Sequencing of SARS-CoV-2 genome using different nanopore chemistries.
Appl Microbiol Biotechnol
; 105(8): 3225-3234, 2021 Apr.
Article
in En
| MEDLINE
| ID: mdl-33792750
ABSTRACT
Nanopore sequencing has emerged as a rapid and cost-efficient tool for diagnostic and epidemiological surveillance of SARS-CoV-2 during the COVID-19 pandemic. This study compared the results from sequencing the SARS-CoV-2 genome using R9 vs R10 flow cells and a Rapid Barcoding Kit (RBK) vs a Ligation Sequencing Kit (LSK). The R9 chemistry provided a lower error rate (3.5%) than R10 chemistry (7%). The SARS-CoV-2 genome includes few homopolymeric regions. Longest homopolymers were composed of 7 (TTTTTTT) and 6 (AAAAAA) nucleotides. The R10 chemistry resulted in a lower rate of deletions in thymine and adenine homopolymeric regions than the R9, at the expenses of a larger rate (~10%) of mismatches in these regions. The LSK had a larger yield than the RBK, and provided longer reads than the RBK. It also resulted in a larger percentage of aligned reads (99 vs 93%) and also in a complete consensus genome. The results from this study suggest that the LSK preparation library provided longer DNA fragments which contributed to a better assembly of the SARS-CoV-2, despite an impaired detection of variants in a R10 flow cell. Nanopore sequencing could be used in epidemiological surveillance of SARS-CoV-2. KEY POINTS ⢠Sequencing SARS-CoV-2 genome is of great importance for the pandemic surveillance. ⢠Nanopore offers a low cost and accurate method to sequence SARS-CoV-2 genome. ⢠Ligation sequencing is preferred rather than the rapid kit using transposases.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Genome, Viral
/
Sequence Analysis, RNA
/
Nanopores
/
SARS-CoV-2
Language:
En
Journal:
Appl Microbiol Biotechnol
Year:
2021
Document type:
Article
Affiliation country:
España
Publication country:
ALEMANHA
/
ALEMANIA
/
DE
/
DEUSTCHLAND
/
GERMANY