Snapshot study of canine distemper virus in Bangladesh with on-site PCR detection and nanopore sequencing.

Canine distemper virus (CDV) is a highly contagious virus that affects domestic and wild animals, causing severe illness with high mortality rates. Rapid monitoring and sequencing can provide valuable information about circulating CDV strains, which may foster effective vaccination strategies and the successful integration of these into conservation programs. During two site visits in Bangladesh in 2023, we tested a mobile, deployable genomic surveillance setup to explore the genetic diversity and phylogenetic patterns of locally circulating CDV strains. We collected and analysed 355 oral swab samples from stray dogs in Rajshahi and Chattogram cities, Bangladesh. CDV-specific real-time RT-PCR was performed to screen the samples. Out of the 355 samples, 7.4% (10/135) from Rajshahi city and 0.9% (2/220) from Chattogram city tested positive for CDV. We applied a real-time RT-PCR assay and a pan-genotype CDV-specific amplicon-based Nanopore sequencing technology to obtain the near-completes. Five near-complete genome sequences were generated, with phylogenetic relation to the India-1/Asia-5 lineage previously identified in India. This is the first study to provide genomic data on CDV in Bangladesh and the first demonstration of a mobile laboratory setup as a powerful tool in rapid genomic surveillance and risk assessment for CDV in low resource regions.

Single nucleotide polymorphisms in candidate genes are significantly associated with resistance to Haemonchus contortus infection in goats.

BACKGROUND: Haemonchosis is a major economic problem in goat production in humid, tropical and subtropical regions. The disease is caused by an abomasal nematode, Haemonchus contortus, which is highly pathogenic in small ruminants. The aim of this study was to identifying single-nucleotide polymorphisms (SNP) that were associated with fecal egg counts (FEC) and could be used as markers to identify resistance to H. contortus in goats. RESULTS: Ten novel variants in the CIITA, ATP2A3, HSPA8, STAT5B, ESYT1, and SERPING1 genes were associated with FEC in goats with a nominal significance level of P < 0.05. Two missense mutation in the exon region of the caprine CIITA gene resulted in replacement of arginine with cysteine at position 9473550 (R9473550C) and aspartic acid with glutamic acid at position 9473870 (D9473870E). Chinese goat breeds had significantly higher FEC than Bangladeshi goat breeds within their respective genotypes. Polymorphism information content (PIC), effective allele number (Ne), and heterozygosity (He) were greatest for the STAT5B_197_A > G SNP locus in all goat breeds. Pairwise coefficients of linkage disequilibrium (D´, r 2) revealed complete LD (r 2 = 1) between significant SNP polymorphisms in CIITA and SERPING1 and strong LD (r 2 = 0.93 and 0.98) between polymorphisms in HSPA8 and ATP2A3, respectively. Correlation coefficient (r) between FEC and body weight (BW) was significantly positive (r = 0.56***, P < 0.001) but that between FEC and packed cell volume (PCV) was negatively significant (r = - 0.47**, P < 0.01) in the total population of goats. On the other hand, correlation coefficient (r) between BW and PCV was not significant in total population of goats. Association analysis revealed that haplotypes within ATP2A3, HSPA8, and SERPING1 were significantly associated with FEC. Quantitative real-time PCR revealed that the relative expression of mRNA was higher (P < 0.001) for resistant, compared to susceptible, groups of goats for all candidate genes except CIITA. CONCLUSIONS: This study identified SNP markers that can potentially be used in marker-assisted selection programs to develop goat breeds that are resistant to H. contortus.

Consequence of dam genotypes on productive and reproductive performance of dairy cows under the rural condition in Bangladesh.

The main objective of the present study was to evaluate the consequence of dam genotypes on productive and reproductive performance of different cross-bred dairy cows under field condition. A total of 313 dairy cow's information were collected from 33 Artificial Insemination (AI) Sub-centers/Points from the District AI center of greater Rajshahi district for a period from 1993 to 2002. The information of the productive and reproductive parameters were analyzed from questionnaires answered by 33 field assistant (artificial inseminator) and owner's of cow in respective of AI Sub-Center/Points as well as from reading the AI and 100% progeny collection Registers. In general, the mean birth weight, age at puberty, age at first fertile service, age at first calving, gestation length, post-partum heat period, days open, wastage day, service per conception, milk production per day, peak milk production per day, lactation length, lactation yield, dry period, weaning period and calving intervals were 18.8 kg, 27.9 month, 29.2 month, 38.7 months, 278.7 days, 139 days, 160 days, 20.3 days, 1.62, 5.13 L, 10.45 L, 282 days, 1445 L, 146 days, 10.65 months and 438 days, respectively. Dam genotype of dairy cows were divided into 5 groups according to their genetic composition. LxF, SxSL, L, LxSLxF and LxSxSL of dam genotype had significant effect on all the productive and reproductive performances of the dairy cows except on age at first calving, gestation length and weaning period. The genotypes of dam's of cows like LxF and LxSL showed a better performance under field condition at greater Rajshahi district and poor performance were recorded in L and LxSxSL of dam genotype. The experiment reflects that the LxF and LxSL genotypes of dam showed the better productive and reproductive performances of dairy cows under rural condition in Bangladesh.