Genome Sequencing of a Camelpox Vaccine Reveals Close Similarity to Modified Vaccinia virus Ankara (MVA)

Marcacci, Maurilia; Khalafalla, Abdelmalik I.; Hammadi, Zulaikha M. Al; Monaco, Federica; Cammà, Cesare; Yusof, Mohammed F.; Yammahi, Saeed M. Al; Mangone, Iolanda; Valleriani, Fabrizia; Alhosani, Mohamed A.; Decaro, Nicola; Lorusso, Alessio; Almuhairi, Salama S; Savini, Giovanni

doi:10.3390/v12080786

Cited by 5 publications

(6 citation statements)

References 25 publications

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“…Except for two con rmed genomic deletions, the whole genome sequence of this vaccine was shown to closely resemble that of VACV-MVA, supporting our earlier study in which we reported that two gene regions of this vaccine resembled the aforementioned strain [33]. Our ndings also corroborate with a previous study that used short read Illumina sequencing, and a reference guided assembly to generate a partial Ducapox genome, wherein the authors noted the putative deletions, but could con rm the validity of the deletions due to the both the assembly pipeline and sequencing technology used [34]. At 159,696 bp in length, the vaccine genome, to our knowledge, is the smallest amongst the non-vector derived orthopoxviruses.…”

Section: Discussionsupporting

confidence: 91%

“…The vaccine has since been found to contain two gene regions that more closely resembled that of VACV strain Modi ed Vaccinia Ankara (VACV-MVA) [33]. A separate study of the strain using second generation WGS found the vaccine genome matches that of VACV-MVA, with the exception of two genomic deletions (5195 and 890 bp in size), however, the authors questioned the authenticity of these genomic deletions due to both the reference-based assembly approach adopted, and the low sequencing coverage of the genome [34]. We present a sequencing and annotation pipeline for long read de novo assembly of Poxvirus genomes and identify putative epigenetic modi cations within the genome.…”

Section: Introductionmentioning

confidence: 99%

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Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides

Saud

Hitchings

Butt

2020

Preprint

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DNA viruses can exploit host cellular epigenetic processes to their advantage; however, the epigenome status of most DNA viruses remains undetermined. Third generation sequencing technologies allow for the identification of modified nucleotides from sequencing experiments without specialized sample preparation, permitting the detection of non-canonical epigenetic modifications that may distinguish viral nucleic acid from that of their host, thus identifying attractive targets for advanced therapeutics and diagnostics. We present a novel nanopore de novo assembly pipeline used to assemble a misidentified Camelpox vaccine. Two confirmed deletions of this vaccine strain in comparison to the closely related Vaccinia virus strain modified vaccinia Ankara make it one of the smallest non-vector derived orthopoxvirus genomes to be reported. Annotation of the assembly revealed a previously unreported signal peptide at the start of protein A38 and several signal peptides that were found to differ from those previously described. Putative epigenetic modifications around various motifs have been identified and the assembly confirmed previous work showing the vaccine genome to most closely resemble that of Vaccinia virus strain Modified Vaccinia Ankara. The pipeline may be used for other DNA viruses, increasing the understanding of DNA virus evolution, virulence, host preference, and epigenomics.

show abstract

Section: Discussionsupporting

confidence: 91%

Section: Introductionmentioning

confidence: 99%

Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides

Saud

Hitchings

Butt

2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Except for two confirmed genomic deletions, the whole genome sequence of this vaccine was shown to closely resemble that of VACV-MVA, supporting our earlier study in which we reported that two gene regions of this vaccine most closely resembled those of the aforementioned strain 34 . Our findings also corroborate with a previous study that used short read Illumina sequencing, and a reference guided assembly to generate a partial Ducapox genome, wherein the authors noted the putative deletions, but could not confirm the validity of the deletions due to the both the assembly pipeline and sequencing technology used 35 . At 159,695 bp in length, the vaccine genome, to our knowledge, is the smallest amongst the non-vector derived orthopoxviruses.…”

Section: Discussionsupporting

confidence: 78%

“…The vaccine has since been found to contain two gene regions that more closely resembled that of VACV strain Modified Vaccinia Ankara (VACV-MVA) 34 . A separate study of the strain using second generation WGS found the vaccine genome matches that of VACV-MVA, with the exception of two genomic deletions (5195 and 890 bp in size), however, the authors questioned the authenticity of these genomic deletions due to both the reference-based assembly approach adopted, and the low sequencing coverage of the genome 35 . We present a sequencing and annotation pipeline for long read de novo assembly of Poxvirus genomes and identify putative epigenetic modifications within the genome.…”

Section: Introductionmentioning

confidence: 99%

Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides

Saud

Hitchings

Butt

2021

Sci Rep

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DNA viruses can exploit host cellular epigenetic processes to their advantage; however, the epigenome status of most DNA viruses remains undetermined. Third generation sequencing technologies allow for the identification of modified nucleotides from sequencing experiments without specialized sample preparation, permitting the detection of non-canonical epigenetic modifications that may distinguish viral nucleic acid from that of their host, thus identifying attractive targets for advanced therapeutics and diagnostics. We present a novel nanopore de novo assembly pipeline used to assemble a misidentified Camelpox vaccine. Two confirmed deletions of this vaccine strain in comparison to the closely related Vaccinia virus strain modified vaccinia Ankara make it one of the smallest non-vector derived orthopoxvirus genomes to be reported. Annotation of the assembly revealed a previously unreported signal peptide at the start of protein A38 and several predicted signal peptides that were found to differ from those previously described. Putative epigenetic modifications around various motifs have been identified and the assembly confirmed previous work showing the vaccine genome to most closely resemble that of Vaccinia virus strain Modified Vaccinia Ankara. The pipeline may be used for other DNA viruses, increasing the understanding of DNA virus evolution, virulence, host preference, and epigenomics.

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“…Camel pox has been reported in all other countries where camel farming takes place. Symptoms of camel pox include the development of fever accompanied by lesions in the form of rash both on the skin and mucous membranes in the respiratory organs and oral cavity of animals ( Marcacci et al , 2020 ). Depending on the severity of the disease, clinical signs of the CMLV include manifestations of different levels of systemic infection, ranging from mild to severe ( Saud et al , 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Characterization of the camel pox virus strain used in producing camel pox virus vaccine

Maikhin,

Berdikulov,

Abishov

et al. 2023

Open Vet J

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Background: The camel pox virus is a widespread infectious viral disease of camels. It is necessary to conduct research on new strains for the development of vaccines. Aim: The research aims to characterize a novel strain isolated from the camel pox virus used to produce a camel pox virus vaccine. Methods: The objects of the study were the “M-0001” strain isolated from a sample of animals infected with the camel pox virus during the epidemic. The cultural and reproductive properties of the virus isolate were studied using primary cell lines from primary trypsinized lamb kidney and testicular cell cultures (LK and LT). Other samples included kidney cell lines from transplanted sheep) as well as a kidney cell line from transplanted cattle, Vero (transplanted green monkey kidney cell line), and calf trachea. The strain was PCR-tested and sequenced for characterization purposes. Results: The PCR results show that the study sample is species specific and corresponds to the camel pox virus by the size of the cumulative amplifications, which is 241 bp. Given the maximum percentage of a sequence match analyzed by the BLAST algorithm based on the international database and the results of phylogenetic analysis, the M0001 sample was determined to belong to the Camel pox virus (gene bank inventory number KP768318.1). Conclusion: The sample “M0001” is located on the same branch with a representative from CMLV (Camel pox virus). Among the cell cultures tested, the LK and LT cell lines were the most sensitive to the isolated CMLV isolate. Reproducing the virus in these cell cultures remains stable even after 15 consecutive passes. The cytopathic effect of the virus was less pronounced and low in transplanted cell lines, and the cytopathic effect was no longer apparent in the third passage. A genome alignment of the virus has identified potentially conserved sites, and analysis of loci in different virus types revealed one maximally conserved locus. An epizootic strain of the camelina virus “M-0001” candidate to produce vaccines for the camels was obtained. An experimental vaccine sample based on an isolated and charred camellia virus will be created in the future.

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Genome Sequencing of a Camelpox Vaccine Reveals Close Similarity to Modified Vaccinia virus Ankara (MVA)

Cited by 5 publications

References 25 publications

Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides

Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides

Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides

Characterization of the camel pox virus strain used in producing camel pox virus vaccine

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