BibTex format
@article{Alrezaihi:2023:10.1016/j.jcv.2023.105620,
author = {Alrezaihi, A and Penrice-Randal, R and Dong, X and Prince, T and Randle, N and Semple, MG and Openshaw, PJM and MacGill, T and Myers, T and Orr, R and Zakotnik, S and Sulji, A and Avi-upanc, T and Petrovec, M and Korva, M and AlJabr, W and Hiscox, JA and ISARIC4C, Investigators},
doi = {10.1016/j.jcv.2023.105620},
journal = {Journal of Clinical Virology},
title = {Enrichment of SARS-CoV-2 sequence from nasopharyngeal swabs whilst identifying the nasal microbiome},
url = {http://dx.doi.org/10.1016/j.jcv.2023.105620},
volume = {171},
year = {2023}
}
RIS format (EndNote, RefMan)
TY - JOUR
AB - Simultaneously characterising the genomic information of coronaviruses and the underlying nasal microbiome from a single clinical sample would help characterise infection and disease. Metatranscriptomic approaches can be used to sequence SARS-CoV-2 (and other coronaviruses) and identify mRNAs associated with active transcription in the nasal microbiome. However, given the large sequence background, unenriched metatranscriptomic approaches often do not sequence SARS-CoV-2 to sufficient read and coverage depth to obtain a consensus genome, especially with moderate and low viral loads from clinical samples. In this study, various enrichment methods were assessed to detect SARS-CoV-2, identify lineages and define the nasal microbiome. The methods were underpinned by Oxford Nanopore long-read sequencing and variations of sequence independent single primer amplification (SISPA). The utility of the method(s) was also validated on samples from patients infected seasonal coronaviruses. The feasibility of profiling the nasal microbiome using these enrichment methods was explored. The findings shed light on the performance of different enrichment strategies and their applicability in characterising the composition of the nasal microbiome.
AU - Alrezaihi,A
AU - Penrice-Randal,R
AU - Dong,X
AU - Prince,T
AU - Randle,N
AU - Semple,MG
AU - Openshaw,PJM
AU - MacGill,T
AU - Myers,T
AU - Orr,R
AU - Zakotnik,S
AU - Sulji,A
AU - Avi-upanc,T
AU - Petrovec,M
AU - Korva,M
AU - AlJabr,W
AU - Hiscox,JA
AU - ISARIC4C,Investigators
DO - 10.1016/j.jcv.2023.105620
PY - 2023///
SN - 1386-6532
TI - Enrichment of SARS-CoV-2 sequence from nasopharyngeal swabs whilst identifying the nasal microbiome
T2 - Journal of Clinical Virology
UR - http://dx.doi.org/10.1016/j.jcv.2023.105620
UR - https://www.ncbi.nlm.nih.gov/pubmed/38237303
VL - 171
ER -
