Complete Genome Sequencing, Annotation, and Mutational Profiling of the Novel Clade I Human Mpox Virus, Kamituga Strain
Introduction: Human Mpox (formerly monkeypox) infection is an emerging zoonotic disease caused by the Mpox virus (MPXV). We describe the complete genome annotation, phylogeny, and mutational profile of a novel, sustained Clade I Mpox outbreak in the city of Kamituga in Eastern Democratic Republic o...
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The Journal of Infection in Developing Countries
2024-04-01
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| Series: | Journal of Infection in Developing Countries |
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| Online Access: | https://jidc.org/index.php/journal/article/view/20136 |
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| author | Leandre Murhula Masirika Anuj Kumar Mansi Dutt Ali Toloue Ostadgavahi Benjamin Hewins Maliyamungu Bubala Nadine Bilembo Kitwanda Steeven Franklin Kumbana Mweshi Léandre Mutimbwa Mambo Justin Bengehya Mbiribindi Freddy Belesi Siangoli Alyson A Kelvin Jean Claude Udahemuka Patricia Kelvin Luis Flores David J Kelvin Gustavo Sganzerla Martinez |
| author_facet | Leandre Murhula Masirika Anuj Kumar Mansi Dutt Ali Toloue Ostadgavahi Benjamin Hewins Maliyamungu Bubala Nadine Bilembo Kitwanda Steeven Franklin Kumbana Mweshi Léandre Mutimbwa Mambo Justin Bengehya Mbiribindi Freddy Belesi Siangoli Alyson A Kelvin Jean Claude Udahemuka Patricia Kelvin Luis Flores David J Kelvin Gustavo Sganzerla Martinez |
| author_sort | Leandre Murhula Masirika |
| collection | DOAJ |
| description |
Introduction: Human Mpox (formerly monkeypox) infection is an emerging zoonotic disease caused by the Mpox virus (MPXV). We describe the complete genome annotation, phylogeny, and mutational profile of a novel, sustained Clade I Mpox outbreak in the city of Kamituga in Eastern Democratic Republic of the Congo (DRC).
Methodology: A cross-sectional, observational, cohort study was performed among patients of all ages admitted to the Kamituga Hospital with Mpox infection symptoms between late September 2023 and late January 2024. DNA was isolated from Mpox swabbed lesions and sequenced followed by phylogenetic analysis, genome annotation, and mutational profiling.
Results: We describe an ongoing Clade I Mpox outbreak in the city of Kamituga, South Kivu Province, Democratic Republic of Congo. Whole-genome sequencing of the viral RNA samples revealed, on average, 201.5 snps, 28 insertions, 81 deletions, 2 indels, 312.5 total variants, 158.3 amino acid changes, 81.66 intergenic variants, 72.16 synonymous mutations, 106 missense variants, 41.16 frameshift variants, and 3.33 inframe deletions across six samples. By assigning mutations at the proteome level for Kamituga MPXV sequences, we observed that seven proteins, namely, C9L (OPG047), I4L (OPG080), L6R (OPG105), A17L (OPG143), A25R (OPG151), A28L (OPG153), and B21R (OPG210) have emerged as hot spot mutations based on the consensuses inframe deletions, frameshift variants, synonymous variants, and amino acids substitutions. Based on the outcome of the annotation, we found a deletion of the D14L (OPG032) gene in all six samples. Following phylogenetic analysis and whole genome assembly, we determined that this cluster of Mpox infections is genetically distinct from previously reported Clade I outbreaks, and thus propose that the Kamituga Mpox outbreak represents a novel subgroup (subgroup VI) of Clade I MPXV.
Conclusions: Here we report the complete viral genome for the ongoing Clade I Mpox Kamituga outbreak for the first time. This outbreak presents a distinct mutational profile from previously sequenced Clade I MPXV oubtreaks, suggesting that this cluster of infections is a novel subgroup (we term this subgroup VI). These findings underscore the need for ongoing vigilance and continued sequencing of novel Mpox threats in endemic regions.
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| format | Article |
| id | doaj-art-b9c07399922b4e96bec51daf8ec4cf0c |
| institution | DOAJ |
| issn | 1972-2680 |
| language | English |
| publishDate | 2024-04-01 |
| publisher | The Journal of Infection in Developing Countries |
| record_format | Article |
| series | Journal of Infection in Developing Countries |
| spelling | doaj-art-b9c07399922b4e96bec51daf8ec4cf0c2025-08-20T02:57:52ZengThe Journal of Infection in Developing CountriesJournal of Infection in Developing Countries1972-26802024-04-01180410.3855/jidc.20136Complete Genome Sequencing, Annotation, and Mutational Profiling of the Novel Clade I Human Mpox Virus, Kamituga StrainLeandre Murhula Masirika0Anuj Kumar1Mansi Dutt2Ali Toloue Ostadgavahi3Benjamin Hewins4Maliyamungu Bubala Nadine5Bilembo Kitwanda Steeven6Franklin Kumbana Mweshi7Léandre Mutimbwa Mambo8Justin Bengehya Mbiribindi9Freddy Belesi Siangoli10Alyson A Kelvin11Jean Claude Udahemuka12Patricia Kelvin13Luis Flores14David J Kelvin15Gustavo Sganzerla Martinez16Centre de Recherche en Sciences Naturelles de Lwiro, South Kivu, DS Bukavu, Democratic Republic of the CongoDepartment of Microbiology and Immunology, Canadian Center for Vaccinology (CCfV), Faculty of Medicine, Dalhousie University, Halifax, CanadaDepartment of Microbiology and Immunology, Canadian Center for Vaccinology (CCfV), Faculty of Medicine, Dalhousie University, Halifax, CanadaDepartment of Microbiology and Immunology, Canadian Center for Vaccinology (CCfV), Faculty of Medicine, Dalhousie University, Halifax, CanadaDepartment of Microbiology and Immunology, Canadian Center for Vaccinology (CCfV), Faculty of Medicine, Dalhousie University, Halifax, CanadaHospital General de Reference de Kamituga, South Kivu, Democratic Republic of the CongoHospital General de Reference de Kamituga, South Kivu, Democratic Republic of the CongoHospital General de Reference de Kamituga, South Kivu, Democratic Republic of the CongoZone de Santé de Kamituga, South Kivu, Democratic Republic of the CongoDivision Provinciale de la Santé, South Kivu, Democratic Republic of the CongoDivision Provinciale de la Santé, South Kivu, Democratic Republic of the CongoVaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, CanadaDepartment of Veterinary Medicine, University of Rwanda, Nyagatare, RwandaDepartment of Microbiology and Immunology, Canadian Center for Vaccinology (CCfV), Faculty of Medicine, Dalhousie University, Halifax, CanadaCentre de Recherche en Sciences Naturelles de Lwiro, South Kivu, DS Bukavu, Democratic Republic of the CongoDepartment of Microbiology and Immunology, Canadian Center for Vaccinology (CCfV), Faculty of Medicine, Dalhousie University, Halifax, CanadaDepartment of Microbiology and Immunology, Canadian Center for Vaccinology (CCfV), Faculty of Medicine, Dalhousie University, Halifax, Canada Introduction: Human Mpox (formerly monkeypox) infection is an emerging zoonotic disease caused by the Mpox virus (MPXV). We describe the complete genome annotation, phylogeny, and mutational profile of a novel, sustained Clade I Mpox outbreak in the city of Kamituga in Eastern Democratic Republic of the Congo (DRC). Methodology: A cross-sectional, observational, cohort study was performed among patients of all ages admitted to the Kamituga Hospital with Mpox infection symptoms between late September 2023 and late January 2024. DNA was isolated from Mpox swabbed lesions and sequenced followed by phylogenetic analysis, genome annotation, and mutational profiling. Results: We describe an ongoing Clade I Mpox outbreak in the city of Kamituga, South Kivu Province, Democratic Republic of Congo. Whole-genome sequencing of the viral RNA samples revealed, on average, 201.5 snps, 28 insertions, 81 deletions, 2 indels, 312.5 total variants, 158.3 amino acid changes, 81.66 intergenic variants, 72.16 synonymous mutations, 106 missense variants, 41.16 frameshift variants, and 3.33 inframe deletions across six samples. By assigning mutations at the proteome level for Kamituga MPXV sequences, we observed that seven proteins, namely, C9L (OPG047), I4L (OPG080), L6R (OPG105), A17L (OPG143), A25R (OPG151), A28L (OPG153), and B21R (OPG210) have emerged as hot spot mutations based on the consensuses inframe deletions, frameshift variants, synonymous variants, and amino acids substitutions. Based on the outcome of the annotation, we found a deletion of the D14L (OPG032) gene in all six samples. Following phylogenetic analysis and whole genome assembly, we determined that this cluster of Mpox infections is genetically distinct from previously reported Clade I outbreaks, and thus propose that the Kamituga Mpox outbreak represents a novel subgroup (subgroup VI) of Clade I MPXV. Conclusions: Here we report the complete viral genome for the ongoing Clade I Mpox Kamituga outbreak for the first time. This outbreak presents a distinct mutational profile from previously sequenced Clade I MPXV oubtreaks, suggesting that this cluster of infections is a novel subgroup (we term this subgroup VI). These findings underscore the need for ongoing vigilance and continued sequencing of novel Mpox threats in endemic regions. https://jidc.org/index.php/journal/article/view/20136DRCMpoxKamituga outbreakhMPXVClade ISequencing |
| spellingShingle | Leandre Murhula Masirika Anuj Kumar Mansi Dutt Ali Toloue Ostadgavahi Benjamin Hewins Maliyamungu Bubala Nadine Bilembo Kitwanda Steeven Franklin Kumbana Mweshi Léandre Mutimbwa Mambo Justin Bengehya Mbiribindi Freddy Belesi Siangoli Alyson A Kelvin Jean Claude Udahemuka Patricia Kelvin Luis Flores David J Kelvin Gustavo Sganzerla Martinez Complete Genome Sequencing, Annotation, and Mutational Profiling of the Novel Clade I Human Mpox Virus, Kamituga Strain Journal of Infection in Developing Countries DRC Mpox Kamituga outbreak hMPXV Clade I Sequencing |
| title | Complete Genome Sequencing, Annotation, and Mutational Profiling of the Novel Clade I Human Mpox Virus, Kamituga Strain |
| title_full | Complete Genome Sequencing, Annotation, and Mutational Profiling of the Novel Clade I Human Mpox Virus, Kamituga Strain |
| title_fullStr | Complete Genome Sequencing, Annotation, and Mutational Profiling of the Novel Clade I Human Mpox Virus, Kamituga Strain |
| title_full_unstemmed | Complete Genome Sequencing, Annotation, and Mutational Profiling of the Novel Clade I Human Mpox Virus, Kamituga Strain |
| title_short | Complete Genome Sequencing, Annotation, and Mutational Profiling of the Novel Clade I Human Mpox Virus, Kamituga Strain |
| title_sort | complete genome sequencing annotation and mutational profiling of the novel clade i human mpox virus kamituga strain |
| topic | DRC Mpox Kamituga outbreak hMPXV Clade I Sequencing |
| url | https://jidc.org/index.php/journal/article/view/20136 |
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