tetano
Editor, Senior Moderator
J Clin Virol
. 2023 Nov 25:171:105620.
doi: 10.1016/j.jcv.2023.105620. Online ahead of print. Enrichment of SARS-CoV-2 sequence from nasopharyngeal swabs whilst identifying the nasal microbiome
Abdulrahman Alrezaihi[SUP] 1 [/SUP], Rebekah Penrice-Randal[SUP] 2 [/SUP], Xiaofeng Dong[SUP] 2 [/SUP], Tessa Prince[SUP] 2 [/SUP], Nadine Randle[SUP] 2 [/SUP], Malcolm G Semple[SUP] 3 [/SUP], Peter J M Openshaw[SUP] 4 [/SUP], Tracy MacGill[SUP] 5 [/SUP], Todd Myers[SUP] 5 [/SUP], Robert Orr[SUP] 5 [/SUP], Samo Zakotnik[SUP] 6 [/SUP], Alen Suljič[SUP] 6 [/SUP], Tatjana Avšič-Županc[SUP] 6 [/SUP], Miroslav Petrovec[SUP] 6 [/SUP], Miša Korva[SUP] 6 [/SUP], Waleed AlJabr[SUP] 7 [/SUP], Julian A Hiscox[SUP] 8 [/SUP]; ISARIC4C Investigators[SUP] 2 [/SUP]
Affiliations
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.
Keywords: Clinical sample; Humans coronaviruses; Microbiome; Nanopore; SARS-CoV-2; Sequencing
. 2023 Nov 25:171:105620.
doi: 10.1016/j.jcv.2023.105620. Online ahead of print. Enrichment of SARS-CoV-2 sequence from nasopharyngeal swabs whilst identifying the nasal microbiome
Abdulrahman Alrezaihi[SUP] 1 [/SUP], Rebekah Penrice-Randal[SUP] 2 [/SUP], Xiaofeng Dong[SUP] 2 [/SUP], Tessa Prince[SUP] 2 [/SUP], Nadine Randle[SUP] 2 [/SUP], Malcolm G Semple[SUP] 3 [/SUP], Peter J M Openshaw[SUP] 4 [/SUP], Tracy MacGill[SUP] 5 [/SUP], Todd Myers[SUP] 5 [/SUP], Robert Orr[SUP] 5 [/SUP], Samo Zakotnik[SUP] 6 [/SUP], Alen Suljič[SUP] 6 [/SUP], Tatjana Avšič-Županc[SUP] 6 [/SUP], Miroslav Petrovec[SUP] 6 [/SUP], Miša Korva[SUP] 6 [/SUP], Waleed AlJabr[SUP] 7 [/SUP], Julian A Hiscox[SUP] 8 [/SUP]; ISARIC4C Investigators[SUP] 2 [/SUP]
Affiliations
- PMID: 38237303
- DOI: 10.1016/j.jcv.2023.105620
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.
Keywords: Clinical sample; Humans coronaviruses; Microbiome; Nanopore; SARS-CoV-2; Sequencing