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 Genome Sequences of Five African Swine Fever Virus Genotype IX Isolates from Domestic Pigs in Uganda

2018 ◽  
Vol 7 (13) ◽  
Author(s):  
Charles Masembe ◽  
Vattipally B. Sreenu ◽  
Ana Da Silva Filipe ◽  
Gavin S. Wilkie ◽  
Peter Ogweng ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
Genome Sequences ◽  
Virus Genotype ◽  
Domestic Pigs ◽  
Genotype Ix ◽  
Virus Isolates

Complete genome sequences of five African swine fever virus isolates were determined directly from clinical material obtained from domestic pigs in Uganda. Four sequences were essentially identical to each other, and all were closely related to the only known genome sequence of p72 genotype IX.

scholarly journals The first genotype II African swine fever virus isolated in Africa provides insight into the current Eurasian pandemic

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Emma P. Njau ◽  
Jean-Baka Domelevo Entfellner ◽  
Eunice M. Machuka ◽  
Edwina N. Bochere ◽  
Sarah Cleaveland ◽  
...  
Keyword(s):  
Complete Genome ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Gene Families ◽  
Fever Virus ◽  
Eastern Africa ◽  
Chinese Isolate ◽  
Genome Sequences ◽  
Genotype I ◽  
Genotype Ii

AbstractAfrican swine fever (ASF) caused by the African swine fever virus (ASFV) is ranked by OIE as the most important source of mortality in domestic pigs globally and is indigenous to African wild suids and soft ticks. Despite two ASFV genotypes causing economically devastating epidemics outside the continent since 1961, there have been no genome-level analyses of virus evolution in Africa. The virus was recently transported from south-eastern Africa to Georgia in 2007 and has subsequently spread to Russia, eastern Europe, China, and south-east Asia with devastating socioeconomic consequences. To date, two of the 24 currently described ASFV genotypes defined by sequencing of the p72 gene, namely genotype I and II, have been reported outside Africa, with genotype II being responsible for the ongoing pig pandemic. Multiple complete genotype II genome sequences have been reported from European, Russian and Chinese virus isolates but no complete genome sequences have yet been reported from Africa. We report herein the complete genome of a Tanzanian genotype II isolate, Tanzania/Rukwa/2017/1, collected in 2017 and determined using an Illumina short read strategy. The Tanzania/Rukwa/2017/1 sequence is 183,186 bp in length (in a single contig) and contains 188 open reading frames. Considering only un-gapped sites in the pairwise alignments, the new sequence has 99.961% identity with the updated Georgia 2007/1 reference isolate (FR682468.2), 99.960% identity with Polish isolate Pol16_29413_o23 (MG939586) and 99.957% identity with Chinese isolate ASFV-wbBS01 (MK645909.1). This represents 73 single nucleotide polymorphisms (SNPs) relative to the Polish isolate and 78 SNPs with the Chinese genome. Phylogenetic analysis indicated that Tanzania/Rukwa/2017/1 clusters most closely with Georgia 2007/1. The majority of the differences between Tanzania/Rukwa/2017/1 and Georgia 2007/1 genotype II genomes are insertions/deletions (indels) as is typical for ASFV. The indels included differences in the length and copy number of the terminal multicopy gene families, MGF 360 and 110. The Rukwa2017/1 sequence is the first complete genotype II genome from a precisely mapped locality in Africa, since the exact origin of Georgia2007/1 is unknown. It therefore provides baseline information for future analyses of the diversity and phylogeography of this globally important genetic sub-group of ASF viruses.

scholarly journals Recombination Drives Emergence of Orf Virus Diversity: Evidence From the First Complete Genome of Indian Orf Virus and Comparative Genomic Analysis

2021 ◽  
Author(s):  
Debasis Nayak ◽  
Basanta Sahu ◽  
Prativa Majee ◽  
Ravi Singh ◽  
Niranjan Sahoo
Keyword(s):  
Complete Genome ◽  
Phylogenetic Trees ◽  
Small Ruminants ◽  
Gc Content ◽  
Genomic Analysis ◽  
Central India ◽  
Purifying Selection ◽  
Orf Virus ◽  
Comparative Genomic ◽  
Virus Diversity

Abstract Contagious pustular dermatitis is a disease that primarily infects small ruminants and has the zoonotic potential evoked by a Parapoxvirus, Orf virus (ORFV). This study evaluated an ORFV outbreak in goats that arose in Madhya Pradesh, a state of central India, during 2017 by constructing phylogenetic trees and unveiling its transboundary potential. Thereafter, the complete genome of an ORFV strain named Ind/MP has revealed the presence of 139,807bp nucleotide sequences, GC content 63.7%, 132 open reading frames (ORFs) circumscribed by inverted terminal repeats (ITRs) of 3,910bp. Evolutionary parameters such as selection pressure (θ=dN/dS), nucleotide diversity (π), etc., demonstrate the ORFV exhibit purifying selection. A total of forty recombination events were observed, out of which Ind/MP strains were engaged in twenty-one recombination events indicating this strain can recombine for the generation of new variants.

Comparative analysis of the complete genome sequences of Kenyan African swine fever virus isolates within p72 genotypes IX and X

Virus Genes ◽  
2015 ◽  
Vol 50 (2) ◽  
pp. 303-309 ◽  
Author(s):  
Richard P. Bishop ◽  
Clare Fleischauer ◽  
Etienne P. de Villiers ◽  
Edward A. Okoth ◽  
Marisa Arias ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Complete Genome ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
Genome Sequences ◽  
Virus Isolates

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.

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 Comparative genomic analysis of 142 bacteriophages infecting Salmonella enterica subsp. enterica

2019 ◽  
Author(s):  
Ruimin Gao ◽  
Sohail Naushad ◽  
Sylvain Moineau ◽  
Lawrence Goodridge ◽  
Dele Ogunremi
Keyword(s):  
Amino Acid ◽  
Salmonella Enterica ◽  
Rational Design ◽  
Gc Content ◽  
Amino Acid Sequences ◽  
Nucleotide Identity ◽  
Comparative Genomic ◽  
Genome Sequences ◽  
Multiple Sequence ◽  
Practical Applications

Abstract Background: Bacteriophages are bacterial parasites and are considered the most abundant and diverse biological entities on the planet. Previously we identified 154 prophages from 151 serovars of Salmonella enterica subsp. enterica . A detailed analysis of Salmonella prophage genomics is required given the influence of phages on their bacterial hosts and should provide a broader understanding of Salmonella biology and virulence and contribute to the practical applications of phages as vectors and antibacterial agents. Results: Comparative analysis of the full genome sequences of 142 prophages of Salmonella enterica subsp. enterica retrieved from public databases revealed an extensive variation in genome sizes (6.4- 358.7 kb) and guanine plus cytosine (GC) content (35.5-65.4%) and a linear correlation between the genome size and the number of open reading frames (ORFs). We used three approaches to compare the phage genomes. The NUCmer/MUMmer genome alignment tool was used to evaluate linkages and correlations based on nucleotide identity between genomes. Multiple sequence alignment was performed to calculate genome average nucleotide identity using the Kalgin program. Finally, genome synteny was explored using dot plot analysis. We found that 90 phage genome sequences grouped into 17 distinct clusters while the remaining 52 genomes showed no close relationships with the other phage genomes and are identified as singletons. We generated genome maps using nucleotide and amino acid sequences which allowed protein-coding genes to be sorted into phamilies (phams) using the Phamerator software. Out of 5796 total assigned phamilies, one phamily was observed to be dominant and was found in 49 prophages, or 34.5% of the 142 phages in our collection. A majority of the phamilies, 4330 out of 5796 (74.7%), occurred in just one prophage underscoring the high degree of diversity among Salmonella bacteriophages. Conclusions: Based on nucleotide and amino acid sequences, a high diversity was found among Salmonella bacteriophages which validate the use of prophage sequence analysis as a highly discriminatory subtyping tool for Salmonella. Thorough understanding of the conservation and variation of prophage genomic characteristics will facilitate their rational design and use as tools for bacterial strain construction, vector development and as anti-bacterial agents.

scholarly journals Comparative genomic analysis of 142 bacteriophages infecting Salmonella enterica subsp. enterica

2020 ◽  
Author(s):  
Ruimin Gao ◽  
Sohail Naushad ◽  
Sylvain Moineau ◽  
Roger Levesque ◽  
Lawrence Goodridge ◽  
...  
Keyword(s):  
Amino Acid ◽  
Salmonella Enterica ◽  
Rational Design ◽  
Gc Content ◽  
Amino Acid Sequences ◽  
Nucleotide Identity ◽  
Comparative Genomic ◽  
Genome Sequences ◽  
Multiple Sequence ◽  
Practical Applications

Abstract Background: Bacteriophages are bacterial parasites and are considered the most abundant and diverse biological entities on the planet. Previously we identified 154 prophages from 151 serovars of Salmonella enterica subsp. enterica . A detailed analysis of Salmonella prophage genomics is required given the influence of phages on their bacterial hosts and should provide a broader understanding of Salmonella biology and virulence and contribute to the practical applications of phages as vectors and antibacterial agents. Results: Comparative analysis of the full genome sequences of 142 prophages of Salmonella enterica subsp. enterica retrieved from public databases revealed an extensive variation in genome sizes (6.4- 358.7 kb) and guanine plus cytosine (GC) content (35.5-65.4%) and a linear correlation between the genome size and the number of open reading frames (ORFs). We used three approaches to compare the phage genomes. The NUCmer/MUMmer genome alignment tool was used to evaluate linkages and correlations based on nucleotide identity between genomes. Multiple sequence alignment was performed to calculate genome average nucleotide identity using the Kalgin program. Finally, genome synteny was explored using dot plot analysis. We found that 90 phage genome sequences grouped into 17 distinct clusters while the remaining 52 genomes showed no close relationships with the other phage genomes and are identified as singletons. We generated genome maps using nucleotide and amino acid sequences which allowed protein-coding genes to be sorted into phamilies (phams) using the Phamerator software. Out of 5796 total assigned phamilies, one phamily was observed to be dominant and was found in 49 prophages, or 34.5% of the 142 phages in our collection. A majority of the phamilies, 4330 out of 5796 (74.7%), occurred in just one prophage underscoring the high degree of diversity among Salmonella bacteriophages. Conclusions: Based on nucleotide and amino acid sequences, a high diversity was found among Salmonella bacteriophages which validate the use of prophage sequence analysis as a highly discriminatory subtyping tool for Salmonella. Thorough understanding of the conservation and variation of prophage genomic characteristics will facilitate their rational design and use as tools for bacterial strain construction, vector development and as anti-bacterial agents.

scholarly journals Complete Genome Sequences of Nine Enterovirus D68 Strains from Patients of the Lower Hudson Valley, New York, 2016

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Weihua Huang ◽  
Changhong Yin ◽  
Jian Zhuge ◽  
Taliya Farooq ◽  
Esther C. Yoon ◽  
...  
Keyword(s):  
New York ◽  
Complete Genome ◽  
Genomic Analysis ◽  
The United States ◽  
Comparative Genomic ◽  
Genome Sequences ◽  
Hudson Valley ◽  
Enterovirus D68 ◽  
Nucleotide Divergence ◽  
Generation Sequencing

Complete genome sequences of nine enterovirus D68 (EV-D68) strains from patients in New York were obtained in 2016 by metagenomic next-generation sequencing. Comparative genomic analysis suggests that a new subclade B3, with ~4.5% nucleotide divergence from subclade B1 strains causing the 2014 outbreak, is circulating in the United States in 2016.

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