Comparative genomic analysis reveals an ‘open’ pan‐genome of African swine fever virus

2020 ◽  
Vol 67 (4) ◽  
pp. 1553-1562 ◽  
Author(s):  
Liang Wang ◽  
Yuzi Luo ◽  
Yuhui Zhao ◽  
George F. Gao ◽  
Yuhai Bi ◽  
...  
Keyword(s):  
African Swine Fever Virus ◽  
Genomic Analysis ◽  
African Swine Fever ◽  
Comparative Genomic Analysis ◽  
Fever Virus ◽  
Comparative Genomic ◽  
Pan Genome

scholarly journals Complete genome analysis of African swine fever virus responsible for outbreaks in domestic pigs in 2018 in Burundi and 2019 in Malawi

2021 ◽  
Vol 53 (4) ◽  
Author(s):  
Jean N. Hakizimana ◽  
Jean B. Ntirandekura ◽  
Clara Yona ◽  
Lionel Nyabongo ◽  
Gladson Kamwendo ◽  
...  
Keyword(s):  
Complete Genome ◽  
African Swine Fever Virus ◽  
Gc Content ◽  
Genomic Analysis ◽  
African Swine Fever ◽  
Eastern Africa ◽  
Nucleotide Identity ◽  
Comparative Genomic ◽  
Genome Sequences ◽  
Domestic Pigs

AbstractSeveral African swine fever (ASF) outbreaks in domestic pigs have been reported in Burundi and Malawi and whole-genome sequences of circulating outbreak viruses in these countries are limited. In the present study, complete genome sequences of ASF viruses (ASFV) that caused the 2018 outbreak in Burundi (BUR/18/Rutana) and the 2019 outbreak in Malawi (MAL/19/Karonga) were produced using Illumina next-generation sequencing (NGS) platform and compared with other previously described ASFV complete genomes. The complete nucleotide sequences of BUR/18/Rutana and MAL/19/Karonga were 176,564 and 183,325 base pairs long with GC content of 38.62 and 38.48%, respectively. The MAL/19/Karonga virus had a total of 186 open reading frames (ORFs) while the BUR/18/Rutana strain had 151 ORFs. After comparative genomic analysis, the MAL/19/Karonga virus showed greater than 99% nucleotide identity with other complete nucleotides sequences of p72 genotype II viruses previously described in Tanzania, Europe and Asia including the Georgia 2007/1 isolate. The Burundian ASFV BUR/18/Rutana exhibited 98.95 to 99.34% nucleotide identity with genotype X ASFV previously described in Kenya and in Democratic Republic of the Congo (DRC). The serotyping results classified the BUR/18/Rutana and MAL/19/Karonga ASFV strains in serogroups 7 and 8, respectively. The results of this study provide insight into the genetic structure and antigenic diversity of ASFV strains circulating in Burundi and Malawi. This is important in order to understand the transmission dynamics and genetic evolution of ASFV in eastern Africa, with an ultimate goal of designing an efficient risk management strategy against ASF transboundary spread.

scholarly journals Pacmanvirus, a New Giant Icosahedral Virus at the Crossroads between Asfarviridae and Faustoviruses

2017 ◽  
Vol 91 (14) ◽  
Author(s):  
Julien Andreani ◽  
Jacques Yaacoub Bou Khalil ◽  
Madhumati Sevvana ◽  
Samia Benamar ◽  
Fabrizio Di Pinto ◽  
...  
Keyword(s):  
African Swine Fever Virus ◽  
Acanthamoeba Castellanii ◽  
Genomic Analysis ◽  
African Swine Fever ◽  
Fever Virus ◽  
Dna Virus ◽  
Dna Viruses ◽  
Content Type ◽  
Double Stranded Dna ◽  
Protein Locus

ABSTRACT African swine fever virus, a double-stranded DNA virus that infects pigs, is the only known member of the Asfarviridae family. Nevertheless, during our isolation and sequencing of the complete genome of faustovirus, followed by the description of kaumoebavirus, carried out over the past 2 years, we observed the emergence of previously unknown related viruses within this group of viruses. Here we describe the isolation of pacmanvirus, a fourth member in this group, which is capable of infecting Acanthamoeba castellanii. Pacmanvirus A23 has a linear compact genome of 395,405 bp, with a 33.62% G+C content. The pacmanvirus genome harbors 465 genes, with a high coding density. An analysis of reciprocal best hits shows that 31 genes are conserved between African swine fever virus, pacmanvirus, faustovirus, and kaumoebavirus. Moreover, the major capsid protein locus of pacmanvirus appears to be different from those of kaumoebavirus and faustovirus. Overall, comparative and genomic analyses reveal the emergence of a new group or cluster of viruses encompassing African swine fever virus, faustovirus, pacmanvirus, and kaumoebavirus. IMPORTANCE Pacmanvirus is a newly discovered icosahedral double-stranded DNA virus that was isolated from an environmental sample by amoeba coculture. We describe herein its structure and replicative cycle, along with genomic analysis and genomic comparisons with previously known viruses. This virus represents the third virus, after faustovirus and kaumoebavirus, that is most closely related to classical representatives of the Asfarviridae family. These results highlight the emergence of previously unknown double-stranded DNA viruses which delineate and extend the diversity of a group around the asfarvirus members.

scholarly journals Genomic analysis of Sardinian 26544/OG10 isolate of African swine fever virus

2016 ◽  
Vol 6 ◽  
pp. 81-89 ◽  
Author(s):  
Donatella Bacciu ◽  
Massimo Deligios ◽  
Giovanna Sanna ◽  
Maria Paola Madrau ◽  
Maria Luisa Sanna ◽  
...  
Keyword(s):  
African Swine Fever Virus ◽  
Genomic Analysis ◽  
African Swine Fever ◽  
Fever Virus

scholarly journals Comparative genomic analysis of Staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Xavier Argemi ◽  
Dorota Matelska ◽  
Krzysztof Ginalski ◽  
Philippe Riegel ◽  
Yves Hansmann ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Staphylococcus Lugdunensis ◽  
Pan Genome

scholarly journals Genomic Analysis of Highly Virulent Georgia 2007/1 Isolate of African Swine Fever Virus

2011 ◽  
Vol 17 (4) ◽  
pp. 599-605 ◽  
Author(s):  
David A.G. Chapman ◽  
Alistair C. Darby ◽  
Melissa Da Silva ◽  
Chris Upton ◽  
Alan D. Radford ◽  
...  
Keyword(s):  
African Swine Fever Virus ◽  
Genomic Analysis ◽  
African Swine Fever ◽  
Fever Virus ◽  
Highly Virulent

scholarly journals The Kaumoebavirus LCC10 Genome Reveals a Unique Gene Strand Bias among “Extended Asfarviridae”

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 148
Author(s):  
Khalil Geballa-Koukoulas ◽  
Julien Andreani ◽  
Bernard La Scola ◽  
Guillaume Blanc
Keyword(s):  
African Swine Fever Virus ◽  
Sequence Divergence ◽  
Genomic Analysis ◽  
African Swine Fever ◽  
Comparative Genomic ◽  
Type I ◽  
Strand Bias ◽  
Sequencing Data ◽  
Capsid Protein Gene ◽  
Distant Relative

Kaumoebavirus infects the amoeba Vermamoeba vermiformis and has recently been described as a distant relative of the African swine fever virus. To characterize the diversity and evolution of this novel viral genus, we report here on the isolation and genome sequencing of a second strain of Kaumoebavirus, namely LCC10. Detailed analysis of the sequencing data suggested that its 362-Kb genome is linear with covalently closed hairpin termini, so that DNA forms a single continuous polynucleotide chain. Comparative genomic analysis indicated that although the two sequenced Kaumoebavirus strains share extensive gene collinearity, 180 predicted genes were either gained or lost in only one genome. As already observed in another distant relative, i.e., Faustovirus, which infects the same host, the center and extremities of the Kaumoebavirus genome exhibited a higher rate of sequence divergence and the major capsid protein gene was colonized by type-I introns. A possible role of the Vermamoeba host in the genesis of these evolutionary traits is hypothesized. The Kaumoebavirus genome exhibited a significant gene strand bias over the two-third of genome length, a feature not seen in the other members of the “extended Asfarviridae” clade. We suggest that this gene strand bias was induced by a putative single origin of DNA replication located near the genome extremity that imparted a selective force favoring the genes positioned on the leading strand.

scholarly journals Comparative Genomics and CAZyme Genome Repertoires of Marine Zobellia amurskyensis KMM 3526T and Zobellia laminariae KMM 3676T

Marine Drugs ◽  
2019 ◽  
Vol 17 (12) ◽  
pp. 661 ◽  
Author(s):  
Nadezhda Chernysheva ◽  
Evgeniya Bystritskaya ◽  
Anna Stenkova ◽  
Ilya Golovkin ◽  
Olga Nedashkovskaya ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Core Genome ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Active Enzyme ◽  
Comparative Genomic ◽  
The Core ◽  
Pan Genome ◽  
Carbohydrate Active Enzyme ◽  
Pharmaceutical Industries

We obtained two novel draft genomes of type Zobellia strains with estimated genome sizes of 5.14 Mb for Z. amurskyensis KMM 3526Т and 5.16 Mb for Z. laminariae KMM 3676Т. Comparative genomic analysis has been carried out between obtained and known genomes of Zobellia representatives. The pan-genome of Zobellia genus is composed of 4853 orthologous clusters and the core genome was estimated at 2963 clusters. The genus CAZome was represented by 775 GHs classified into 62 families, 297 GTs of 16 families, 100 PLs of 13 families, 112 CEs of 13 families, 186 CBMs of 18 families and 42 AAs of six families. A closer inspection of the carbohydrate-active enzyme (CAZyme) genomic repertoires revealed members of new putative subfamilies of GH16 and GH117, which can be biotechnologically promising for production of oligosaccharides and rare monomers with different bioactivities. We analyzed AA3s, among them putative FAD-dependent glycoside oxidoreductases (FAD-GOs) being of particular interest as promising biocatalysts for glycoside deglycosylation in food and pharmaceutical industries.

scholarly journals Comparative genomic analysis of Mycobacterium tuberculosis reveals evolution and genomic instability within Uganda I sub-lineage

2020 ◽  
Author(s):  
Stephen Kanyerezi ◽  
Patricia Nabisubi
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Core Genome ◽  
Variant Calling ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Genome Wide Association ◽  
Comparative Genomic ◽  
Pan Genome ◽  
Genome Wide

AbstractIntroductionTuberculosis (TB) is the leading cause of morbidity and mortality globally, responsible for an estimated annual 10.0 million new cases and 1.3 million deaths among infectious diseases with Africa contributing a quarter of these cases in 2019. Classification of Mycobacterium tuberculosis (MTB) strains is important in understanding their geographical predominance and pathogenicity. Different studies have gone ahead to classify MTB using different methods. Some of these include; RFLP, spoligotyping, MIRU-VNTR and SNP set based phylogeny. The SNP set based classification has been found to be in concordance with the region of difference (RD) analysis of MTB complex classification system. In Uganda, the most common cause of pulmonary tuberculosis (PTB) is Uganda genotype of MTB and accounts for up to 70 % of isolates.MethodsSequenced MTB genome samples were retrieved from NCBI and others from local sequencing projects. The genomes were subjected to snippy (a rapid haploid variant calling and core genome alignment) to call variants and annotate them. Outputs from snippy were used to classify the isolates into Uganda genotypes and Non Ugandan genotypes based on 62 SNP set. The Ugandan genotype isolates were later subjected to 413 SNP set and then to a pan genome wide association analysis.Results6 Uganda genotype isolates were found not to classify as either Uganda I or II genotypes based on the 62 SNP set. Using the 413 SNP set, the 6 Uganda genotype isolates were found to have only one SNP out of the 7 SNPs that classify the Uganda I genotypes. They were also found to have both missense and frameshift mutations within the ctpH gene whereas the rest of Uganda I that had a mutation within this gene, was a missense.ConclusionAmong the Uganda genotypes genomes, Uganda I genomes are unstable. We used publicly available datasets to perform analysis like mapping, variant calling, mixed infection, pan-genome analysis to investigate and compare evolution of the Ugandan genotype.

scholarly journals Pan-Genomic Analysis of African Swine Fever Virus

2019 ◽  
Vol 35 (5) ◽  
pp. 662-665 ◽  
Author(s):  
Ziming Wang ◽  
Lijia Jia ◽  
Jing Li ◽  
Haizhou Liu ◽  
Di Liu
Keyword(s):  
African Swine Fever Virus ◽  
Genomic Analysis ◽  
African Swine Fever ◽  
Fever Virus
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