Coronavirus Mutations In The Era Of Increasing Cases. Situation in India.

 

Changes to the SARS-CoV-2 genome—including some of those found in currently circulating variants—can negatively affect the detection of the virus by reverse transcription (RT) PCR, according to a study published on April 26 in the Journal of Clinical Microbiology. The researchers propose that mutations in the loci recognized by DNA primers may reduce the amplification of viral sequences and, as a result, potentially hinder the detection of the virus in samples from COVID-19–positive individuals.

 

This finding isn’t cause for full-blown panic, the authors say. “We thought maybe this could be more common than not. But it turns out, it’s actually fairly rare,” says coauthor David Wang, a virologist at Washington University. Wang and his colleagues recommend that diagnostic tests include more than one target to ensure proper SARS-CoV-2 detection. While a number of products already include multiple genetic targets, some COVID-19 RT-PCR assays authorized for emergency use check only one.

 

The primers used for RT-PCR test were developed early in the pandemic, when the SARS-CoV-2 virus was first sequenced. Based on information about other coronaviruses, researchers designed PCR primers to amplify sequences in the viral genome thought to remain relatively stable. The approach has been used to great success, detecting SARS-CoV-2 in samples from nasopharyngeal swabs, saliva, and even sewage.

“If you have a high value in one gene, you have a high value in the other gene—and vice versa,” says coauthor Bijal Parikh, a clinical pathologist at Washington University and the medical director of the molecular diagnostics laboratory. While most samples his team has processed have had similar cycle threshold values for the two targets, a handful strayed from the expected correlation: at times, the E gene wasn’t amplified to the same degree as was ORF1ab.

 

Despite this curious result, the tests still correctly identified SARS-CoV-2–positive samples based on the ORF1ab signal. To figure out what was going on with the E gene, the team sequenced a handful of viral samples. They found three samples had a common mutation in the E gene, one does not present in any of the common variants now circulating in the population. The researchers propose that the mutation affects the binding of the PCR primer and interferes with amplification.