Multi-locus sequence typing of African swine fever viruses from endemic regions of Kenya and Eastern Uganda (2011–2013) reveals rapid B602L central variable region evolution

Onzere, Cynthia; Bastos, Armanda D.S.; Okoth, Edward; Lichoti, Jacqueline Kasiiti; Bochere, Edwina N.; Owido, Milton; Ndambuki, Gideon; Bronsvoort, Mark; Bishop, Richard P.

doi:10.1007/s11262-017-1521-4

Cited by 36 publications

(35 citation statements)

References 24 publications

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“…Similar to our findings, asymptomatic pigs in Uganda and on the Kenya–Uganda border also carried genotype IX viruses (Abworo et al, ; Atuhaire et al, ). The discovery of ASFV genotype IX virus in asymptomatic pigs is surprising, as ASFV genotype IX isolates are usually highly virulent (Gallardo et al, ; Masembe et al, ; Onzere et al, ). The reasons for the apparent resistance of some pigs to potentially virulent isolates of ASFV are still unclear.…”

Section: Discussionmentioning

confidence: 99%

Symptomatic and asymptomatic cases of African swine fever in Tanzania

Chang’a¹,

Mayenga²,

Settypalli

et al. 2019

Transbound Emerg Dis

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African swine fever (ASF) is an acute, highly contagious and deadly viral haemorrhagic disease of domestic pigs caused by African swine fever virus (ASFV). In ASF endemic countries, there are an increasing number of reports on circulating ASFV strains with different levels of virulence causing a broad range of clinical symptoms in susceptible animals. Tanzania, where ASFV is endemic since 2001, recorded several outbreaks including symptomatic and asymptomatic cases between 2015 and 2017. We collected 35 clinical samples from four outbreaks for diagnostic confirmation and sequenced the partial B646L (p72), the full E183L (p54) gene, the central variable region of the B602L gene and the intergenic region between the I73R and I329L genes to characterize molecularly the new ASFV isolates and analyse their relatedness with previously reported Tanzanian and foreign isolates. We detected ASFV in 21 samples, 15 from symptomatic and six from asymptomatic pigs. Phylogenetic analyses based on the partial p72 gene and the complete p54 (E183L) genes revealed that the ASFVs in samples from symptomatic pigs belonged to genotypes II and those in samples from asymptomatic pigs belonged to genotype IX. The CVR profiles of the p72 genotype II and genotype IX isolates differed between each other and from previously published Tanzanian sequences. The sequence analysis of the intergenic region between the I73R and I329L for the 2017 genotype II isolates showed the absence of one GGAATATATA motif in those isolates. This study showed the simultaneous circulation of two different ASFV genotypes with different levels of pathogenicity in Tanzania. Since the existence of sub‐clinically infected pigs may contribute to the persistence of the virus, our findings suggest continuous surveillance and characterization of ASFV isolates in disease‐endemic regions.

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Section: Discussionmentioning

confidence: 99%

Symptomatic and asymptomatic cases of African swine fever in Tanzania

Chang’a¹,

Mayenga²,

Settypalli

et al. 2019

Transbound Emerg Dis

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“…An insertion observed at the I73R / I329L TRS marker also confirmed allele variation in Russia or elsewhere in the Caucasus prior to the detection of the virus in Baltic countries [7, 8]. While existing ASFV marker-based assays provide genetic discrimination among isolates, higher-resolution genomic comparisons may facilitate more robust epidemiological tracing [18]. Lack of whole genome data for both closely related endemic strains as well as those generated during intra-epidemic transmission remain unavailable.…”

Section: Introductionmentioning

confidence: 99%

Intra-epidemic genome variation in highly pathogenic African swine fever virus (ASFV) from the country of Georgia

Farlow

Donduashvili²,

Kokhreidze³

et al. 2018

Virol J

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BackgroundAfrican swine fever virus (ASFV) causes an acute hemorrhagic infection in suids with a mortality rate of up to 100%. No vaccine is available and the potential for catastrophic disease in Europe remains elevated due to the ongoing ASF epidemic in Russia and Baltic countries. To date, intra-epidemic whole-genome variation for ASFV has not been reported. To provide a more comprehensive baseline for genetic variation early in the ASF outbreak, we sequenced two Georgian ASFV samples, G-2008/1 and G-2008/2, derived from domestic porcine blood collected in 2008.MethodsGenomic DNA was extracted directly from low-volume ASFV PCR-positive porcine blood samples and subjected to next generation sequencing on the Illumina Miseq platform. De novo and mapped sequence assemblies were performed using CLCBio software. Genomic illustrations, sequence alignments and assembly figures were generated using Geneious v10.2.4. Sequence repeat architecture was analyzed using DNASTAR GeneQuest 14.1.0.ResultsThe G-2008/1 and G-2008/2 genomes were distinguished from each other by coding changes in seven genes, including MGF 110-1 L, X69R, MGF 505-10R, EP364R, H233R, E199L, and MGF 360-21R in addition to eight homopolymer tract variations. The 2008/2 genome possessed a novel allele state at a previously undescribed intergenic repeat locus between genes C315R and C147L. The C315R/C147L locus represents the earliest observed variable repeat sequence polymorphism reported among isolates from this epidemic. No sequence variation was observed in conventional ASFV subtyping markers. The two genomes exhibited complete collinearity and identical gene content with the Georgia 2007/1 reference genome. Approximately 56 unique homopolymer A/T-tract variations were identified that were unique to the Georgia 2007/1 genome. In both 2008 genomes, within-sample sequence read heterogeneity was evident at six homopolymeric G/C-tracts confined to the known hypervariable ~ 7 kb region in the left terminal region of the genome.ConclusionsThis is the first intra-epidemic comparative genomic analysis reported for ASFV and provides insight into the intra-epidemic microevolution of ASFV. The genomes reported here, in addition to the G-2007/1 genome, provide an early baseline for future genome-level comparisons and epidemiological tracing efforts.Electronic supplementary materialThe online version of this article (10.1186/s12985-018-1099-z) contains supplementary material, which is available to authorized users.

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“…The virus was isolated from O. porcinus ticks from Kenya on swine peripheral blood mononuclear cells (PBMCs), passaged twice and titrated on PBMCs as described elsewhere [52]. By sequencing the p72, B602L and p54 genes, we compared 'ASFV ken.rie1' to known ASFV isolates from GenBank and grouped it into p72 genotype X, which is known to circulate in East Africa between ticks and indigenous pigs [53]. 'ASFV-Sardinia' and 'ASFV ken06.bus' (originally received from the European reference laboratory for ASFV (CISA-INIA)) were stored at the German National Reference Laboratory for ASFV as reference material.…”

Section: Virus Strainsmentioning

confidence: 99%

Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution

Forth

Lycett

et al. 2020

BMC Biol

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Background African swine fever virus (ASFV) is a most devastating pathogen affecting swine. In 2007, ASFV was introduced into Eastern Europe where it continuously circulates and recently reached Western Europe and Asia, leading to a socio-economic crisis of global proportion. In Africa, where ASFV was first described in 1921, it is transmitted between warthogs and soft ticks of the genus Ornithodoros in a so-called sylvatic cycle. However, analyses into this virus’ evolution are aggravated by the absence of any closely related viruses. Even ancient endogenous viral elements, viral sequences integrated into a host’s genome many thousand years ago that have proven extremely valuable to analyse virus evolution, remain to be identified. Therefore, the evolution of ASFV, the only known DNA virus transmitted by arthropods, remains a mystery. Results For the identification of ASFV-like sequences, we sequenced DNA from different recent Ornithodoros tick species, e.g. O. moubata and O. porcinus, O. moubata tick cells and also 100-year-old O. moubata and O. porcinus ticks using high-throughput sequencing. We used BLAST analyses for the identification of ASFV-like sequences and further analysed the data through phylogenetic reconstruction and molecular clock analyses. In addition, we performed tick infection experiments as well as additional small RNA sequencing of O. moubata and O. porcinus soft ticks. Conclusion Here, we show that soft ticks of the Ornithodoros moubata group, the natural arthropod vector of ASFV, harbour African swine fever virus-like integrated (ASFLI) elements corresponding to up to 10% (over 20 kb) of the ASFV genome. Through orthologous dating and molecular clock analyses, we provide data suggesting that integration could have occurred over 1.47 million years ago. Furthermore, we provide data showing ASFLI-element specific siRNA and piRNA in ticks and tick cells allowing for speculations on a possible role of ASFLI-elements in RNA interference-based protection against ASFV in ticks. We suggest that these elements, shaped through many years of co-evolution, could be part of an evolutionary virus-vector ‘arms race’, a finding that has not only high impact on our understanding of the co-evolution of viruses with their hosts but also provides a glimpse into the evolution of ASFV.

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Multi-locus sequence typing of African swine fever viruses from endemic regions of Kenya and Eastern Uganda (2011–2013) reveals rapid B602L central variable region evolution

Cited by 36 publications

References 24 publications

Symptomatic and asymptomatic cases of African swine fever in Tanzania

Symptomatic and asymptomatic cases of African swine fever in Tanzania

Intra-epidemic genome variation in highly pathogenic African swine fever virus (ASFV) from the country of Georgia

Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution

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