Genomic and single nucleotide polymorphism analysis of infectious bronchitis coronavirus

Infectious bronchitis virus (IBV) is a Gammacoronavirus that causes a highly contagious respiratory disease in chickens. A QX-like strain was analysed by high-throughput Illumina sequencing and genetic variation across the entire viral genome was explored at the sub-consensus level by single nucleotide polymorphism (SNP) analysis. Thirteen open reading frames (ORFs) in the order 50-UTR-1a-1ab-S-3a- 3b-E-M-4b-4c-5a-5b-N-6b-30UTR were predicted. The relative frequencies of missense: silent SNPs were calculated to obtain a comparative measure of variability in specific genes. The most variable ORFs in descending order were E, 3b, 50UTR, N, 1a, S, 1ab, M, 4c, 5a, 6b. The E and 3b protein products play key roles in coronavirus virulence, and RNA folding demonstrated that the mutations in the 50UTR did not alter the predicted secondary structure. The frequency of SNPs in the Spike (S) protein ORF of 0.67% was below the genomic average of 0.76%. Only three SNPS were identified in the S1 subunit, none of which were located in hypervariable region (HVR) 1 or HVR2. The S2 subunit was considerably more variable containing 87% of the polymorphisms detected across the entire S protein. The S2 subunit also contained a previously unreported multi-A insertion site and a stretch of four consecutive mutated amino acids, which mapped to the stalk region of the spike protein. Template-based protein structure modelling produced the first theoretical model of the IBV spike monomer. Given the lack of diversity observed at the sub-consensus level, the tenet that the HVRs in the S1 subunit are very tolerant of amino acid changes produced by genetic drift is questioned.The Poultry Section, Department of Production Animal Studieshttp://www.elsevier.com/locate/meegid2016-06-30hb201

Molecular epidemiology of Newcastle disease and avian influenza in South Africa

Please read the abstract in the secton 00front of this document.Thesis (PhD (Zoology))--University of Pretoria, 2007.Zoology and Entomologyunrestricte

History of Newcastle disease in South Africa

Poultry production in South Africa, a so-called developing country, may be seen as a gradient between two extremes with highly integrated commercial enterprises with world-class facilities on one hand and unimproved rural chickens kept by households and subsistence farmers on the other. Although vaccination against Newcastle disease is widely applied to control this devastating infection, epizootics continue to occur. Since the first official diagnosis in 1945, through the sporadic outbreaks of the 1950s and early 1960s, to serious epizootics caused by genotype VIII (late 1960s–2000), genotype VIIb (1993–1999), genotype VIId (2003–2012) and most recently genotype VIIh (2013 to present), South Africa’s encounters with exotic Newcastle disease follow global trends. Importation – probably illegal – of infected poultry, poultry products or exotic birds and illegal swill dumping are likely routes of entry. Once the commercial sector is affected, the disease spreads rapidly within the region via transportation routes. Each outbreak genotype persisted for about a decade and displaced its predecessor.http://www.ojvr.orgam2017Production Animal Studie

Extended survival times of Mycoplasma gallisepticum and Mycoplasma synoviae on kanekalon synthetic hair fibres

The survival times of Mycoplasma gallisepticum (Mg) and Mycoplasma synoviae (Ms) on washed and unwashed natural and synthetic kanekalon hair samples over a 5-d period were evaluated using the color changing unit method for comparison with results of previous studies conducted on natural hair. Regardless of whether synthetic or natural hair samples prewashed with a disinfectant shampoo were spiked with Mg or Ms, all viable organisms rapidly dropped below a count of 1 × 101/mL of culture. unwashed natural hair seeded with a titer of approximately 1 × 106/mL of viable Mg or Ms decreased to 6 × 105/mL and 6 × 103/ mL, respectively, by 4 h postseeding, but no viable Mg or Ms were detected on natural hair from 8 h onwards. By contrast, the titers of Mg and Ms on synthetic hair did not decline from the initial 1 × 106/mL seed dose up to 96 h postseeding, and, in fact, viable Mg and Ms was still detectable at 9 d postinfection. Application of a real-time quantitative single-tube duplex PCR assay confirmed that no proliferation of Mg or Ms had occurred on the synthetic hair samples, the cells simply remained viable. The unexpected finding that Mg and Ms survive for extended periods on synthetic kanekalon hair fibers raises the question of whether attachment to a surface is a prerequisite for the survival and persistence of Mg and Ms in the extra-host environment. Future studies should be aimed at determining whether other synthetic hair types or indeed other types of plastics commonly found in the poultry house offer similar survival advantages to mycoplasmas.The Southern African Poultry Association (Johannesburg).http://ps.oxfordjournals.orgam201

Salmonella gallinarum strains from outbreaks of fowl typhoid fever in Southern Africa closely related to SG9R vaccines

DATA AVAILABILITY STATEMENT : The data presented in the study are deposited in the NCBI repository (https://www.ncbi.nlm.nih.gov/ genbank/), accession numbers CP118112–CP118133 and SRR23450481–SRR23450491.INTRODUCTION : Salmonella enterica subspecies enterica serovar Gallinarum biovar Gallinarum (SG) is associated with fowl typhoid fever, and the attenuated rough strain SG9R is widely used as a vaccine in many regions. Reversion to virulence of vaccine strains was suspected as the cause during recent fowl typhoid fever outbreaks in poultry in South Africa and Eswatini. METHODS : To compare nine field isolates with global wild-type SG9 strains and the two commercial SG9R vaccines in use, Nobilis ® SG9R and Cevac ® -SG, we used whole-genome comparison with single-nucleotide polymorphism (SNP) detection. RESULTS : SNP phylogenic analysis showed that all the southern African field isolates were more closely related to the vaccine strains than wild-type SG9 strains. Furthermore, SNPs in the pyruvate dehydrogenase (aceE) and/or lipopolysaccharide 1,2-glucosyltransferase (rfaJ) genes, which are knownmarkers of attenuation, were found in four of the field isolates along with intact spv, SPI- 1, and SPI-2 gene clusters, providing conclusive evidence that these four isolates were originally vaccine strains that reverted to virulence. Five other field isolates lacked the SG9R attenuation markers, but variant analysis identified an SNP in the yihX gene, insertions in the ybjX and hydH genes, and deletions in the ftsK and sadA genes that were shared between the field isolates and vaccine strains but absent in wild-type SG9, indicating that these field isolates were also likely revertant vaccines. DISCUSSION : Overall, this study highlights different mechanisms of reversion of two commercial vaccines, where virulence caused by field isolates closely related to the Nobilis ® SG9R vaccine was associated with the restoration of intact virulence gene clusters, and those derived fromthe Cevac ® -SG vaccine were characterized by point mutations resulting in restored aceE and rfaJ genes. A possible new marker of attenuation was identified as a point mutation in the yihX gene, as well as four new candidate genes that could potentially be used to distinguish current vaccine strains from wild-type strains using PCR assays.The National Research Foundation SA.https://www.frontiersin.org/journals/veterinary-science#am2024Production Animal StudiesSDG-03:Good heatlh and well-bein

Complete genome sequence of mycoplasma pullorum isolated from domestic chickens

The 1,007,172-bp complete genome of Mycoplasma pullorum strain B359_6, isolated from domestic chickens, has been sequenced, assembled, and annotated.The Technology Innovation Agency (TIA) under the Tshwane Animal Health Innovation Cluster (TAHC) initiative, grant number TAHC12-00034. A.B. is funded by bursaries from the Health and Welfare Sector Education and Training Authority (HWSETA) and the University of Pretoria.http://genomea.asm.orgam2018Production Animal Studie

Complete genome sequence of a Newcastle disease genotype XIII virus isolated from indigenous chickens in Zambia

The first complete genome sequence of an African-origin Newcastle disease virus belonging to genotype XIII is described here. The virulent strain chicken/Zambia /Chiwoko/2015 was isolated from diseased chickens in 2015

Salmonella gallinarum strains from outbreaks of fowl typhoid fever in Southern Africa closely related to SG9R vaccines

IntroductionSalmonella enterica subspecies enterica serovar Gallinarum biovar Gallinarum (SG) is associated with fowl typhoid fever, and the attenuated rough strain SG9R is widely used as a vaccine in many regions. Reversion to virulence of vaccine strains was suspected as the cause during recent fowl typhoid fever outbreaks in poultry in South Africa and Eswatini.MethodsTo compare nine field isolates with global wild-type SG9 strains and the two commercial SG9R vaccines in use, Nobilis® SG9R and Cevac®-SG, we used whole-genome comparison with single-nucleotide polymorphism (SNP) detection.ResultsSNP phylogenic analysis showed that all the southern African field isolates were more closely related to the vaccine strains than wild-type SG9 strains. Furthermore, SNPs in the pyruvate dehydrogenase (aceE) and/or lipopolysaccharide 1,2-glucosyltransferase (rfaJ) genes, which are known markers of attenuation, were found in four of the field isolates along with intact spv, SPI-1, and SPI-2 gene clusters, providing conclusive evidence that these four isolates were originally vaccine strains that reverted to virulence. Five other field isolates lacked the SG9R attenuation markers, but variant analysis identified an SNP in the yihX gene, insertions in the ybjX and hydH genes, and deletions in the ftsK and sadA genes that were shared between the field isolates and vaccine strains but absent in wild-type SG9, indicating that these field isolates were also likely revertant vaccines.DiscussionOverall, this study highlights different mechanisms of reversion of two commercial vaccines, where virulence caused by field isolates closely related to the Nobilis® SG9R vaccine was associated with the restoration of intact virulence gene clusters, and those derived from the Cevac®-SG vaccine were characterized by point mutations resulting in restored aceE and rfaJ genes. A possible new marker of attenuation was identified as a point mutation in the yihX gene, as well as four new candidate genes that could potentially be used to distinguish current vaccine strains from wild-type strains using PCR assays

Coinfeccio´n entre el gyrovirus aviar 2 y el virus de la enfermedad de Newcastle avirulento en una parvada de pollo de engorde con signos neurolo´gicos y alta mortalidad

A disease with severe neurologic symptoms caused 100% mortality in a small broiler operation in the Gauteng Province, South Africa in late March 2013. Routine diagnostic PCR testing failed to identify a possible cause of the outbreak; thus, samples were submitted for virus isolation, serology, and bacteriology. An avirulent Newcastle disease virus (NDV) strain isolated was identified as a V4-like genotype 1 strain, by DNA sequencing, with a cleavage site of 112GKQGRQL117. Real-time reverse transcription PCR identified NDV in the brain but not in cecal tonsils or pooled tracheas, spleens, lungs, and livers. A random amplification deep sequencing of a transcriptome library generated from pooled tissues produced 927,966 paired-end reads. A contig of 2,309 nucleotides was identified as a near-complete avian gyrovirus 2 (AGV2) genome. This is the first report on the African continent of AGV2, which has been reported in southern Brazil, the Netherlands, and Hong Kong thus far. A real-time PCR for AGV2 only detected the virus in the brain but not in cecal tonsils or pooled tracheas, spleens, lungs, and livers. Sequence reads also mapped to the genomes of mycoplasma, Escherichia coli, avian leukosis virus subtype J, and Marek’s disease virus but excluded influenza A virus, Ornithobacterium rhinotracheale, avian rhinotracheitis virus, avian encephalomyelitis virus, and West Nile virus. Air sac swabs were positive on bacterial culture for E. coli. The possibility of a synergistic pathogenic effect between avirulent NDV and AGV2 requires further investigation.Una enfermedad con signos neurolo´gicos graves causo´ una mortalidad del 100 % en una operacio´n pequen˜a de pollos de engorde en la provincia de Gauteng, en Suda´frica a finales de marzo del 2013. Las pruebas rutinarias de diagno´stico por PCR no lograron identificar una posible causa del brote, por lo que las muestras fueron sometidas al aislamiento viral, serologı´a y bacteriologı´a. Se aislo´ e identifico´ un virus de la enfermedad de Newcastle no virulento (NDV) como una cepa similar al genotipo 1 V4, por secuenciacio´n de ADN, en el sitio de disociacio´n 112GKQGR Q L117. Mediante un me´todo de transcripcio´n reversa y PCR en tiempo real se identifico´ la presencia del virus de Newcastle en el cerebro, pero no en las tonsilas cecales o en las muestras agrupadas de tra´quea, bazo, pulmones, e hı´gado. Una amplificacio´n con secuenciacio´n profunda y aleatoria de una biblioteca de transcriptoma generada a partir de muestras agrupadas de tejidos produjo 927,966 lecturas emparejadas. Se identifico´ un contig de 2309 nucleo´tidos como un genoma casi completo de un Gyrovirus aviar 2 (AGV2). Este es el primer informe en el continente africano de la presencia del AGV2, que se ha reportado hasta el momento en el sur de Brasil, los Paı´ses Bajos y Hong Kong. Un me´todo de PCR en tiempo real para AGV2 so´lo detecto´ al virus en el cerebro, pero no se detecto´ en las tonsilas cecales, o en las muestras agrupadas de tra´quea, bazos, pulmones e hı´gado. Las lecturas de las secuencias tambie´n se relacionaron con el genoma de mycoplasma, Escherichia coli, con el virus de la leucosis aviar subtipo J, y con el virus de la enfermedad de Marek, pero excluyo´ al virus de la influenza A, Ornithobacterium rhinotracheale, al virus de la rinotraqueı´tis aviar, al virus de la encefalomielitis aviar y al virus del Nilo Occidental. Los hisopos de sacos ae´reos fueron positivos para el cultivo bacteriano de E. coli. La posibilidad de un efecto patoge´nico sine´rgico entre el virus de Newcastle avirulento y el AGV2 requiere de ma´s investigacio´n.http://www.aaapjournals.info/loi/avdiam2014ab201

Evolutionary consequences of a decade of vaccination against subtype H6N2 influenza

The evolutionary dynamics of chicken-origin H6N2 viruses isolated in South Africa between 2002 and 2013 were investigated. Sub-lineages I and II continued to co-circulate under vaccination pressure, but sublineage I, from which the inactivated vaccine was derived, displayed a markedly higher mutation rate and a three-fold increase in the emergence of potential antigenic sites on the globular head of HA compared to sub-lineage II. Immunological pressure culminated in a critical phenotypic change as four of the five isolates from 2012-2013 had lost the ability to haemagglutinate chicken erythrocytes, correlating with a pattern of predicted O-glycosylation sites at residues 134, 137 and 141 within the critical 130 loop of the receptor binding domain site. Coassortment of the HA, NA and M genes in the respective sub-lineages contrasted reassortment of the other internal protein genes, and the vaccine seed strain itself was the probable donor of segments to sub-lineage II field strains.Deltamune (Pty) Ltd, and an Incentive Funding for Rated Researchers grant from the National Research Foundation (C Abolnik). D. Rauff was supported by a grant from the Health and Welfare Sector Education and Training Authority (HWSETA).http://www.elsevier.com/locate/yviro2017-11-30hb2016Production Animal StudiesVeterinary Tropical Disease