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The Pirbright Institute publication directory contains details of selected publications written by our researchers.

There were a total of 2606 results for your search.
Munir M (2013)

Bioinformatics analysis of large-scale viral sequences: from construction of data sets to annotation of a phylogenetic tree

Virulence 4 (1), 97-106
Publisher’s version: http://dx.doi.org/10.4161/viru.23161

Abstract

Due to a significant decrease in the cost of DNA sequencing, the number of sequences submitted to the public databases has dramatically increased in recent years. Efficient analysis of these data sets may lead to a significant understanding of the nature of pathogens such as bacteria, viruses, parasites, etc. However, this has raised questions about the efficacy of currently available algorithms for the study of pathogen evolution and construction of phylogenetic trees. While the advanced algorithms and corresponding programs are being developed, it is crucial to optimize the available ones in order to cope with the current need. The protocol presented in this study is optimized using a number of strategies currently being proposed for handling large-scale DNA sequence data sets, and offers a highly efficacious and accurate method for computing phylogenetic trees with limited computer resources. The protocol may take up to 36 h for construction and annotation of a final tree of about 20,000 sequences.
Munir M (2013)

Mononegaviruses of veterinary importance. Volume I: Pathobiology and molecular diagnosis

, 363
Publisher’s version: http://dx.doi.org/10.1079/9781780641799.0000

Abstract

The purpose of this book is to provide a timely and comprehensive review on all the mononegaviruses of veterinary importance. The book is divided into two sections. Section I deals with 13 mononegaviruses (Bornaviruses, Avian Paramyxoviruses serotypes 1 to 10, Hendra and Nipah viruses, Canine distemper virus, Peste des petits ruminants virus, Rinderpest virus, Bovine parainfluenza virus, Swine parainfluenza virus, Porcine rubulavirus (PoRV -LPMV), Bovine respiratory syncytial virus, Avian metapneumoviruses, Bovine ephemeral fever virus and Rabies virus) of livestock, horses, dogs and cats; whereas Section II comprises of 9 other mononegaviruses (Ebolavirus, Marburgvirus, Phocine distemper virus, Morbilliviruses, Sendai virus, pneumonia virus, Infectious hematopoietic necrosis virus, Viral haemorrhagic septicaemia virus and Snakehead rhabdovirus) of rodents, primates, fish and sea mammals. A full chapter is dedicated to each virus which provides up-to-date literature on historical distribution, genome structure, viral proteins, reverse genetics, immunity, viral pathogenesis, clinical and molecular diagnosis and future challenges. Every chapter is written by renowned scientists who have made seminal contributions in their respective mononegavirus fields of expertise. Each chapter is attempted to make as stand-alone document, making it a valuable reference source for virologists, field veterinarians, infection and molecular biologists, immunologists, scientists in related fields and veterinary school libraries.
Munir M, Berg M (2013)

The multiple faces of proteinkinase R in antiviral defense

Virulence 4 (1), 85-89
Publisher’s version: http://dx.doi.org/10.4161/viru.23134

Abstract

Various pattern recognition receptors (PRRs) have been implicated in the detection of viral RNA and subsequent interferon (IFN) gene expression, including the double-stranded RNA-dependent proteinkinase R (PKR). Now, a novel role of PKR has been unveiled, as it was shown that, upon the infection with certain viruses, PKR is crucial for the integrity of newly synthesized IFN mRNA, thereby generating an optimal host antiviral immune response. There is a need of future studies to investigate additional roles of PKR in innate immunity and the molecular understanding of this novel function of PKR.
Munir M, Zohari S, Abbas M, Shabbir M Z, Zahid M N, Latif M S, Iqbal M, Qureshi Z U A, Berg M (2013)

Isolation and characterization of low pathogenic H9N2 avian influenza A viruses from a healthy flock and its comparison to other H9N2 isolates

Indian Journal of Virology 24 (3), 342-348
Publisher’s version: http://dx.doi.org/10.1007/s13337-013-0144-1

Abstract

Several outbreaks of avian influenza (AI) caused by H9N2 subtype, have been reported in the poultry industry during 1990 around the globe. Currently, H9N2 are endemic in the large area of Middle and Far East, including Pakistan. Since H9N2 AI viruses are sporadically reported from humans, extensive incidence of H9N2 in poultry imposes a great risk for human health. In this context, continuous monitoring of the poultry and determining the genetic nature of these viruses are fundamental to predict any future threat. Thus gene sequences of one isolate of H9N2, isolated from commercial poultry flocks, were analyzed. The results of this investigation, based on hemagglutinin (HA), neuraminidase (NA) and non-structural genes, showed that Pakistani H9N2 isolates are closely related to each other and to other H9N2 isolates from the Middle East. However, several unusual substitutions with unknown functional consequences were observed in HA and NA proteins and thus warrant further investigations for their possible role in viral biology. In conclusion, these findings provide information regarding the genetic nature of H9N2 avian influenza viruses in Pakistani poultry and necessitate the sequencing of more H9N2 viruses from both naturally infected and vaccinated flocks.
Munir M, Zohari S, Berg M (2013)

Molecular Biology and Pathogenesis of Peste des Petits Ruminants Virus. (book)

, 151
Publisher’s version: https://www.springer.com/gp/book/9783642314506

Abstract

Peste de Petits Ruminants (PPR) is a highly contagious viral disease of domestic and wild small ruminants that can significantly affect economies. The authors are experts in the field and provide an up-to-date and comprehensive review covering all aspects of the disease. The book is divided into seven chapters highlighting genome organization, virus replication and the determinants of virulence, pathophysiology and clinical disease, immunology and immunopathogenesis, epidemiology, diagnostic assays and vaccines, and the challenges concerning global eradication. It is an invaluable reference work, presenting the latest information for virologists, microbiologists, immunologists, veterinarians, and scientists working in PPR research.

Munir M, Zohari S, Iqbal M, Abbas M, Perez D R, Berg M (2013)

The non-structural (NS) gene segment of H9N2 influenza virus isolated from backyard poultry in Pakistan reveals strong genetic and functional similarities to the NS gene of highly pathogenic H5N1

Virulence 4 (7), 612-623
Publisher’s version: http://dx.doi.org/10.4161/viru.26055

Abstract

Apart from natural reassortment, co-circulation of different avian influenza virus strains in poultry populations can lead to generation of novel variants and reassortant viruses. In this report, we studied the genetics and functions of a reassorted non-structural gene (NS) of H9N2 influenza virus collected from back yard poultry (BYP) flock. Phylogenetic reconstruction based on hemagglutinin and neuraminidase genes indicates that an isolate from BYP belongs to H9N2. However, the NS gene-segment of this isolate cluster into genotype Z, clade 2.2 of the highly pathogenic H5N1. The NS gene plays essential roles in the host-adaptation, cell-tropism, and virulence of influenza viruses. However, such interpretations have not been investigated in naturally recombinant H9N2 viruses. Therefore, we compared the NS1 protein of H9N2 (H9N2/NS1) and highly pathogenic H5N1 (H5N1/NS1) in parallel for their abilities to regulate different signaling pathways, and investigated the molecular mechanisms of IFN-beta production in human, avian, and mink lung cells. We found that H9N2/NS1 and H5N1/NS1 are comparably similar in inhibiting TNF-alpha induced nuclear factor kappaB and double stranded RNA induced activator protein 1 and interferon regulatory factor 3 transcription factors. Thus, the production of IFN-beta was inhibited equally by both NS1s as demonstrated by IFN stimulatory response element and IFN-beta promoter activation. Moreover, both NS1s predominantly localized in the nucleus when transfected to human A549 cells. This study therefore suggests the possible increased virulence of natural reassortant viruses for their efficient invasion of host immune responses, and proposes that these should not be overlooked for their epizootic and zoonotic potential.
Muniraju M, El Harrak M, Bao J, Ramasamy Parthiban A B, Banyard A C, Batten C, Parida S (2013)

Complete genome sequence of a peste des petits ruminants virus recovered from an alpine goat during an outbreak in Morocco in 2008

Genome Announcements 1 (3), e00096-13
Publisher’s version: http://dx.doi.org/10.1128/genomeA.00096-13

Abstract

Here, we announce the first complete genome sequence of a field isolate of a peste des petits ruminants virus (PPRV) from northern Africa. This isolate is derived from an Alpine goat that suffered from severe clinical disease during the 2008 outbreak in Morocco. The full genome sequence of this isolate clusters phylogenetically with the lineage IV isolates of PPRV, sharing high levels of sequence identity with other lineage IV isolates.

Murphy L, Kisielewski D, Brown D, Piccardo P, Hogan K, Fragkoudis R, Fazakerley J, Freeman T, Perry H, Manson J (2013)

The impact of viral infection on the innate immune response within the brain during chronic neurodegeneration

Journal of Neurovirology 19, S60
Publisher’s version:
Murray L, Edwards L, Tuppurainen E S M, Bachanek-Bankowska K, Oura C A L, Mioulet V, King D P (2013)

Detection of capripoxvirus DNA using a novel loop-mediated isothermal amplification assay

BMC Veterinary Research 9, 90
Publisher’s version: http://dx.doi.org/10.1186/1746-6148-9-90

Abstract

Sheep poxvirus (SPPV), Goat poxvirus (GTPV) and Lumpy skin disease virus (LSDV) are the most serious poxviruses of ruminants. They are double stranded DNA viruses of the genus Capripoxvirus, (subfamily Chordopoxvirinae) within the family Poxviridae. The aim of this study was to develop a Loop-mediated isothermal AMPlification (LAMP) assay for the detection of Capripoxvirus (CaPV) DNA. A single LAMP assay targeting a conserved region of the CaPV P32 gene was selected from 3 pilot LAMP assays and optimised by adding loop primers to accelerate the reaction time. This LAMP assay successfully detected DNA prepared from representative CaPV isolates (SPPV, GTPV and LSDV), and did not cross-react with DNA extracted from other mammalian poxviruses. The analytical sensitivity of the LAMP assay was determined to be at least 163 DNA copies/?l which is equivalent to the performance reported for diagnostic real-time PCR currently used for the detection of CaPV. LAMP reactions were monitored with an intercalating dye using a real-time PCR machine, or by agarose-gel electrophoresis. Furthermore, dual labelled LAMP products (generated using internal LAMP primers that were conjugated with either biotin or fluorescein) could be readily visualised using a lateral-flow device. This study provides a simple and rapid approach to detect CaPV DNA that may have utility for use in the field, or in non-specialised laboratories where expensive equipment is not available.
Mussa T, Ballester M, Silva-Campa E, Baratelli M, Busquets N, Lecours M P, Dominguez J, Amadori M, Fraile L, Hernandez J, Montoya M (2013)

Swine, human or avian influenza viruses differentially activates porcine dendritic cells cytokine profile

Veterinary Immunology and Immunopathology 154 (1-2), 25-35
Publisher’s version: http://dx.doi.org/10.1016/j.vetimm.2013.04.004

Abstract

Swine influenza virus (SwIV) is considered a zoonosis and the fact that swine may act as an intermediate reservoir for avian influenza virus, potentially infectious for humans, highlights its relevance and the need to understand the interaction of different influenza viruses with the porcine immune system. Thus, in vitro porcine bone marrow-derived dendritic cell (poBMDCs) were infected with a circulating SwIV A/Swine/Spain/SF32071/2007(H3N2), 2009 human pandemic influenza virus A/Catalonia/63/2009(H1N1), low pathogenic avian influenza virus (LPAIV) A/Anas plathyrhynchos/Spain/1877/2009(aH7N2) or high pathogenic avian influenza virus (HPAIV) A/Chicken/Italy/5093/1999(aH7N1). Swine influenza virus H3N2 infection induced an increase of SLA-I and CD80/86 at 16 and 24 h post infection (hpi), whereas the other viruses did not. All viruses induced gene expression of NF-kappa B, TGF-beta, IFN-beta and IL-10 at the mRNA level in swine poBMDCs to different extents and in a time-dependent manner. All viruses induced the secretion of IL-12 mostly at 24 hpi whereas IL-18 was detected at all tested times. Only swH3N2 induced IFN-alpha in a time-dependent manner. Swine H3N2, aH7N2 and aH7N1 induced secretion of TNF-alpha also in a time-dependent manner. Inhibition of NF-kappa B resulted in a decrease of IFN-alpha and IL-12 secretion by swH3N2-infected poBMDC at 24 hpi, suggesting a role of this transcription factor in the synthesis of these cytokines. Altogether, these data might help in understanding the relationship between influenza viruses and porcine dendritic cells in the innate immune response in swine controlled through soluble mediators and transcription factors.

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