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Dicrocoelium lancet flukes cause significant production loss in ruminant livestock. Although co-infection with multiple Dicrocoelium species within a host is common, techniques for studying the composition of these complex parasite communities are lacking. The pathogenicity, epidemiology, and therapeutic susceptibility of different helminth species vary, and little is known about the interactions that take place between co-infecting species and their hosts. Here, we describe the first applicationof metabarcoding deep amplicon sequencing method to studythe Dicrocoelium species in sheep and goats. First, rDNA ITS-2 sequences of four Dicrocoelium species (Dicrocoelium dendriticum, Dicrocoelium hospes, Dicrocoelium orientalis, and Dicrocoelium chinensis) were extracted from the NCBI public database. Phylogenetic analysis revealed separate clades of Dicrocoelium species; hence, molecular differentiation between each species is possible in co-infections. Second, 202 flukes belonging to seventeen host populations (morphologically verified as belonging to the Dicrocoelium genus) were evaluated to determine the deep amplicon sequencing read threshold of an individual fluke for each of the four species. The accuracy of the method in proportional quantification of samples collected from single hosts was further assessed. Overall, 198 (98.01%) flukes were confirmed as D. dendriticum and 1.98% produced no reads. The comparison of genetic distances between rDNA ITS-2 revealed 86% to 98% identity between the Dicrocoelium species. Phylogenetic analysis demonstrated a distinct clustering of species, apart from D. orientalis and D. chinensis, which sit very close to each other in a single large clade whereas D. hospes and D. dendriticum are separated into their own clade. In conclusion each sample was identified as D. dendriticum based on the proportion of MiSeq reads and validated the presence of this group of parasites in the Gilgit Baltistan and Khyber Pakhtunkhwa provinces of Pakistan. The metabarcoding deep amplicon sequencing technology and bioinformatics pathway have several potential applications, including species interactions during co-infections, identifying the host and geographical distribution of Dicrocoelium in livestock, drug therapy response evaluation and understanding of the emergence and spread of drug resistance. [ABSTRACT FROM AUTHOR]

Simple Summary: Warble fly is a globally important pest of domesticated and wild animals in the northern hemisphere. Goat warble fly infestation (GWFI), triggered by the obligatory parasite Przhevalskiana silenus larvae, has detrimental consequences for livestock. GWFI is usually not accurately detected by the traditional methods of detection. This study aimed to identify the best diagnostic method for the early detection of GWFI by comparing three enzyme-linked immunosorbent assay (ELISA) methods using Hypoderma purified antigen (Hypodermin C), the crude antigen of P. silenus, and a commercially available hypodermosis ELISA kit, in the Pothwar region of Punjab, Pakistan. The sampling was carried out in 1000 goats, randomly selected from four districts (Rawalpindi, Attock, Jhelum, and Attock) of the Pothwar region, Punjab Pakistan. The seroprevalence, determined via ELISA with the crude P. silenus antigen, hypodermin C (HyC) antigen, and the commercial ELISA kit, was 17%, 15.5%, and 18.6%, respectively. Cohen's Kappa test confirmed that all the three assays could be employed for the early detection of GWFI, while an indirect crude P. silenus antigen ELISA was more sensitive and accurate. Przhevalskiana silenus (warble fly) grubs cause myiasis in goats, in mountainous and semi-mountainous areas and different regions in Pakistan, and cause substantial losses to livestock. The palpation method for detecting warble flies generally neglects the infestation intensity; therefore, the development of a reliable and efficient diagnostic technique is extremely necessary. This study compared three indirect enzyme-linked immunosorbent assay (ELISA) methods for detecting anti-P. silenus antibodies using the hypodermin C (HyC) purified from Hypoderma spp. Larvae collected in cattle (local isolate, Microbiology Laboratory, PMAS-Arid Agriculture University, Rawalpindi), the crude antigen from the first instar stage of P. silenus, and a commercial Bovine Hypodermosis Antibody ELISA kit (IDEXX Laboratory), for accurately estimating the seroprevalence of goat warble fly infestation (GWFI) in the Pothwar plateau, Punjab, Pakistan. The ELISA with the crude antigen of P. silenus proved very sensitive and specific, 91% and 93%, respectively. The optical density exhibited a monthly variation, and the antibody titer began increasing from June, continually increased from July to December, and gradually decreased thereafter until March. The study confirmed the endemic status of GWFI in the Pothwar region and identified that ELISA based on the crude antigen of P. silenus was a more sensitive and specific immunodiagnostic method for determining seroprevalence, and could be employed for initiating nationwide eradication campaigns. [ABSTRACT FROM AUTHOR]

Pastoralism is mostly related to specific ethnic group or group of people whose livelihoods generally depend on production of livestock in the rangelands. Pastoralists' livelihood regarding livestock is hastily becoming indefensible due to mounting pressure of population growth on rangelands and desertification of vast rangeland, the reason for severe climate change. This study attempted to investigate the impact of violent conflicts and environmental hazards on sustainability of pastoral in Punjab, Pakistan. Muzaffargarh, Rahim Yar Khan and Bahawalpur districts of southern Punjab due to significant contribution in livestock and grazing rangeland locations were purposively selected for this study. This research work used the data of 840 pastoralists' and employed instrumental variable regression model for empirical estimation of the study. Estimates of the study indicated livestock holding negatively influenced from violent conflicts and environmental hazards as this effect can initiate without any exception of livestock holding size. Finding also highlighted pastoralists significant welfare indicators such as income and expenses were negatively influenced due to livestock losses. Pastoralist's livelihood sustainability is feasible by overcoming such negative impacts of violent conflicts and environmental hazards. There is need to sure pastoralists' community sustainability by priority focusing on environment sustainable agenda not only internationally but also on national and regional levels. More particularly, implementation proper policy measures regarding climate change coping strategies, controlling violent conflicts, land management and managing programs for reducing poverty more specifically for pastoralist's rangeland households is needed. [ABSTRACT FROM AUTHOR]

Foot and mouth disease (FMD) causes severe economic losses to the livestock industry of endemic countries, including Pakistan. Pakistan is part of the endemic pool 3 for foot and mouth disease viruses (FMDV), characterized by co-circulating O, A, and Asia 1 serotypes, as designated by the world reference laboratory for FMD (WRL-FMD). FMDV serotype A lineage ASIA/Iran-05 is widespread in buffalos and cattle populations and was first reported in Pakistan in 2006. This lineage has a high turnover, with as many as 10 sub-lineages reported from Pakistan over the years. In this study, we reconstructed the evolutionary, demographic, and spatial history of serotype A and one of its sub-lineages, A/ASIA/Iran-05/SIS-13, prevalent in Pakistan. We sequenced nearly complete genomes of three isolates belonging to sub-lineage A/ASIA/Iran-05/SIS-13. We estimated recombination patterns and natural selection acting on the serotype A genomes. Source and transmission routes in Pakistan were inferred, and the clustering pattern of isolates of the SIS-13 sub-lineage were mapped on a tree. We hereby report nearly complete genome sequences of isolates belonging to sub-lineage A/ASIA/Iran-05/SIS-13, along with purported recombinant genomes, and highlight that complete coding sequences can better elucidate the endemic history and evolutionary pressures acting on long-term co-circulating FMDV strains. [ABSTRACT FROM AUTHOR]

Ixodid ticks are in varying distribution patterns throughout Pakistan. They cause substantial losses to livestock industry in terms of hide loss and vector-borne disease transmission. This study was conducted in three districts of Khyber Pakhtunkhwa (KPK) from March 2018 to February 2019 with the aim of determining the prevalence and seasonal variation in tick species belonging to Ixodidae family in cattle population. A total of 1145 adult ticks were collected by a convenient method of sampling from 434 infested cattle of various breeds, age groups and sexes. Identification of ticks up to genus and species level was done with the help of specific morphological keys. The results showed higher prevalence of Rhipicephalus (Boophilus) microplus (77%) followed by R. (B) annulatus (70%), R. (B) decoloratus (54%), H. anatolicum (52%) and the leastprevalence was recorded inR. (B) turanicus (12%). The prevalence of all ixodid tick species with exception of R. (B) annulatus and R. (B) decoloratus was significantly associated (p<0.05) with districts, breed, age and sex of cattle. Tick prevalence was higher in Achai and Friesian breeds, young stock and male animals. Prevalence of tick infestation was at its peak during summer and rainy seasons and remained low during winter season. In conclusions, that cattle tick R. (B) microplus was the dominant tick species infesting cattle population of KPK province and tick burden presented the highestrecord in summer season. [ABSTRACT FROM AUTHOR]

In pan Pamir Plateau countries, Peste des petits ruminants (PPR) has brought huge losses to the livestock industry and threaten the endangered wildlife. In unknown regions, revealing PPRV transmission among countries is the premise of effective prevention and control, therefore calls for quantified monitoring on disease communication among countries. In this paper, a MaxEnt model was built for the first time to predict the PPR risk within the research area. The least cost path (LCP) for PPR transboundary communication were calculated and referred to as the maximum available paths (MAP). The results show that there are many places with high-risk in the research area, and the domestic risk in China is lower than that in foreign countries and is mainly determined by human activities. Five LCPs representing corridors among Kazakhstan, Tajikistan, Pakistan, India and China were obtained. This study proves for the first time that there is the possibility of cross-border transmission of diseases by wild and domestic animals. In the future, it will play an important role in monitoring the PPR epidemic and blocking-up its cross-border transmission. [ABSTRACT FROM AUTHOR]

Background: In tropical and subtropical countries, tick infestation causes major public health problems and considerable financial losses to the livestock industry. This study was aimed to assess the species composition of richness and analyze the phylogeny of Rhipicephalus microplus in the District Bannu of Khyber Pakhtunkhwa, Pakistan. Methods: Collected ticks were identified morphologically and DNA extracted from R. microplus was amplified and subjected to sequencing. Results: A total of 3,600 animals were examined among them 1,494 animals were found to be infested with ticks, including 669 cows, 476 buffaloes, 163 goats, and 186 sheep (p = 0.001). Tick infestation was significantly high (43.58%) in animals of age group (<1 year) (p-value = 0.027). Female animals were more (44.05%) infested with ticks than males (34.43%) (p = 0.001). The intensity of infestation was significantly higher in summer (77.49%) (p = 0.001). A total of 5,557 ticks were collected comprising three genera and six species. R. microplus was predominantly prevalent (n = 1,474; 26.52%), followed by Rhipicephalus annulatus (n = 1,215; 21.86%), Hyalomma anatolicum (n = 1,139; 20.49%), Hyalomma marginatum (n = 1,086; 19.54%), and Rhipicephalus turanicus (n = 761; 13.69%), while the least common was Haemaphysalis aciculifer (n = 80; 1.43%) (p = 0.001). Morphologically identified R. microplus species were also analyzed genetically by using two genetic markers 16S ribosomal RNA (16S rRNA) and internal transcribed spacer 2 (ITS2) genes. The phylogenetic study revealed that R. microplus is genetically diversified and clustered in clade B with R. microplus species from China, India, and Pakistan. Conclusion: Ticks infestation was significantly correlated with various factors including age, sex, season, and animal type. R. microplus genetically resembled species reported from India and China. However, major knowledge gaps concerning various species of ticks exist and many areas are still unexplored in Pakistan. Therefore, it is necessary to explore the epidemiological and molecular aspects of various tick species in other regions of southern Khyber Pakhtunkhwa. [ABSTRACT FROM AUTHOR]

Climate change has adversely affected pastoral community in Pakistan through increased severity of livestock diseases, floods, and drought. These climatic hazards caused extensive livestock loss and worsen livelihood of pastoralists' households. Pastoralists are higher vulnerable to these climate shocks and livestock major source of their nutrition and income. This research work focused to analyze the factors affecting resilience of pastoral community in Punjab province of Pakistan. Understanding shocks of climate change in historical perspective of pastoral community, consultation for key information, and focus group discussions were managed. The study collected data of 768 pastoral households' regarding pastoral shocks experience, long-term adaptation measures, and coping strategies through external support for resilience upright. Principal component analysis was used for construction of resilience index of pastoral households. In estimating institutional factors, adaptive practice and socio-demographic effects on pastoral households' resilience structured probit regression were employed in the study. Extension services access, availability of adequate formal credit, pastoral household income, schooling years and adaptive practice like afforestation, the practice of ethno-veterinary, improved stock breeding, beekeeping, enclosures, and grazing of crop fields post-harvest affect significantly and positively in developing pastoral household resilience to shocks. In the past scenario long-term adaptation strategies, policy measures ignored, while investment priority was focused on risk-reducing measures. To enhance long-run pastoral household resilience status regarding climate change shocks, there is need for direct investment to increase adaptive capacity pastoral community. [ABSTRACT FROM AUTHOR]

Globally, climate change is an alarming threat to the livestock industry. Such changes in the climate can also adversely affect the returns of livestock farmers in Pakistan. Improvement in the production process could decrease the risk of losses. This study analyzes the efficacy of silage to abate the losses in livestock profitability resulting from the climate change. The study employed cross-sectional survey data of 492 livestock farmers collected from six districts of Punjab Province, Pakistan. The data are analyzed with endogenous switching regression, considering the possibility of selection bias and endogeneity in adopting silage as a climate change adaptation measure. The study findings show a significant difference in material well-being between silage users and conventional feed users. Furthermore, training programs such as silage training and livestock development programs could be meaningful provisions to abate climate change and improve food security. It is suggested that training and development programs should be incorporated in policy plans to improve the well-being of farmers in terms of their farm revenues. [ABSTRACT FROM AUTHOR]

The gastrointestinal tract (GIT) of animals contains various helminth parasites, responsible for subclinical and clinical parasitism. The health situation of animals is seriously affected by these parasites and leads massive financial losses for the livestock trade. The present study was conducted to determine the prevalence and associated risk factors of GIT parasites in small and large ruminants of Mardan district and zoo animals of Golden Life Safari Park Khyber Pakhtunkhwa. A total of 419 fecal samples were collected including 117 from goats, 110 from cattle, 80 from sheep, 66 from buffaloes, 40 from birds, four from deer, and two from leopards. The fecal samples were subjected to sedimentation and floatation to identify parasite eggs. Of a total of 419 fecal samples, 215 (51.31%) were found positive for GIT parasites eggs. The prevalence of GIT parasites was high in sheep (65%), followed by goats (62.39%), cattle (42.70%), and buffaloes (37.87%). In birds, GIT parasite eggs were identified in 11 (45.83%) and 7 (43.75%) fecal samples of Pheasant and Peacock, respectively. However, an absence of infection was noted in fecal samples from deer and leopards. Eggs of GIT Parasites belonging to one superfamily and four different genera were recognized in fecal samples of domestic animals and buffaloes, which were Trichostrongyloidea (19.81%), Strongyloides (9.31%), Trichuris (7.77%), Monezia (6.44%), and Fasciola (4.53%). For bird, the coccidia group comprises the highest representation of parasites (2.63%), followed by the Trichuris genus (1.67%). Settlement, management system, anthelminthic medications and body condition score were significantly associated with the occurrence of GIT parasites in feces (P < 0.05). Animals from rural settlements, rearing under poor management systems, with thin (poor) body condition and under warmed were more affected by GIT parasites. The diversity and the high prevalence of GIT parasites reported in this study highlights the urgent need for intervention through treatment and modification of management practices in the investigated areas of Pakistan. [ABSTRACT FROM AUTHOR]

Foot-and-mouth disease is one of the devastating transboundary animal diseases causing heavy losses to the livestock industry. Different vaccines based on the inactivated FMD virus are used against this disease, but lack of immunological memory and the need for high biocontainment are the major drawbacks of these vaccines. A novel vaccine comprising recombinant antigenic regions is effective, as they lack viruses for production. Considering the fact, capsid proteins vp4, vp2, vp3, and vp1 with 3C protease of FMDV serotype Asia-1 were analyzed through reverse vaccinology approaches in this study. The sequence and structural analysis of the proteins is carried out through various bioinformatic tools and the sequence analysis has figured out the acidic nature and thermal stability of the proteins, likewise, the phylogenetic analysis helped us to trace the FMDV isolates, elucidating that selected proteins belong to the strain (Group VII), which is currently circulating in Pakistan. Next, the B-cell and MHC Class-I epitopes are identified from the antigenic proteins by immunoinformatic tools. The highly conserved, antigenic, and non-allergenic epitopes are used to design the vaccine. Accordingly, the codon adaptation and in silico cloning of the corresponding genes is performed. Thus, the bacterial expression vector could be used for efficient expression and large-scale production of the vaccine. [Display omitted] • Sindh-08 strain of serotype Asia-1, currently circulating in Pakistan. • Vp3, vp2 and vp1; the most antigenic ones among capsid proteins. • Highly antigenic and non-allergenic epitopes identified by immunoinformatic tools. • Alleles present in BoLA haplotypes taken from IPD-MHC database. • Highly conserved epitopes of vp3 and vp2 conjugated with CTB, an effective vaccine. [ABSTRACT FROM AUTHOR]