Integrated approach for detection of SARS-CoV-2 and its variant by utilizing LAMP and ARMS-PCR

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F62156489%3A43210%2F24%3A43924727" target="_blank" >RIV/62156489:43210/24:43924727 - isvavai.cz</a>

Result on the web

<a href="https://doi.org/10.1186/s12941-023-00665-0" target="_blank" >https://doi.org/10.1186/s12941-023-00665-0</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1186/s12941-023-00665-0" target="_blank" >10.1186/s12941-023-00665-0</a>

Result language

angličtina

Original language name

Integrated approach for detection of SARS-CoV-2 and its variant by utilizing LAMP and ARMS-PCR

Original language description

Global impact of COVID-19 pandemic has heightened the urgency for efficient virus detection and identification of variants such as the Q57H mutation. Early and efficient detection of SARS-CoV-2 among densely populated developing countries is paramount objective. Although RT-PCR assays offer accuracy, however, dependence on expansive kits and availability of allied health resources pose an immense challenge for developing countries. In the current study, RT-LAMP based detection of SARS-Cov-2 with subsequent confirmation of Q57H variant through ARMS-PCR was performed. Among the 212 collected samples, 134 yielded positive results, while 78 tested negative using RT-LAMP. Oropharyngeal swabs of suspected individuals were collected and processed for viral RNA isolation. Isolated viral RNA was processed further by using either commercially available WarmStart Master Mix or our in house developed LAMP master mix separately. Subsequently, the end results of each specimen were evaluated by colorimetry. For LAMP assays, primers targeting three genes (ORF1ab, N and S) were designed using PrimerExplorer software. Interestingly, pooling of these three genes in single reaction tube increased sensitivity (95.5%) and specificity (93.5%) of LAMP assay. SARS-CoV-2 positive specimens were screened further for Q57H mutation using ARMS-PCR. Based on amplicon size variation, later confirmed by sequencing, our data showed 18.5% samples positive for Q57H mutation. Hence, these findings strongly advocate use of RT-LAMP-based assay for SARS-CoV-2 screening within suspected general population. Furthermore, ARMS-PCR also provides an efficient mean to detect prevalent mutations against SARS-Cov-2.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

30401 - Health-related biotechnology

Project

—

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2024

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Annals of Clinical Microbiology and Antimicrobials

ISSN

1476-0711

e-ISSN

1476-0711

Volume of the periodical

23

Issue of the periodical within the volume

1 February

Country of publishing house

GB - UNITED KINGDOM

Number of pages

9

Pages from-to

11

UT code for WoS article

001155011400001

EID of the result in the Scopus database

2-s2.0-85183712229