Base-By-Base Version 3: New Comparative Tools for Large Virus Genomes

Tu, Shin Lin; Staheli, Jeannette P.; McClay, Colum; McLeod, Kathleen; Rose, Timothy M.; Upton, Chris

doi:10.3390/v10110637

Cited by 23 publications

(18 citation statements)

References 23 publications

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“…The causative agent, ASF virus (ASFV), is a large enveloped virus containing a double-stranded (ds) DNA genome of approximately 190 kilobase pairs. ASFV shares aspects of genome structure and replication strategy with other large dsDNA viruses, including the Poxviridae, Iridoviridae, and Phycodnaviridae [1]. ASF causes a spectrum of disease that ranges from highly lethal to subclinical, depending on host characteristics and the virulence of circulating virus strains [2].…”

Section: Introductionmentioning

confidence: 99%

Differential Effect of the Deletion of African Swine Fever Virus Virulence-Associated Genes in the Induction of Attenuation of the Highly Virulent Georgia Strain

Ramírez-Medina

Vuono

O’Donnell

et al. 2019

Viruses

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African swine fever virus (ASFV) is the etiological agent of an often lethal disease of domestic pigs, African swine fever (ASF). The ASFV Georgia 2007 isolate (ASFV-G) is responsible for the current epidemic situation in Europe and Asia. Genetically modified ASFVs containing deletions of virulence-associated genes have produced attenuated phenotypes and induced protective immunity in swine. Here we describe the differential behavior of two viral genes, NL (DP71L) and UK (DP96R), both originally described as being involved in virus virulence. Deletion of either of these genes efficiently attenuated ASFV strain E70. We demonstrated that deletion of the UK gene from the ASFV-G genome did not decrease virulence when compared to the parental virus. Conversely, deletion of the NL gene produced a heterogeneous response, with early death in one of the animals and transient fever in the other animals. With this knowledge, we attempted to increase the safety profile of the previously reported experimental vaccine ASFV-GΔ9GL/ΔUK by deleting the NL gene. A triple gene-deletion virus was produced, ASFV-GΔ9GL/ΔNL/ΔUK. Although ASFV-GΔ9GL/ΔNL/ΔUK replicated in primary cell cultures of swine macrophages, it demonstrated a severe replication deficiency in pigs, failing to induce protection against challenge with parental ASFV-G.

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Section: Introductionmentioning

confidence: 99%

Differential Effect of the Deletion of African Swine Fever Virus Virulence-Associated Genes in the Induction of Attenuation of the Highly Virulent Georgia Strain

Ramírez-Medina

Vuono

O’Donnell

et al. 2019

Viruses

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“…By scanning for blocks of unusually lowered percent amino acid identities (red highlighting in Table S1), we discovered regions with unusually high single nucleotide polymorphism (SNP) density. Therefore, the distribution of SNPs among the genomes was examined in greater detail using the Base-By-Base sequence editor (BBB) (17). Figure 4 displays a number of sequence blocks that clearly have more SNPs than the general overall density found when AKMV-VANI10 is compared to both subclades of the AKMV genomes.…”

Section: Resultsmentioning

confidence: 99%

Isolation and Characterization of Akhmeta Virus from Wild-Caught Rodents ( Apodemus spp.) in Georgia

Doty

Maghlakelidze

Sikharulidze

et al. 2019

J Virol

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Akhmeta virus is a unique Orthopoxvirus that was described in 2013 from the country of Georgia. This paper presents the first isolation of this virus from small mammal (Rodentia; Apodemus spp.) samples and the molecular characterization of those isolates. The identification of the virus in small mammals is an essential component to understanding the natural history of this virus and its transmission to human populations and could guide public health interventions in Georgia. Akhmeta virus genomes harbor evidence suggestive of recombination with a variety of other orthopoxviruses; this has implications for the evolution of orthopoxviruses, their ability to infect mammalian hosts, and their ability to adapt to novel host species.

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“…For identifying SNPs, we used a combination of the MismatchTable function from Biostrings and the BasebyBase tool from the Viral Bioinformatics Research Centre [11]. We used the results from both the tools in our subsequent comparisons.…”

Section: Methodsmentioning

confidence: 99%

Genome Analysis of SARS-CoV-2 Isolate from Bangladesh

Hasan

Khan

Ahsan

et al. 2020

Preprint

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Recently the first genome sequence for a Severe acute respiratory syndrome coronavirus 2 or SARS-CoV-2 isolate from Bangladesh became available. The sequencing was carried out by the Child Health Research Foundation and provided the first insight into the genetic details of the viral strain responsible for the SARS-CoV-2 infections in Bangladesh. Here we carried out a comparative study were we explored the phylogenetic relationship between the Bangladeshi isolate with other isolates from different parts of the world. Afterwards we identified single nucleotide variants in the Bangladeshi isolate, using the Wuhan virus reference sequence. We found a total of 9 variants in the Bangladeshi isolate using 2 separate tools. Barring 2, the rest of these variants were also observed in other isolates from different countries. Most of the variants occurred in the ORF1ab gen. Another noteworthy finding was a sequence of three consecutive variants in the N protein gene that were observed in other isolates as well. Lastly the phylogenetic analysis revealed a close relationship between the Bangladeshi isolate and those from Taiwan,

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Base-By-Base Version 3: New Comparative Tools for Large Virus Genomes

Cited by 23 publications

References 23 publications

Differential Effect of the Deletion of African Swine Fever Virus Virulence-Associated Genes in the Induction of Attenuation of the Highly Virulent Georgia Strain

Differential Effect of the Deletion of African Swine Fever Virus Virulence-Associated Genes in the Induction of Attenuation of the Highly Virulent Georgia Strain

Isolation and Characterization of Akhmeta Virus from Wild-Caught Rodents ( Apodemus spp.) in Georgia

Genome Analysis of SARS-CoV-2 Isolate from Bangladesh

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