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Whole-Genome Sequence and Assembly of Eight Africa Horse Sickness Virus Strains Collected in Namibia and South Africa.

ABSTRACT: In this report, we describe eight complete genome sequences of African horse sickness virus (AHSV) strains belonging to four different serotypes, namely, AHSV-5, AHSV-6, AHSV-8, and AHSV-9. Samples were collected in Namibia and South Africa from infected horses between 2000 and 2011. As expected, phylogenetic analyses of the variable outer capsid protein VP2 genomic sequences of AHSV-6 and AHSV-8 show higher nucleotide identity between the isolated viruses than that of the relevant reference strains. The full-genome sequence of AHSV will provide useful information on its geographical origin, and it will also be instrumental for comparing the distribution of the Namibian isolate with that of global isolates.

SUBMITTER: Serroni A

PROVIDER: S-EPMC10112199 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature

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Whole-Genome Sequence and Assembly of Eight Africa Horse Sickness Virus Strains Collected in Namibia and South Africa.

Serroni Anna A Traini Sara S Iorio Mariangela M Mangone Iolanda I Di Gialleonardo Luigina L Molini Umberto U Khaiseb Siegfried S Mercante Maria Teresa MT Di Ventura Mauro M Caporale Marco M

Microbiology resource announcements 20230315 4

In this report, we describe eight complete genome sequences of African horse sickness virus (AHSV) strains belonging to four different serotypes, namely, AHSV-5, AHSV-6, AHSV-8, and AHSV-9. Samples were collected in Namibia and South Africa from infected horses between 2000 and 2011. As expected, phylogenetic analyses of the variable outer capsid protein VP2 genomic sequences of AHSV-6 and AHSV-8 show higher nucleotide identity between the isolated viruses than that of the relevant reference str ...[more]

PMID: 36920210

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Project description:African horse sickness is a devastating, transboundary animal disease, that is 'listed' by the Office International des Epizooties (OIE). Although attenuated, inactivated and subunit vaccines have been developed for African horse sickness virus (AHSV), these are serotype-specific and their effective deployment therefore relies on rapid and reliable identification of virus type. AHSV serotype is controlled by the specificity of interactions between neutralising antibodies, and components of the outer-capsid, particularly protein VP2 (encoded by AHSV genome segment 2 (Seg-2)). We report the development and evaluation of novel gel based reverse transcription-PCR (RT-PCR) assays targeting AHSV Seg-2, which can be used to very significantly increase the speed and reliability of detection and identification (compared to virus neutralisation tests) of the nine serotypes of AHSV. Primer sets were designed targeting regions of Seg-2 that are conserved between strains within each of the AHSV serotype (types 1 to 9). These assays were evaluated using multiple AHSV strains from the orbivirus reference collection at IAH (www.reoviridae.org/dsRNA_virus_proteins/ReoID/AHSV-isolates.htm). In each case the Seg-2 primers showed a high level of specificity and failed to cross-amplify the most closely related heterologous AHSV types, or other related orbiviruses (such as bluetongue virus (BTV), or equine encephalosis virus (EEV)). The assays are rapid and sensitive, and can be used to detect and type viral RNA in blood, tissue samples, or cultivated viral suspensions within 24 h. They were used to identify AHSV strains from recent outbreaks in sub-Saharan African countries. These methods also generate cDNAs suitable for sequencing and phylogenetic analyses of Seg-2, identifying distinct virus lineages within each virus-type and helping to identify strain movements/origins. The RT-PCR methods described here provide a robust and versatile tool for rapid and specific detection and identification of AHSV serotypes 1 to 9.

Project description:Background. The bacterial foodborne pathogen Campylobacter jejuni is a common cause of acute gastroenteritis and is also associated with the postinfectious neuropathies, Guillain-Barré and Miller Fisher syndromes. This study described the use of multilocus sequence typing and DNA microarrays to examine the genetic content of a collection of South African C. jejuni strains, recovered from patients with enteritis, Guillain-Barré or Miller Fisher syndromes. Methodology/Principal Findings. The comparative genomic analysis by using multilocus sequence typing and DNA microarrays demonstrated that the South African strains with Penner heat-stable (HS) serotype HS:41 were clearly distinct from the other South African strains. Further analysis of the DNA microarray data demonstrated that the serotype HS:41 strains from South African GBS and enteritis patients are highly similar in gene content. Interestingly, the South African HS:41 strains were distinct in gene content when compared to serotype HS:41 strains from other geographical locations due to the presence of genomic islands, referred to as Campylobacter jejuni integrated elements. Only the genomic integrated element CJIE1, a Campylobacter Mu-like prophage, was present in the South African HS:41 strains whereas absent in the closely-related HS:41 strains from Mexico. A more distantly-related HS:41 strain from Canada possessed both genomic integrated elements CJIE1 and CJIE2. Conclusion/Significance. These findings demonstrated that these C. jejuni integrated elements may contribute to the differentiation of closely-related C. jejuni strains. In addition, the presence of bacteriophage-related genes in CJIE1 may probably contribute to increasing the genomic diversity of these C. jejuni strains. This comparative genomic analysis of the foodborne pathogen C. jejuni provides fundamental information that potentially could lead to improved methods for analyzing the epidemiology of disease outbreaks and their sources. Keywords: comparative genomic indexing analysis

Project description:BackgroundCulicoides biting midges exhibit a global spatial distribution and are the main vectors of several viruses of veterinary importance, including bluetongue (BT) and African horse sickness (AHS). Many environmental and anthropological factors contribute to their ability to live in a variety of habitats, which have the potential to change over the years as the climate changes. Therefore, as new habitats emerge, the risk for new introductions of these diseases of interest to occur increases. The aim of this study was to model distributions for two primary vectors for BT and AHS (Culicoides imicola and Culicoides bolitinos) using random forest (RF) machine learning and explore the relative importance of environmental and anthropological factors in a region of South Africa with frequent AHS and BT outbreaks.MethodsCulicoides capture data were collected between 1996 and 2022 across 171 different capture locations in the Western Cape. Predictor variables included climate-related variables (temperature, precipitation, humidity), environment-related variables (normalised difference vegetation index-NDVI, soil moisture) and farm-related variables (livestock densities). Random forest (RF) models were developed to explore the spatial distributions of C. imicola, C. bolitinos and a merged species map, where both competent vectors were combined. The maps were then compared to interpolation maps using the same capture data as well as historical locations of BT and AHS outbreaks.ResultsOverall, the RF models performed well with 75.02%, 61.6% and 74.01% variance explained for C. imicola, C. bolitinos and merged species models respectively. Cattle density was the most important predictor for C. imicola and water vapour pressure the most important for C. bolitinos. Compared to interpolation maps, the RF models had higher predictive power throughout most of the year when species were modelled individually; however, when merged, the interpolation maps performed better in all seasons except winter. Finally, midge densities did not show any conclusive correlation with BT or AHS outbreaks.ConclusionThis study yielded novel insight into the spatial abundance and drivers of abundance of competent vectors of BT and AHS. It also provided valuable data to inform mathematical models exploring disease outbreaks so that Culicoides-transmitted diseases in South Africa can be further analysed.

Project description:Background. The bacterial foodborne pathogen Campylobacter jejuni is a common cause of acute gastroenteritis and is also associated with the postinfectious neuropathies, Guillain-BarrÃ© and Miller Fisher syndromes. This study described the use of multilocus sequence typing and DNA microarrays to examine the genetic content of a collection of South African C. jejuni strains, recovered from patients with enteritis, Guillain-BarrÃ© or Miller Fisher syndromes. Methodology/Principal Findings. The comparative genomic analysis by using multilocus sequence typing and DNA microarrays demonstrated that the South African strains with Penner heat-stable (HS) serotype HS:41 were clearly distinct from the other South African strains. Further analysis of the DNA microarray data demonstrated that the serotype HS:41 strains from South African GBS and enteritis patients are highly similar in gene content. Interestingly, the South African HS:41 strains were distinct in gene content when compared to serotype HS:41 strains from other geographical locations due to the presence of genomic islands, referred to as Campylobacter jejuni integrated elements. Only the genomic integrated element CJIE1, a Campylobacter Mu-like prophage, was present in the South African HS:41 strains whereas absent in the closely-related HS:41 strains from Mexico. A more distantly-related HS:41 strain from Canada possessed both genomic integrated elements CJIE1 and CJIE2. Conclusion/Significance. These findings demonstrated that these C. jejuni integrated elements may contribute to the differentiation of closely-related C. jejuni strains. In addition, the presence of bacteriophage-related genes in CJIE1 may probably contribute to increasing the genomic diversity of these C. jejuni strains. This comparative genomic analysis of the foodborne pathogen C. jejuni provides fundamental information that potentially could lead to improved methods for analyzing the epidemiology of disease outbreaks and their sources. The genomic diversity of 33 South African, 2 Mexican and 1 Canadian Campylobacter jejuni strains from humans were examined by microarray-based comparative genomic indexing (CGI) analysis. The CGI analysis allowed the assessment of CDS content for each C. jejuni strain relative to the C. jejuni DNA microarray, which comprises ORFs from strains NCTC 11168, RM1221. ORFs were spotted in duplicate. Genomic DNA from strains NCTC 11168/RM1221 were used as a reference DNA and competitively hybridized with genomic DNA from each of the other C. jejuni strains. Two or three replicates for each strain were performed. Data normalization was performed as in Parker et al. J Clin Microbiol 2006, 44(11):4125-4135.

Dataset Information

Whole-Genome Sequence and Assembly of Eight Africa Horse Sickness Virus Strains Collected in Namibia and South Africa.

Publications

Whole-Genome Sequence and Assembly of Eight Africa Horse Sickness Virus Strains Collected in Namibia and South Africa.

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