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 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.

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 Evolutionary Analysis of Plastid Genomes of Seven Lonicera L. Species: Implications for Sequence Divergence and Phylogenetic Relationships

2018 ◽  
Vol 19 (12) ◽  
pp. 4039 ◽  
Author(s):  
Mi-Li Liu ◽  
Wei-Bing Fan ◽  
Ning Wang ◽  
Peng-Bin Dong ◽  
Ting-Ting Zhang ◽  
...  
Keyword(s):  
Molecular Genetic ◽  
Phylogenetic Reconstruction ◽  
Sequence Divergence ◽  
Genomic Analysis ◽  
Repeat Sequence ◽  
Biological Research ◽  
Comparative Genomic ◽  
Sequence Evolution ◽  
Evolutionary Analysis ◽  
Plastid Genomes

Plant plastomes play crucial roles in species evolution and phylogenetic reconstruction studies due to being maternally inherited and due to the moderate evolutionary rate of genomes. However, patterns of sequence divergence and molecular evolution of the plastid genomes in the horticulturally- and economically-important Lonicera L. species are poorly understood. In this study, we collected the complete plastomes of seven Lonicera species and determined the various repeat sequence variations and protein sequence evolution by comparative genomic analysis. A total of 498 repeats were identified in plastid genomes, which included tandem (130), dispersed (277), and palindromic (91) types of repeat variations. Simple sequence repeat (SSR) elements analysis indicated the enriched SSRs in seven genomes to be mononucleotides, followed by tetra-nucleotides, dinucleotides, tri-nucleotides, hex-nucleotides, and penta-nucleotides. We identified 18 divergence hotspot regions (rps15, rps16, rps18, rpl23, psaJ, infA, ycf1, trnN-GUU-ndhF, rpoC2-rpoC1, rbcL-psaI, trnI-CAU-ycf2, psbZ-trnG-UCC, trnK-UUU-rps16, infA-rps8, rpl14-rpl16, trnV-GAC-rrn16, trnL-UAA intron, and rps12-clpP) that could be used as the potential molecular genetic markers for the further study of population genetics and phylogenetic evolution of Lonicera species. We found that a large number of repeat sequences were distributed in the divergence hotspots of plastid genomes. Interestingly, 16 genes were determined under positive selection, which included four genes for the subunits of ribosome proteins (rps7, rpl2, rpl16, and rpl22), three genes for the subunits of photosystem proteins (psaJ, psbC, and ycf4), three NADH oxidoreductase genes (ndhB, ndhH, and ndhK), two subunits of ATP genes (atpA and atpB), and four other genes (infA, rbcL, ycf1, and ycf2). Phylogenetic analysis based on the whole plastome demonstrated that the seven Lonicera species form a highly-supported monophyletic clade. The availability of these plastid genomes provides important genetic information for further species identification and biological research on Lonicera.

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 Predicting Insect Invasiveness With Whole-genome Sequencing Data

2020 ◽  
Author(s):  
Cong Huang ◽  
Nianwan Yang ◽  
Shuping Wang ◽  
Xiaodan Fan ◽  
Cong Pian ◽  
...  
Keyword(s):  
Insect Pest ◽  
Genomic Analysis ◽  
Gene Families ◽  
Insect Species ◽  
Whole Genome Sequencing Data ◽  
Comparative Genomic ◽  
Nucleic Acid Metabolism ◽  
Sequencing Data ◽  
Invasive Insects ◽  
Invasive Insect

Abstract Background Invasive alien insects threaten agriculture, biodiversity, and human livelihoods globally. Unfortunately, insect invasiveness still cannot be reliably predicted. Empirical policies of insect pest quarantine and inspection are mainly designed against species that are already problematic. Results We conducted a comparative genomic analysis of 37 invasive insect species and six non-invasive insect species, showing that the gene families associated with defense, protein and nucleic acid metabolism, chemosensory function, and transcriptional regulation were significantly expanded in invasive insects, suggesting that enhanced abilities in self-protection, nutrition exploitation, and locating food or mates are intrinsic features conferring invasiveness in insects. By using these intrinsic genome features, we proposed an invasiveness index and estimated the invasiveness of 99 other insect species with genome data, classifying them as highly, moderately, or minimally invasive. Insects possessing all these aforementioned enhanced abilities are predicted to be highly invasive, and vice versa. Next, a logistic-regression classifier was trained to predict insect invasiveness, achieving 93.2% accuracy. Conclusions We present evidence that several traits may confer invasiveness in insects and these features can be used to predict insect invasiveness accurately, and we quantify insect invasiveness with an invasiveness index.

scholarly journals Organization of the multigene families of African Swine Fever Virus

Fine Focus ◽  
2017 ◽  
Vol 3 (2) ◽  
pp. 155-170 ◽  
Author(s):  
Jacob Imbery ◽  
Chris Upton
Keyword(s):  
African Swine Fever Virus ◽  
Sequence Divergence ◽  
African Swine Fever ◽  
Fever Virus ◽  
Multigene Families ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Viral Genomes ◽  
Gene Maps

African swine fever virus is a complex DNA virus that infects swine and is spread by ticks. Mortality rates in domestic pigs are very high and the virus is a significant threat to pork farming. The genomes of 16 viruses have been sequenced completely, but these represent only a few of the 23 genotypes. The viral genome is unusual in that it contains 5 multigene families, each of which contain 3-19 duplicated copies (paralogs). There is significant sequence divergence between the paralogs in a single virus and between the orthologs in the different viral genomes. This, together with the fact that in most of the multigene families there are numerous gene indels that create truncations and fusions, makes annotation of these regions very difficult; it has led to inconsistent annotation of the 16 viral genomes. In this project, we have created multiple sequence alignments for each of the multigene families and have produced gene maps to help researchers more easily understand the organization of the multigene families among the different viruses. These gene maps will help researchers ascertain which members of the multigene families are present in each of the viruses. This is critical because some of the multigene families are known to be associated with virus virulence.

scholarly journals Deletion of the Gene for the Type I Interferon Inhibitor I329L from the Attenuated African Swine Fever Virus OURT88/3 Strain Reduces Protection Induced in Pigs

Vaccines ◽  
2020 ◽  
Vol 8 (2) ◽  
pp. 262 ◽  
Author(s):  
Ana Luisa Reis ◽  
Lynnette C. Goatley ◽  
Tamara Jabbar ◽  
Elisabeth Lopez ◽  
Anusyah Rathakrishnan ◽  
...  
Keyword(s):  
Type I Interferon ◽  
African Swine Fever Virus ◽  
Clinical Signs ◽  
African Swine Fever ◽  
Type I ◽  
Lethal Challenge ◽  
Host Innate Immune Response ◽  
Antibody Levels

Live attenuated vaccines are considered to be the fastest route to the development of a safe and efficacious African swine fever (ASF) vaccine. Infection with the naturally attenuated OURT88/3 strain induces protection against challenge with virulent isolates from the same or closely related genotypes. However, adverse clinical signs following immunisation have been observed. Here, we attempted to increase the OURT88/3 safety profile by deleting I329L, a gene previously shown to inhibit the host innate immune response. The resulting virus, OURT88/3ΔI329L, was tested in vitro to evaluate the replication and expression of type I interferon (IFN) and in vivo by immunisation and lethal challenge experiments in pigs. No differences were observed regarding replication; however, increased amounts of both IFN-β and IFN-α were observed in macrophages infected with the deletion mutant virus. Unexpectedly, the deletion of I329L markedly reduced protection against challenge with the virulent OURT88/1 isolate. This was associated with a decrease in both antibody levels against VP72 and the number of IFN-γ-producing cells in the blood of non-protected animals. Furthermore, a significant increase in IL-10 levels in serum was observed in pigs immunised with OURT88/3ΔI329L following challenge. Interestingly, the deletion of the I329L gene failed to attenuate the virulent Georgia/2007 isolate.

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