Show simple item record

Files in this item

Thumbnail

Item metadata

dc.contributor.authorUlhuq, Fatima R
dc.contributor.authorBarge, Madhuri
dc.contributor.authorFalconer, Kerry
dc.contributor.authorWild, Jonathan
dc.contributor.authorFernandes, Goncalo
dc.contributor.authorGallagher, Abbie
dc.contributor.authorMcGinley, Suzie
dc.contributor.authorSugadol, Ahmad
dc.contributor.authorTariq, Muhammad
dc.contributor.authorMaloney, Daniel
dc.contributor.authorKenicer, Juliet
dc.contributor.authorDewar, Rebecca
dc.contributor.authorTempleton, Kate
dc.contributor.authorMcHugh, Martin P
dc.date.accessioned2023-05-04T11:30:20Z
dc.date.available2023-05-04T11:30:20Z
dc.date.issued2023-04-21
dc.identifier.citationUlhuq , F R , Barge , M , Falconer , K , Wild , J , Fernandes , G , Gallagher , A , McGinley , S , Sugadol , A , Tariq , M , Maloney , D , Kenicer , J , Dewar , R , Templeton , K & McHugh , M P 2023 , ' Analysis of the ARTIC V4 and V4.1 SARS-CoV-2 primers and their impact on the detection of Omicron BA.1 and BA.2 lineage-defining mutations ' , Microbial Genomics , vol. 9 , no. 4 , 000991 . https://doi.org/10.1099/mgen.0.000991en
dc.identifier.issn2057-5858
dc.identifier.otherPURE: 285390365
dc.identifier.otherPURE UUID: a581bb76-54d3-4e8c-915f-425c3965f9d6
dc.identifier.otherPubMed: 37083576
dc.identifier.otherScopus: 85153550374
dc.identifier.otherORCID: /0000-0002-0370-3700/work/134491535
dc.identifier.urihttps://hdl.handle.net/10023/27512
dc.description.abstractThe ARTIC protocol uses a multiplexed PCR approach with two primer pools tiling the entire SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) genome. Primer pool updates are necessary for accurate amplicon sequencing of evolving SARS-CoV-2 variants with novel mutations. The suitability of the ARTIC V4 and updated V4.1 primer scheme was assessed using whole genome sequencing of Omicron from clinical samples using Oxford Nanopore Technology. Analysis of Omicron BA.1 genomes revealed that 93.22 % of clinical samples generated improved genome coverage at 50× read depth with V4.1 primers when compared to V4 primers. Additionally, the V4.1 primers improved coverage of BA.1 across amplicons 76 and 88, which resulted in the detection of the variant-defining mutations G22898A, A26530G and C26577G. The Omicron BA.2 sub-variant (VUI-22JAN-01) replaced BA.1 as the dominant variant by March 2022, and analysis of 168 clinical samples showed reduced coverage across amplicons 15 and 75. Upon further interrogation of primer binding sites, a mutation at C4321T [present in 163/168 (97 %) of samples] was identified as a possible cause of complete dropout of amplicon 15. Furthermore, two mutations were identified within the primer binding regions for amplicon 75: A22786C (present in 90 % of samples) and C22792T (present in 12.5 % of samples). Together, these mutations may result in reduced coverage of amplicon 75, and further primer updates would allow the identification of the two BA.2-defining mutations present in amplicon 75: A22688G and T22679C. This work highlights the need for ongoing surveillance of primer matches as circulating variants evolve and change.
dc.format.extent9
dc.language.isoeng
dc.relation.ispartofMicrobial Genomicsen
dc.rightsCopyright © 2023 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License.en
dc.subjectBA.1en
dc.subjectBA.2en
dc.subjectNanoporeen
dc.subjectSARS-CoV-2en
dc.subjectWhole genome sequencingen
dc.subjectCOVID-19en
dc.subjectQR355 Virologyen
dc.subjectDASen
dc.subjectNISen
dc.subjectMCCen
dc.subject.lccQR355en
dc.titleAnalysis of the ARTIC V4 and V4.1 SARS-CoV-2 primers and their impact on the detection of Omicron BA.1 and BA.2 lineage-defining mutationsen
dc.typeJournal articleen
dc.description.versionPublisher PDFen
dc.contributor.institutionUniversity of St Andrews. Infection and Global Health Divisionen
dc.contributor.institutionUniversity of St Andrews. School of Medicineen
dc.identifier.doihttps://doi.org/10.1099/mgen.0.000991
dc.description.statusPeer revieweden


This item appears in the following Collection(s)

Show simple item record