality in Japanese native chicks can be attributed to dual infection with both CAV and IBV. The results of the experimental infection suggest that CAV/Japan/HS1/17 has a pathogenic potential to specific-pathogen-free chicks and a relatively higher pathogenicity than previous Japanese CAV strains.