Complete genome constellation of a dominant Bovine rotavirus genotype circulating in Bangladesh reveals NSP4 intragenic recombination with human strains.

Rotavirus A is a leading cause of non-bacterial gastroenteritis in humans and domesticated animals. Despite the vast diversity of bovine Rotavirus A strains documented in South Asian countries, there are very few whole genomes available for phylogenetic study. A cross-sectional study identified a high prevalence of the G6P[11] genotype of bovine Rotavirus A circulating in the commercial cattle population in Bangladesh. Next-generation sequencing and downstream phylogenetic analysis unveiled all 11 complete gene segments of this strain (BD_ROTA_CVASU), classifying it under the genomic constellation G6P[11]-I2-R2-C2-M2-A13-N2-T6-E2-H3, which belongs to a classical DS-1-like genomic backbone. We found strong evidence of intragenic recombination between human and bovine strains in the Non-structural protein 4 (NSP4) gene, which encodes a multifunctional enterotoxin. Our analyses highlight frequent zoonotic transmissions of rotaviruses in diverse human-animal interfaces, which might have contributed to the evolution and pathogenesis of this dominant genotype circulating in the commercial cattle population in Bangladesh.

Investigation of koala retrovirus in captive koalas with pneumonia and comparative analysis of subtype distribution.

This study focused on the involvement of koala retrovirus (KoRV) in pneumonia in koalas. Three deceased pneumonic koalas from a Japanese zoo were examined in this study. Hematological and histopathological findings were assessed, and KoRV proviral DNA loads in the blood and tissues were compared with those of eight other KoRV-infected koalas from different zoos. Demographic data and routine blood profiles were collected, and blood and tissue samples were analyzed to rule out concurrent infections in pneumonic koalas. KoRV subtyping and measurement of the KoRV proviral DNA load were performed by polymerase chain reaction (PCR) using specific primers targeting the pol and env genes. The results showed that the koalas had histopathologically suppurative and fibrinous pneumonia. Chlamydiosis was not detected in any of the animals. PCR analysis revealed KoRV-A, -B, and -C infections in all koalas, except for animals K10-11, which lacked KoRV-B. Significant variations in the proviral DNA loads of these KoRV subtypes were observed in all tissues and disease groups. Most tissues showed reduced KoRV loads in koalas with pneumonia, except in the spleen, which had significantly higher loads of total KoRV (2.54 × 107/µg DNA) and KoRV-A (4.74 × 107/µg DNA), suggesting potential immunosuppression. This study revealed the intricate dynamics of KoRV in various tissues, indicating its potential role in koala pneumonia via immunosuppression and opportunistic infections. Analysis of the levels of KoRV proviral DNA in different tissues will shed light on viral replication and the resulting pathogenesis in future studies.

Novel Mutation in the Feline NPC2 Gene in Cats with Niemann-Pick Disease.

Niemann-Pick disease (NP) type C is an autosomal, recessive, and inherited neurovisceral genetic disorder characterized by the accumulation of unesterified cholesterol and glycolipids in cellular lysosomes and late endosomes, with a wide spectrum of clinical phenotypes. This study aimed to determine the molecular genetic alterations in two cases of felines with NP in Japan, a Siamese cat in 1989 and a Japanese domestic (JD) cat in 1998. Sanger sequencing was performed on 25 exons of the feline NPC1 gene and 4 exons of the feline NPC2 gene, using genomic DNA extracted from paraffin-embedded tissue specimens. The sequenced exons were compared with reference sequences retrieved from the GenBank database. The identified mutations and alterations were then analyzed using different prediction algorithms. No pathogenic mutations were found in feline NPC1; however, c.376G>A (p.V126M) was identified as a pathogenic mutation in the NPC2 gene. The Siamese cat was found to be homozygous for this mutation. The JD cat was heterozygous for the same mutation, but no other exonic NPC2 mutation was found. Furthermore, the JD cat had a homozygous splice variant (c.364-4C>T) in the NPC2 gene, which is not known to be associated with this disease. The NPC2:c.376G>A (p.V126M) mutation is the second reported pathogenic mutation in the feline NPC2 gene that may be present in the Japanese cat population.

Novel Mutation in the Feline GAA Gene in a Cat with Glycogen Storage Disease Type II (Pompe Disease).

Glycogen storage disease type II (Pompe disease: PD) is an autosomal recessively inherited fatal genetic disorder that results from the deficiency of a glycogen hydrolyzing enzyme, acid α-glucosidase encoded by the GAA gene. Here, we describe the molecular basis of genetic defects in an 8-month-old domestic short-haired cat with PD. The cat was previously diagnosed with PD based on the clinical and pathological findings of hypertrophic cardiomyopathy and excessive accumulation of glycogen in the cardiac muscles. Sanger sequencing was performed on 20 exons of the feline GAA gene using genomic DNA extracted from paraffin-embedded liver tissues. The affected cat was found to be homozygous for the GAA:c.1799G>A mutation resulting in an amino acid substitution (p.R600H) of acid α-glucosidase, a codon position of which is identical with three missense mutations (p.R600C, p.R600L, and p.R600H) causing human infantile-onset PD (IOPD). Several stability and pathogenicity predictors have also shown that the feline mutation is deleterious and severely decreases the stability of the GAA protein. The clinical, pathological, and molecular findings in the cat were similar to those of IOPD in humans. To our knowledge, this is the first report of a pathogenic mutation in a cat. Feline PD is an excellent model for human PD, especially IOPD.

Molecular Epidemiological Survey for Degenerative Myelopathy in German Shepherd Dogs in Japan: Allele Frequency and Clinical Progression Rate.

Canine degenerative myelopathy (DM) is an adult-onset, chronic, progressive neurodegenerative disease reported in multiple canine breeds, including the German Shepherd Dog (GSD). Clinical signs include progressive motor neuron paralysis, which begins in the pelvic limbs and eventually leads to respiratory distress, which may necessitate euthanasia. A common DM-associated mutation is a single nucleotide substitution that causes an amino acid substitution (c.118G>A, p.E40K) in the canine SOD1 gene. This SOD1 mutation and the clinical progression rate of A/A risk genotype in the Japanese GSD population have not been analyzed before. Therefore, the aim of this study was to determine the frequency of the mutated allele and analyze the clinical progression rate in the Japanese GSD population. We studied 541 GSDs registered with the Japanese German Shepherd Dog Registration Society between 2000 and 2019. Genotyping was performed using real-time PCR with DNA extracted from the hair roots of each dog. The study revealed 330 G/G dogs (61%), 184 G/A dogs (34%), and 27 A/A dogs (5%), indicating a frequency of the mutant allele of 0.220, which are in Hardy−Weinberg equilibrium. We analyzed the clinical signs in A/A dogs with an age limit of 10 years based on information obtained from the dogs' owners. Of the seven A/A dogs older than 10 years, owners reported DM-related clinical signs, indicating a clinical progression rate of 100%. These results, further genotyping, and thorough clinical examinations of SOD1 A/A risk genotype will help control and prevent DM in the Japanese GSD population.

Screening and Carrier Rate of Neuronal Ceroid Lipofuscinosis in Chihuahua Dogs in Japan.

Neuronal ceroid lipofuscinosis (NCL) is a group of rare lethal neurodegenerative lysosomal storage diseases that occur in a range of dog breeds, including Chihuahuas. Recently, a homozygous single base-pair deletion (c.846delT), which causes a frame shift generating a premature stop codon (p.Phe282Leufs13*) in the canine CLN7/MFSD8 gene, has been identified as a causative mutation for NCL in Chihuahuas. The objective of this study was to determine the frequency of the mutant allele and/or carrier rate of NCL in Chihuahuas in Japan using a newly designed real-time PCR assay. Samples of saliva were randomly collected from 1007 Chihuahua puppies during physical examinations prior to the transportation to pet shops. Screening results revealed a carrier rate of 1.29%, indicating a mutant allele frequency (0.00645) that is considered sufficiently high to warrant measures for the control and prevention of this lethal disease. The genotyping assay designed in this study could make a valuable contribution to the control and prevention of NCL.

Carrier Rate and Mutant Allele Frequency of GM1 Gangliosidosis in Miniature Shiba Inus (Mame Shiba): Population Screening of Breeding Dogs in Japan.

GM1 gangliosidosis is a progressive, recessive, autosomal, neurodegenerative, lysosomal storage disorder that affects the brain and multiple systemic organs due to an acid ß-galactosidase deficiency encoded by the GLB1 gene. This disease occurs in the Shiba Inu breed, which is one of the most popular traditional breeds in Japan, due to the GLB1:c.1649delC (p.P550Rfs*50) mutation. Previous surveys performed of the Shiba Inu population in Japan found a carrier rate of 1.02-2.94%. Currently, a miniature type of the Shiba Inu called "Mame Shiba", bred via artificial selection to yield smaller individuals, is becoming more popular than the standard Shiba Inu and it is now one of the most popular breeds in Japan and China. The GM1 gangliosidosis mutation has yet to be surveyed in the Mame Shiba population. This study aimed to determine the frequency of the mutant allele and carrier rate of GM1 gangliosidosis in the Mame Shiba breed. Blood samples were collected from 1832 clinically healthy adult Mame Shiba Inus used for breeding across 143 Japanese kennels. The genotyping was performed using a real-time PCR assay. The survey found nine carriers among the Mame Shibas, indicating that the carrier rate and mutant allele frequency were 0.49% and 0.00246, respectively. This study demonstrated that the mutant allele has already been inherited by the Mame Shiba population. There is a risk of GM1 gangliosidosis occurrence in the Mame Shiba breed if breeders use carriers for mating. Further genotyping surveys are necessary for breeding Mame Shibas to prevent the inheritance of this disease.

Frequency of an X-Linked Maternal Variant of the Bovine FOXP3 Gene Associated with Infertility in Different Cattle Breeds: A Pilot Study.

Immune adaptation plays an essential role in determining pregnancy, which has been shown to be dependent on sufficient immunological tolerance mediated by FOXP3+ regulatory T cells. Recently, an X-linked maternal single-nucleotide polymorphism (SNP), located 2175 base pairs upstream of the start codon in the bovine FOXP3 gene (NC_037357.1: g.87298881A>G, rs135720414), was identified in Japanese Black (JB: Bos taurus) cows in association with recurrent infertility. However, with the exception of JB cows, the frequency of this SNP has yet to be studied in other cow populations. In this study, we thus aimed to evaluate the frequency of this SNP in different cow breeds. Between 2018 and 2021, a total of 809 DNA samples were obtained from 581 JB, 73 Holstein Friesian (HF: B. taurus), 125 Korean Hanwoo (KH: B. taurus coreanae), and 30 Indonesian Madura (IM: a crossbreed between B. indicus and B. javanicus) cows, which were genotyped using a TaqMan probe-based real-time polymerase chain reaction assay designed in this study. The frequency of the G allele was found to be relatively high in local IM (0.700), moderate in dairy HF (0.466), and low in beef JB (0.250) and KH (0.112) cows, with differences in the frequencies between each group being shown to be statistically significant (p < 0.005) using Fisher's exact test. The results obtained in this study indicate that the G allele frequencies of the identified the SNP differ markedly in different breeds of taurine and indicine cattle. Given these findings, it would thus be important to evaluate the relationships between high frequencies of the G allele and infertility in different breeds.

Retrospective Genotyping and Whole Genome Sequencing of a Canine Parvovirus Outbreak in Bangladesh.

Canine parvovirus 2 (CPV-2) outbreaks in close quarters such as kennels or shelters can cause substantial case fatality. Thirteen dead Labradors from a secluded kennel of security dogs presented with typical clinical signs and gross pathology of parvovirus infection. Whole genome shotgun sequencing from tissue-extracted genomic DNA detected new CPV-2a as the contributing antigenic variant. Further genotyping using polymerase chain reaction coupled with high-resolution melt assays (PCR-HRM) confirmed new CPV-2a infection in all deceased dogs. PCR-HRM of additional thirty-four clinically suspected dogs suggested that this variant is in wider community circulation, at least in the southeastern part of Bangladesh. We present complete genome sequence of the new CPV-2a variant circulating in the domestic canine population of Bangladesh.

Carrier rate of the c.235G>C mutation in the bovine isoleucyl-tRNA synthetase (IARS) gene of Japanese Black cows at Kagoshima prefecture, Japan, and analysis of the metabolic profiling and reproductive performance of heterozygous cows.

Bovine isoleucyl-tRNA synthetase (IARS) disorder, a major cause of weak calf syndrome, is caused by a homozygous missense (c.235G>C) mutation in the bovine IARS gene of Japanese Black (JB) cattle, which was identified in 2013. However, the extent to which the carrier rate has changed at Kagoshima prefecture, Japan, and whether the carrier status is associated with any clinical or reproductive problems, have yet to be ascertained. In this study, using a real-time polymerase chain reaction-based genotyping assay, we determined the carrier rate in a regional JB cow population at Kagoshima prefecture. Comparative analyses were performed on the metabolic profile test (MPT) results and reproductive performance data obtained for heterozygous carrier and homozygous wild-type cows. In 2009 and 2018, DNA samples were collected from 130 and 462 clinically healthy JB cows, respectively, in Kagoshima prefecture. MPT results and reproductive performance data were evaluated for 62 cows, comprising four heterozygous carriers and 58 wild-type cows. Genotyping revealed that the carrier rate was 6.9% in 2009 and 1.5% in 2018, the difference of which was statistically significant (P<0.005). There were no statistically significant differences between the carrier and wild-type cows with respect to either MPT results or reproductive performance, indicating that the carrier cows have necessary IARS activity to maintain minimal health and reproductive potential.

Assessment of transport stress on cattle travelling a long distance (≈648 km), from Jessore (Indian border) to Chittagong, Bangladesh.

The effect of long-distance transport on cattle health has not frequently been studied in Bangladesh. The current study investigated the health conditions, and the extent and pattern of cattle injuries, along with haemato-biochemical and hormonal changes, before and after long-distance transportation (≈648 km) from the market of origin to the market of destination. A total of 100 adult cattle were selected at the Benapole live cattle market, Bangladesh, for physical examination before and after transportation. Fifty of these cattle were randomly selected for additional haemato-biochemical evaluation just before the start of transportation (0 hour), immediately after arrival at the destination market (13.8±0.9 hours after the start of transportation) and 24 hours after arrival at the destination market. The external health conditions and injuries were assessed. Animals were fasting in the vehicle during transportation and provided only with paddy straw and water before sale at the destination market. Before and after transportation, the overall frequency of cattle injuries varied significantly (26 per cent before v 47 per cent after transportation; P<0.001). Cattle health conditions diverged significantly (such as nasal discharge: 15 per cent v 28 per cent; P=0.03). The values of haemoglobin (P=0.01), total erythrocyte count (P=0.001), total leucocyte count (P<0.001), lymphocyte (P=0.005), neutrophil (P=0.01) and eosinophil (P=0.01) varied significantly. The values of serum total protein (P=0.006), creatine kinase (P<0.001), triglyceride (P=0.04), calcium (P=0.003), phosphorus (P<0.001) and alkaline phosphatase (P=0.04) significantly differed. The overall findings indicate a high degree of transport stress and poor animal welfare.

The first complete mitogenome of Indian star tortoise (Geochelone elegans).

The complete mitochondrial genome of Indian star tortoise (Geochelone elegans) was characterized having 16,446 bp nucleotides encoding 37 genes in circular orientation comprising 13 protein-coding genes, 22 tRNA genes and two rRNA genes. The lengths of 12S and 16S ribosomal RNA were 973 bp and 1600 bp. A non-coding control region (D-Loop) of 966 bp was identified between tRNAPro and tRNAPhe having seven interrupted tandem repeats. A single A + 1 frameshift insertion in the ND3 gene (ND3-174) was also discovered. The complete mitogenome of G. elegans would contribute in deeper understanding of the evolutionary dynamics and conservation effort of vulnerable testudine families.

Molecular identification of Mycoplasma synoviae from seroprevalent commercial breeder farms at Chittagong district, Bangladesh.

AIM: Worldwide, Mycoplasma synoviae (MS) is an important pathogen of poultry, especially for chicken and turkey. It causes respiratory tract infection and infectious sinusitis. The study was conducted to determine the seroprevalence of MS infection with associated risk factors and identification of MS organism in unvaccinated flocks of commercial breeder farms of the Chittagong district, Bangladesh. MATERIALS AND METHODS: A total of 365 serum samples were collected and tested for MS using serum plate agglutination (SPA) test for determination of MS seroprevalence. On the other hand, tracheal swabs were collected from each seropositive flocks for polymerase chain reaction (PCR) to determine the presence of MS organism. RESULTS: Among the farms, the highest prevalence was found to be 69% and the lowest prevalence was 28% with the average 60%. The seroprevalence of MS infection in breeder farms was highest 70% with the flock size >10,000 birds, whereas it was lowest 57% in the flocks ranging from 4000 to 7000. According to age group, the prevalence was found highest 70% in >60 weeks age group of birds and lowest 42% in 10-19 weeks group. The seroprevalence of MS in winter season was found as highest as 64%, whereas it was found lowest 60% in the summer season. There was a statistically significant difference (p<0.01) among the seroprevalence of MS in different breeder farms, flock size, and age groups, but there was no significant (p>0.05) difference in the winter, summer, and rainy season. To confirm the presence of MS in the samples, PCR test was applied using specific primers to amplify a 214 bp region of the 16S rRNA gene of the organism. In PCR, all seropositive flocks showed a positive result for MS. CONCLUSION: As the plate agglutination test result showed 100% similar with PCR result, it can be suggested that agglutination test is better than molecular and culture techniques for MS detection and it is also cheaper and less time-consuming method.