A New SARS-CoV-2 Variant Poorly Detected by RT-PCR

A new variant of SARS-CoV-2 designated as B.1.616 first reported in France, tests repeatedly negative with RT-PCR tests on nasopharyngeal samples but positive on lower respiratory tract samples. Detection failure of B.1.616-related COVID-19 using RT-PCR led to the emergence of several clusters as infection control measures were relieved once RT-PCR showed negative results. Whole-genome sequencing of the B.1.616 strain revealed that the strain is characterized by nine amino acid changes ( D66H; Y144V; D215G; V483A; D614G; H655Y; G669S; Q949R; and N1187D) and one amino acid deletion (G142 deletion) in the spike protein. The mutations give rise to proteins that have antagonistic effects on type-1interferon (INF-1) production and signaling pathway. V483A mutation is associated with reduced neutralization of antibodies post COVID-19 infection or vaccination.

The reason for the B.1.616  variant to escape the RT-PCR which is a gold-standard diagnostic test for COVID-19 and post-infection complications of B.1.616  was thoroughly analyzed. The outcomes showed that B.1.616 is associated with a higher 28 days mortality rate. B.1.616 infected patients displayed worse clinical outcomes reaching a WHO score >5. The B.1.616 was not detected with RT-PCR tests on nasopharyngeal samples due to low viral load on the nosocomial site when compared to lower respiratory tract samples. From this, it could be assumed that nasopharyngeal virus shedding of the B.1.616 variant is lower than the other variants of concern. But the reason for the worst clinical outcomes and higher fatality rate post-infection is yet to be determined. 

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Ref link: https://www.medrxiv.org/content/10.1101/2021.05.05.21256690v1