Molecular characterization of porcine reproductive and respiratory syndrome virus identified in 2021 from Nepal.

Porcine reproductive and respiratory syndrome (PRRS), an important viral disease of swine caused by PRRS virus (PRRSV) was first confirmed in Nepal in 2013. Since then, the virus has spread throughout the country and has now become endemic affecting the pig production nationally. However, molecular characterization of circulating strains has not been done in Nepal yet. In the present study, serum samples were collected from outbreak areas of different districts of Nepal and samples positive for PRRSV by ELISA were sent to Animal and Plant Health Agency (APHA), United Kingdom for sequence analysis. Out of 35 samples that were sent to APHA, only one sample was found positive by PCR and subjected to sequence analysis based on ORF5, ORF7 and Nsp2. The results from the phylogenetic analysis demonstrated that the PRRSV strain belongs to PRRSV-2 and lineage 8 strain. The sequences from the Nepalese PRRSV strain revealed a high degree of similarity with the strains isolated from India, China and Vietnam, with the closest genetic relatedness to the Indian isolates from 2020 and 2018. This is the first study on molecular characterization of PRRS virus circulating in Nepal. Further studies on strains circulating in Nepal are very essential to understand the virus diversity, its spread and evolution.

Farm characteristics and sero-prevalence of porcine reproductive and respiratory syndrome virus (PRRSV) antibodies in pigs of Nepal.

BACKGROUND: Porcine reproductive and respiratory syndrome is a highly infectious disease of swine caused by PRRS virus (PRRSV). OBJECTIVES: To evaluate the prevalence of PRRSV antibodies in the four districts of hilly and terai regions of Nepal. Toassess the farm characteristics through a questionnaire interview of farmersregarding management practices and PRRS. METHODS: A cross-sectional study was conducted from July 2020 to June 2021 to determine the sero-prevalence of PRRSV in pigs. A total of 180 porcine serum samples were collected from 23 pig farms and tested for PRRSV antibodies by ELISA. Alongside, farm characteristics were also assessed through questionnaire to determine the level of biosecurity measures in the farm, knowledge of the disease and possible control mechanisms. RESULTS: Out of 180 samples, 37 were tested positive resulting the overall sero-prevalence of 20.5%. There was significant association between different districts (p < 0.05) and PRRS prevalence. Prevalence of PRRSV antibody was found higher in Kaski district (10.5%) followed by Sunsari (8.8%) district. Based on age groups, highest prevalence was found in age groups of above 18 months (9.4%), followed by 13-18 months age groups (7.7%). Regarding the knowledge level of the disease, 43% of the farmers responded that they have heard about the disease. Biosecurity practices in the farm was found very poor where only 40% of the farms had disinfectant at the entrance of the farm and 25% pig farmers were found using separate boots while dealing with pigs. CONCLUSIONS: The findings of this study reveal the presence of PRRSV antibodies in pigs of Nepal. In addition poor biosecurity measures, management practices and poor knowledge level about the disease among farmers highly affect in the control and prevention of disease thereby affecting the pig production and productivity. Therefore, government should develop and implement effective control measures and biosecurity programs.

Hamlet-Pattern-Based Automated COVID-19 and Influenza Detection Model Using Protein Sequences.

SARS-CoV-2 and Influenza-A can present similar symptoms. Computer-aided diagnosis can help facilitate screening for the two conditions, and may be especially relevant and useful in the current COVID-19 pandemic because seasonal Influenza-A infection can still occur. We have developed a novel text-based classification model for discriminating between the two conditions using protein sequences of varying lengths. We downloaded viral protein sequences of SARS-CoV-2 and Influenza-A with varying lengths (all 100 or greater) from the NCBI database and randomly selected 16,901 SARS-CoV-2 and 19,523 Influenza-A sequences to form a two-class study dataset. We used a new feature extraction function based on a unique pattern, HamletPat, generated from the text of Shakespeare's Hamlet, and a signum function to extract local binary pattern-like bits from overlapping fixed-length (27) blocks of the protein sequences. The bits were converted to decimal map signals from which histograms were extracted and concatenated to form a final feature vector of length 1280. The iterative Chi-square function selected the 340 most discriminative features to feed to an SVM with a Gaussian kernel for classification. The model attained 99.92% and 99.87% classification accuracy rates using hold-out (75:25 split ratio) and five-fold cross-validations, respectively. The excellent performance of the lightweight, handcrafted HamletPat-based classification model suggests that it can be a valuable tool for screening protein sequences to discriminate between SARS-CoV-2 and Influenza-A infections.

Decarbonizing agriculture through the conversion of animal manure to dietary protein and ammonia fertilizer.

The decarbonization of agriculture faces many challenges and has received a level of attention insufficient to abate the worst effects of climate change and ensure a sustainable bioeconomy. Agricultural emissions are caused both by fossil-intensive fertilizer use and land-use change, which in turn are driven in part by increasing demand for dietary protein. To address this challenge, we present a synergistic system in which organic waste-derived biogas (a mixture of methane and carbon dioxide) is converted to dietary protein and ammonia fertilizer. This system produces low-carbon fertilizer inputs alongside high-quality protein, addressing the primary drivers of agricultural emissions. If the proposed system were implemented across the United States utilizing readily available organic waste from municipal wastewater, landfills, animal manure, and commercial operations, we estimate 30% of dietary protein intake and 127% of ammonia usage could be displaced while reducing land use, water consumption, and greenhouse gas emissions.

Detection of antibodies against Bluetongue virus among domestic ruminants in the highlands of Nepal.

Bluetongue (BT) is one of the most economically important transboundary animal diseases. In recent years, it has been considered a disease related to climate change. A study was undertaken in 2013 in Nepal to measure the prevalence of Bluetongue virus (BTV) infection among domestic ruminants inhabiting the 3 agro-climatic zones with altitudes ranging from 150 to 2,400 metres above sea level. Twelve clusters representing the 3 altitudes were selected. The presence of antibodies against BTV was demonstrated in serum samples of sheep, goats, cattle, buffaloes, yaks/chauries, and chyangra goats (Himalayan goat) of Nepal. For this purpose, a total of 2,084 sera were collected from a population of 202 sheep, 739 goats, 590 cattle, 379 buffaloes, 105 yaks/chauries, and 69 chyangra goats between February 2013 and January 2014. The presence of antibodies against BTV was investigated using competitive enzyme-linked immunosorbent assay (c-ELISA). Of the 2,084 collected sera, 45.20% were positive for BTV antibodies. Species-wise prevalence was 17.82%, 47.50%, 53.05%, 58.05%, 7.62%, and 20.29% in sheep, goats, cattle, buffaloes, yak, and chyangra goats, respectively. Contrary to the general belief, maximum numbers of seropositive cases were recorded in buffaloes followed by cattle, goats, chyangra goats, sheep, and yak/chauries. The samples collected in the post-monsoon period (July-August is the monsoon period) show a seroprevalence higher than the pre-monsoon samples. This study shows the seroprevalence of BT in domestic ruminant population of Nepal at all altitudes. The highest prevalence has been reported in the plains of Terai followed by gradual decline in the mid-hills, and in the high mountains. Furthermore, detection of antibodies against BTV in both small and large ruminants (chyangra goats and yak/chauries) dwelling in high altitudes in the absence of BT vaccination is suggesting vector movement to the highlands as a consequence of warmer climate. These findings suggest that the climatic conditions, even at the higher elevation, are suitable for the survival of biting midges responsible for the transmission of BTV.