Variant-specific RT-qPCR for rapid screening of B.1.617 mutations in SARS-CoV-2

Abstract

The continuous emergence of new SARS-CoV-2 variants required rapid and reliable diagnostic methods for early detection and monitoring of the spread of the virus, especially in low-resource countries where whole genome sequencing is not available. We aimed to evaluate and compare the performance of two different RT-qPCR screening assays for the detection of B.1.617 lineage mutations. A total of 85 SARS-CoV-2 positive samples were collected between 9 th August and 10 September 2021 and screened by two mutation-specific RT-qPCR assays for simultaneous detection of B.1.617.1 and B.1.617.2 lineage mutations. VIASURE Variant II PCR assay identified 2 Delta variant-specific mutations (L452R, and P681 R) in 80% of tested samples, while the PKamp™ Variant Detect™ assay was only able to detect one Delta variant specific mutation (L452R) in 75% of tested samples. This is the first report to show the Delta variant as the cause of the third wave in Libya. The use of multiplex RT-qPCR assays has allowed the identification of new variants for rapid screening. However, RT-qPCR results should be confirmed by whole genome sequencing of SARS-COV-2.

Impact of vaccination and risk factors on COVID-19 mortality amid delta wave in Libya: a single centre cohort study

“…In addition, Pfizer-BioNtech vaccination started later in the beginning of August. Our study period (mid-June to October) coincided with the emergence of the Delta SARS-COV-2 variant (16). SARS-COV-2 samples from Libya were regrettably not confirmed by genome sequencing during that time; instead, tracking relied on RT-qPCR assays that targeted the presence of the L452R and P681R mutations.…”

“…The mortality rates were calculated for each month as follows: 33.3% in May, 48.8% in June, 63.1% in July, 78.3% in August and 44.7% in September and October (p value≤0.0001) [Figure .2]. From mid-June to October, this period was predominantly Delta strain in Libya (16).…”

Impact of vaccination and risk factors on COVID-19 mortality amid delta wave in Libya: A single center cohort study

“…The mortality rates were calculated for each month as follows: 33.3% in May, 48.8% in June, 63.1% in July, 78.3% in August and 44.7% in September and October (p value�0.0001) [ Fig 2]. From mid-June to October, infections in Libya were caused primarily by the Delta strain [16].…”

“…Our study period (mid-June to October) coincided with the emergence of the Delta SARS--COV-2 variant [16]. SARS-COV-2 samples from Libya were regrettably not confirmed by genome sequencing during that time; instead, tracking relied on RT-qPCR assays that targeted the presence of the L452R and P681R mutations.…”

A polyethylene glycol enhanced ligation-triggered self-priming isothermal amplification for the detection of SARS-CoV-2 D614G mutation

“…However, qRT-PCR is not suitable for direct mutation detection [ [10] , [11] , [12] , [13] ]. There are many PCR-based methods including amplification refractory mutation system-PCR (ARMS-PCR) [ 14 , 15 ], variant-specific RT-qPCR [ 16 ], and high-resolution melting analysis [ 17 ] which have been developed for SARS-CoV-2 mutation detection. Unfortunately, these methods are limited to the problems of complicated procedures, easy contamination and requirement for professional personnel which hinder their application outside central laboratories [ 18 ].…”