How to tackle the emerging COVID-19 variants

With multiple variants of SARS-CoV-2 spreading rapidly across the globe and proving to be more infectious than previously observed strains, the fight against the pandemic has become even more complex and challenging. The high transmissibility of these mutant strains is making control of COVID-19 particularly difficult, increasing the urgency of vaccine programs.

Here, we speak with Arvind Kothandaraman, specialty diagnostics leader at PerkinElmer, to find out more about these new variants and what impact they could have on the pandemic, as well as discussing the importance of reverse transcription-polymerase chain reaction (RT-PCR) assays, emerging COVID-19 trends, and how PerkinElmer’s tools can be used to detect the U.K. and South Africa variant within a population.

SS: Tell us about your role at PerkinElmer

AK: I am the general manager of the specialty diagnostics business at PerkinElmer. My primary interest is in equipping clinical laboratories with the tools needed to meet their technical and operational goals.

SS: Why is it so important for a reverse transcription-polymerase chain reaction (RT-PCR) assay to be unaffected by COVID-19 variants?

AK: On January 15, 2021, the U.S. CDC projected the U.K. variant, a highly contagious variant of SARS-CoV-2, will become the dominant strain in the U.S. by March. Earlier in the month, the U.S. FDA issued an alert stating potential false-negative results can occur from the use of molecular tests that rely on detection of SARS-CoV-2 regions affected by mutations identified in this variant. The U.S. FDA analysis also named three molecular assays whose performance could be impacted by SARS-CoV-2 variants.

To accurately diagnose patients and reduce the spread of the pandemic, any assay used for COVID-19 detection needs to be able to diagnose the variants within a population. Both the U.K. variant (B.1.1.7 lineage a.k.a. 20B/501Y.V1 VOC 202012/01) and the South Africa variant (B.1.351 lineage a.k.a. 20C/501Y.V2) contain multiple mutations in the spike protein gene. The 69-70 deletion in the spike protein of the U.K. variant has been reported to cause a negative result using RT-PCR assays targeting the S-gene. PerkinElmer’s SARS-CoV-2 RT-PCR assays target two specific genomic regions of the virus (N and ORF1ab) and are not affected by S-gene mutations associated with the dropouts described by the U.S. FDA.

PerkinElmer regularly monitors SARS-CoV-2 variant databases in the National Centre for Biotechnology Information (NCBI), the global initiative on sharing avian influenza data (GISAID) and SARS-CoV-2 publications and works closely with the U.S. government and commercial testing partners. Based on in silico analysis supplemented by wet lab data, the performance of the kit is not impacted by identified SARS-CoV-2 mutations.

SS: How are new variants detected?

AK: New variants are identified by sequencing the genome of the virus using next-generation sequencing (NGS) and comparing this to the original reference strain that was first identified in Wuhan. RT-PCR assays can be designed to specifically detect variants identified using NGS. Such an RT-PCR assay can be used to determine if an individual who tested positive was infected by one of the known variants. Variant detection using NGS or RT-PCR can provide clues about the spread of infection, transmissibility, and vaccine effectiveness.

SS: How do you see variant detection techniques being used in the lab?

AK: Once a patient is confirmed as being infected by SARS-CoV-2, the same RNA that was extracted from this individual for COVID-19 diagnosis can be used for a follow-up assay to detect variants. This could mean testing thousands of additional samples every day, depending on the infection rate in the region. Labs need to increasingly rely on automation to manage this throughput. Labs will benefit from working with vendors who can provide a comprehensive solution for COVID-19 testing as this will save resources and offer much-needed reliability. PerkinElmer can offer a broad range of options including best-in-class RT-PCR detection kits, antibody tests, sequencing consumables, automation instruments and even lab testing services that may be needed.

SS: What are some of the other emerging trends in COVID-19 diagnostics?

AK: Testing is critical to stop the spread of infection – sensitivity matters here, as false negatives will only exacerbate the problem. This is particularly relevant to testing asymptomatic carriers, as a high percentage of cases are known to be spread by this population. Labs are looking for solutions that can be implemented for mass testing. As one of a few commercial kits that has been authorized for emergency use by the U.S. FDA to test asymptomatic individuals, PerkinElmer’s FDA EUA and CE-marked RT-PCR kits are ideally suited for travelers, students, workforce and other such predominantly asymptomatic groups. This test can also be used to detect SARS-CoV-2 in pooled or batch samples containing up to five specimens. When used effectively, sample pooling can generally enable testing of more individuals while conserving time, labor, and materials.

For emergency use authorization only. Please check with your local representative for availability.

Find out more about PerkinElmer’s RT-PCR assays>>