Using Multiplex Amplicon PCR Technology to Efficiently and Timely Generate Rift Valley Fever Virus Sequence Data for Genomic Surveillance

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dc.contributor.authorJuma, John
dc.contributor.authorKonongoi, Samson L.
dc.contributor.authorNsengimana, Isidore
dc.contributor.authorMwangi, Reuben
dc.contributor.authorAkoko, James
dc.contributor.authorNyamota, Richard
dc.contributor.authorMuli, Collins
dc.contributor.authorDobi, Paul O.
dc.contributor.authorKiritu, Edward
dc.contributor.authorOsiany, Shebbar
dc.contributor.authorOnwong’a, Amos A.
dc.contributor.authorGachogo, Rachael W.
dc.contributor.authorSang, Rosemary
dc.contributor.authorChristoffels, Alan
dc.contributor.authorRoesel, Kristina
dc.contributor.authorBett, Bernard
dc.contributor.authorOyola, Samuel O.
dc.date.accessioned2024-04-29T10:31:10Z
dc.date.available2024-04-29T10:31:10Z
dc.date.issued2023-02-09
dc.date.updated2023-02-24T14:09:30Z
dc.description.abstractRift Valley fever (RVF) is a febrile vector-borne disease endemic in Africa and continues to spread in new territories. It is a climate-sensitive disease mostly triggered by abnormal rainfall patterns. The disease is associated with high mortality and morbidity in both humans and livestock. RVF is caused by the Rift Valley fever virus (RVFV) of the genus <i>Phlebovirus</i> in the family <i>Phenuiviridae</i>. It is a tripartite RNA virus with three genomic segments: small (S), medium (M) and large (L). Pathogen genomic sequencing is becoming a routine procedure and a powerful tool for understanding the evolutionary dynamics of infectious organisms, including viruses. Inspired by the utility of amplicon-based sequencing demonstrated in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and Ebola, Zika and West Nile viruses, we report an RVFV sample preparation based on amplicon multiplex polymerase chain reaction (amPCR) for template enrichment and reduction of background host contamination. The technology can be implemented rapidly to characterize and genotype RVFV during outbreaks in a near-real-time manner. To achieve this, we designed 74 multiplex primer sets covering the entire RVFV genome to specifically amplify the nucleic acid of RVFV in clinical samples from an animal tissue. Using this approach, we demonstrate achieving complete RVFV genome coverage even from samples containing a relatively low viral load. We report the first primer scheme approach of generating multiplex primer sets for a tripartite virus which can be replicated for other segmented viruses.
dc.identifierdoi: 10.3390/v15020477
dc.identifier.apacitationJuma, J., Konongoi, Samson L., Nsengimana, I., Mwangi, R., Akoko, J., Nyamota, R., ... Oyola, Samuel O. (2023). Using Multiplex Amplicon PCR Technology to Efficiently and Timely Generate Rift Valley Fever Virus Sequence Data for Genomic Surveillance. http://hdl.handle.net/11427/39489en_ZA
dc.identifier.chicagocitationJuma, John, Samson L. Konongoi, Isidore Nsengimana, Reuben Mwangi, James Akoko, Richard Nyamota, Collins Muli, et al "Using Multiplex Amplicon PCR Technology to Efficiently and Timely Generate Rift Valley Fever Virus Sequence Data for Genomic Surveillance." (2023) http://hdl.handle.net/11427/39489en_ZA
dc.identifier.citationViruses 15 (2): 477 (2023)
dc.identifier.ris TY - Journal Article AU - Juma, John AU - Konongoi, Samson L. AU - Nsengimana, Isidore AU - Mwangi, Reuben AU - Akoko, James AU - Nyamota, Richard AU - Muli, Collins AU - Dobi, Paul O. AU - Kiritu, Edward AU - Osiany, Shebbar AU - Onwong’a, Amos A. AU - Gachogo, Rachael W. AU - Sang, Rosemary AU - Christoffels, Alan AU - Roesel, Kristina AU - Bett, Bernard AU - Oyola, Samuel O. AB - Rift Valley fever (RVF) is a febrile vector-borne disease endemic in Africa and continues to spread in new territories. It is a climate-sensitive disease mostly triggered by abnormal rainfall patterns. The disease is associated with high mortality and morbidity in both humans and livestock. RVF is caused by the Rift Valley fever virus (RVFV) of the genus <i>Phlebovirus</i> in the family <i>Phenuiviridae</i>. It is a tripartite RNA virus with three genomic segments: small (S), medium (M) and large (L). Pathogen genomic sequencing is becoming a routine procedure and a powerful tool for understanding the evolutionary dynamics of infectious organisms, including viruses. Inspired by the utility of amplicon-based sequencing demonstrated in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and Ebola, Zika and West Nile viruses, we report an RVFV sample preparation based on amplicon multiplex polymerase chain reaction (amPCR) for template enrichment and reduction of background host contamination. The technology can be implemented rapidly to characterize and genotype RVFV during outbreaks in a near-real-time manner. To achieve this, we designed 74 multiplex primer sets covering the entire RVFV genome to specifically amplify the nucleic acid of RVFV in clinical samples from an animal tissue. Using this approach, we demonstrate achieving complete RVFV genome coverage even from samples containing a relatively low viral load. We report the first primer scheme approach of generating multiplex primer sets for a tripartite virus which can be replicated for other segmented viruses. DA - 2023-02-09 DB - OpenUCT DP - University of Cape Town LK - https://open.uct.ac.za PY - 2023 T1 - Using Multiplex Amplicon PCR Technology to Efficiently and Timely Generate Rift Valley Fever Virus Sequence Data for Genomic Surveillance TI - Using Multiplex Amplicon PCR Technology to Efficiently and Timely Generate Rift Valley Fever Virus Sequence Data for Genomic Surveillance UR - http://hdl.handle.net/11427/39489 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/39489
dc.identifier.vancouvercitationJuma J, Konongoi Samson L, Nsengimana I, Mwangi R, Akoko J, Nyamota R, et al. Using Multiplex Amplicon PCR Technology to Efficiently and Timely Generate Rift Valley Fever Virus Sequence Data for Genomic Surveillance. 2023; http://hdl.handle.net/11427/39489.en_ZA
dc.titleUsing Multiplex Amplicon PCR Technology to Efficiently and Timely Generate Rift Valley Fever Virus Sequence Data for Genomic Surveillance
dc.typeJournal Article
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