Implementation of an In-House Platform for Rapid Screening of SARS-CoV-2 Genome Variations.
Arch Iran Med
; 26(2): 69-75, 2023 02 01.
Article
en En
| MEDLINE
| ID: mdl-37543926
ABSTRACT
BACKGROUND:
Global real-time monitoring of SARS-CoV-2 variants is crucial to controlling the COVID-19 outbreak. The purpose of this study was to set up a Sanger-based platform for massive SARS-CoV-2 variant tracking in laboratories in low-resource settings.METHODS:
We used nested RT-PCR assay, Sanger sequencing and lineage assignment for 930-bp of the SARS-CoV-2 spike gene, which harbors specific variants of concern (VOCs) mutations. We set up our platform by comparing its results with whole genome sequencing (WGS) data on 137 SARS-CoV-2 positive samples. Then, we applied it on 1028 samples from March-September 2021.RESULTS:
In total, 125 out of 137 samples showed 91.24% concordance in mutation detection. In lineage assignment, 123 out of 137 samples demonstrated 89.78% concordance, 65 of which were assigned as VOCs and showed 100% concordance. Of 1028 samples screened by our in-house method, 78 distinct mutations were detected. The most common mutations were SD614G (21.91%), SP681R (12.19%), SL452R (12.15%), ST478K (12.15%), SN501Y (8.91%), SA570D (8.89%), SP681H (8.89%), ST716I (8.74%), SL699I (3.50%) and SS477N (0.28%). Of 1028 samples, 980 were attributed as VOCs, which include the Delta (B.1.617.2) and Alpha (B.1.1.7) variants.CONCLUSION:
Our proposed in-house Sanger-based assay for SARS-CoV-2 lineage assignment is an accessible strategy in countries with poor infrastructure facilities. It can be applied in the rapid tracking of SARS-CoV-2 VOCs in the SARS-CoV-2 pandemic.Palabras clave
Texto completo:
1
Base de datos:
MEDLINE
Asunto principal:
SARS-CoV-2
/
COVID-19
Tipo de estudio:
Diagnostic_studies
/
Screening_studies
Idioma:
En
Revista:
Arch Iran Med
Año:
2023
Tipo del documento:
Article