A comparative genomic and evolutionary analysis of circulating strains of Avian avulavirus 1 in Pakistan

Newcastle disease, caused by Avian avulavirus 1 (AAvV 1), is endemic to many developing countries around the globe including Pakistan. Frequent epidemics are not uncommon even in vaccinated populations and are largely attributed to the genetic divergence of prevailing isolates and their transmission in the environment. With the strengthening of laboratory capabilities in Pakistan, a number of genetically diverse AAvV 1 strains have recently been isolated and individually characterized in comparison with isolates reported elsewhere in the world. However, there lacks sufficient comparative genomic and phylogenomic analyses of field circulating strains that can elucidate the evolutionary dynamics over a period of time. Herein, we enriched the whole genome sequences of AAvV reported so far (n = 35) from Pakistan and performed comparative genomic, phylogenetic and evolutionary analyses. Based on these analyses, we found only isolates belonging to genotypes VI, VII and XIII of AAvV 1 in a wide range of avian and human hosts. Comparative phylogeny revealed the concurrent circulation of avulaviruses representing different sub-genotypes such as VIg, VIm, VIIa, VIIb, VIIe, VIIf, VIIi, XIIIb and XIIId. We found that the isolates of genotype VII were more closely associated with viruses of genotype XIII than genotype VI. An inter-genotype comparative residue analysis revealed a few substitutions in structurally and functionally important motifs. Putative recombination events were reported for only one of the captive-wild bird (pheasant)-origin isolates. The viruses of genotype VII had a high genetic diversity as compared to isolates from genotypes VI and XIII and, therefore, have more potential to evolve over a period of time. Taken together, the current study provides an insight into the genetic diversity and evolutionary dynamics of AAvV 1 strains circulating in Pakistan. Such findings are expected to facilitate better intervention strategies for the prevention and control of ND in disease-endemic countries across the globe particularly Pakistan

A comparative phylogenomic analysis of peste des petits ruminants virus isolated from wild and unusual hosts

Peste des petits ruminants virus (PPRV) infects a wide range of domestic and wild ruminants, and occasionally unusual hosts such as camel, cattle and pig. Given their broad host-spectrum and disease endemicity in several developing countries, it is imperative to elucidate the viral evolutionary insights for their dynamic pathobiology and differential host-selection. For this purpose, a dataset of all available (n = 37) PPRV sequences originating from wild and unusual hosts was composed and in silico analysed. Compared to domestic small ruminant strains of same geographical region, phylogenomic and residue analysis of PPRV sequences originating from wild and unusual hosts revealed a close relationship between strains. A lack of obvious difference among the studied sequences and deduced residues suggests that these are the host factors that may play a role in their susceptibility to PPRV infection, immune response, pathogenesis, excretion patterns and potential clinical signs or resistance to clinical disease. Summarizing together, the comparative analysis enhances our understanding towards molecular epidemiology of the PPRV in wild and unusual hosts for appropriate intervention strategies particularly at livestock-wildlife interface

Comparative evolutionary and phylogenomic analysis of Avian avulaviruses 1 to 20

Avian avulaviruses (avulaviruses or AAvVs) infect a wide range of avian species worldwide with variable clinical outcomes and economic impacts. Owing to broad host spectrum, several novel avulaviruses are being reported from both wild and domesticate birds that highlight the potential of the virus to evolve, adapt and emerge in susceptible population. Pathobiological and phylogenetic characterizations of individual avulaviruses are often demonstrated, however, a cumulative and comparative assessment of avulaviruses remains elusive. To assess evolutionary dynamics and potential emergence of novel avulaviruses, we enriched existing databases of all known avulaviruses (specie-type 1-20), and determined their genomics features based on both complete genomes and individual complete genes. While a high nucleotide divergence (up to 65.4%) was observed among avulaviruses, phylogenomic analysis revealed clustering of all avulaviruses into three distinct clades. The major clade (Clade-I) included both oldest and newest avulaviruses (2, 5, 6, 7, 8, 10, 11, 14, 15 and 20) and the second clade (Clade-II) consisted of avulaviruses 1, 9, 12, 13, 16, 17, 18 and 19, whereas the third clade (Clade-III) carried only avulaviruses 3 and 4. Intriguingly, clustering pattern was descriptive for individual gene-based analysis, however, the hemagglutinin-neuraminidase (HN) and polymerase (L) genes showed clear and discrete branching patterns similar to complete genome-based clustering. Therefore, we propose the use of HN, or L genes or complete genome to study epidemiological aspects of the avulaviruses. Genomic and residue characteristics of all genes indicated a continuous evolution of the virus, and substitutions in biologically important motifs warrant future investigations to assess their roles in the pathobiology of the virus. Taken together, this comprehensive analysis of all known avulaviruses ascertains continuous monitoring and surveillance of wild/water-fowls and commercial poultry. These findings further our understanding on the evolutionary dynamics and potential emergence of novel avulaviruses and will establish bases to identify potential of wild-bird origin apathogenic viruses to cause infections in commercial poultry

Rationale to understand anthelmintic resistance in parasitic nematodes

With extensive use of the anthelmintic in many tropical and parasite-endemic countries, the graveness of parasite resistance is exaggerating. The trend in the use of excessive medication in animal is also posing threats to public health. The governmental bodies are either lacking understanding or underestimating the regime of this emergingissue. This brief overview highlights the need, rationale and urgency of the matter to establish foundations for unifiedaction plans at the national levels as well as international levels in mitigating the development of resistance

An overview of the trichostorngyloidea

Among helminthes, the trichostrongyloidea consists of most significant parasites of ruminants, which are posing significant threats to livestock productivity, health and well-being. This brief commentary provides an overview of this important group of parasite to showcase the crucial roles these play in hosts

Genetic characterization of small ruminant morbillivirus from recently emerging wave of outbreaks in Pakistan

Peste des petits ruminants (PPR) is an endemic and highly infectious disease of several tropical countries, including Pakistan. Despite exhaustive vaccination, outbreaks are on the rise annually across different parts of the country. Clinical outcomes are largely employed to diagnose disease, while comprehensive genomic features of prevailing field strains of SRMV largely remain elusive. Here, we present comparative sequence-based phylogenomics of field strains from three districts representing different agro-livestock production systems during an emerging wave of outbreaks in 2015, together with the first complete genome sequencing of a strain from Pakistan. The analysis revealed clustering of study strain (SRMV/Lahore/UVAS/Pak/2015) to lineage IV, close to isolates characterized previously from India and China. Investigations of inter- and intralineage genetic distances showed a higher genetic distance between SRMV/Lahore/UVAS/Pak/2015 to lineage III viruses than lineages I and II. The characterized Pakistani strain also showed a high percentage of genetic distance from isolates originated from Nigerian and other African small ruminants. Based on these observations, an integrated cross-protection investigation is warranted in the future, not only to define the protective efficacy of currently applied vaccines, but also to continuously elucidate the genomic and evolutionary nature of circulating viruses in the country to achieve disease eradication by 2030

Understanding of the molecular genetics of benzimidazole resistance in haemonchus

Parasitic infestations are continuously posing enormous threats to food security and poverty alleviation. While different drugs are proposed to minimize the impact of parasite, these come with established genetic resistance. Understanding markers of genetic resistance will streamline the process of use of alternative medication as well as assessing the affect of currently applied anthelmintic. This review briefly outlines the roles of parasites in diseases and proposes the use of different genetic markers to mitigate the emerging resistance in parasite

Peste des petits ruminants in wild ungulates

Peste des petits ruminants (PPR) is a contagious viral disease of domestic small ruminants. It also affects wild ungulates but there are comparatively few studies of the incidence of natural infection, clinical signs and pathology, and confirmation of the virus, and in these species. In this article, we list the wild ungulates in which PPRV infection has been confirmed and summarize available information about the presentation of the disease, its identification, and impact of virus on wildlife populations. Considering recent reports of outbreaks by the World Organization for Animal Health (OIE), it is important to understand the transmission of this disease within wildlife populations in PPR endemic regions

Evaluation of transmission potential and pathobiological characteristics of mallard originated Avian orthoavulavirus 1 (sub-genotype VII.2) in commercial broilers

Newcastle disease (ND), caused by Avian orthoavulavirus 1 (AOAV-1), affects multiple avian species around the globe. Frequent disease outbreaks are not uncommon even in vaccinates despite routine vaccination and, in this regards, viruses of diverse genotypes originating from natural reservoirs (migratory waterfowls) play an important role in a disease endemic setting. Though genomic characterization of waterfowl originated viruses has been well-elucidated previously, there is a paucity of data on clinico-pathological assessment of mallard-originated sub-genotype VII.2 in commercial chickens. Hence, the current study was designed to evaluate its transmission potential, tissue tropism and micro- and macroscopic lesions in commercial broilers. Based on complete genome and complete F gene, phylogenetic analysis clustered the study isolate within genotype VII and sub-genotype VII.2 in close association with those reported previously from multiple avian species worldwide. The study strain was found to be velogenic on the basis of typical residue pattern in the F-protein cleavage site (112R-RQ-K-R↓F117), sever disease induction in chicken, tissue tropism and subsequent clinico-pathological characteristics. Giving a clear evidence of horizontal transmission, a 100% mortality was observed by 4th and 6th day post infection (dpi) in chickens challenged with the virus and those kept with the challenged birds (contact birds), respectively. The observed clinical signs, particularly the greenish diarrhea, and macroscopic lesions such as pinpoint hemorrhages in proventriculus and caecal tonsils were typical of the infection caused by an AOAV-1 in chickens. The virus exhibited a broad tissue tropism where genomic RNA corresponding to study virus was detected in all of the tissues collected from recently mortile and necropsied birds. The study concludes that mallard-originated Avian orthoavulavirus 1 is highly velogenic to commercial chicken and therefore ascertain continuous disease monitoring and surveillance of migratory/aquatic fowls to better elucidate infection epidemiology and subsequent potential impacts on commercial poultry