Assam doctor infected with two COVID-19 variants simultaneously; when this pattern was first discovered, why it's dangerous

A woman doctor in Assam emerged as the country's first case of a COVID-19 patient infected with two different variants of the virus at the same time.

The doctor, despite being fully vaccinated, was infected with both Alpha and Delta variants of SARS-CoV-2. The ICMR's Regional Medical Research Centre in Dibrugarh detected the double infection in the patient in May. A month after receiving the second dose, the woman and her husband, both doctors at a COVID Care Centre, tested COVID-19 positive and the latter was infected with the Alpha variant.

"We collected their samples again and the second round of tests re-confirmed the double infection in her. We also did whole genome sequencing and it made us sure that it was a case of being infected by both variants at the same time," said a senior scientist at RMRC Dr B Borkakoty. The woman who had a mild sore throat, body ache and insomnia, recovered without hospitalisation, he added.

While this is new territory for India, similar instances have occurred before in the UK, Brazil and Portugal. The detection in Brazil in January was the first such case globally.

"A dual infection happens when two variants infect one person simultaneously or within a very short period. It occurs when someone gets infected with one variant and before immunity can develop, the person gets infected with another variant usually within two to three days of the first infection," Borkakoty said.

Most cases of dual infection may be missed if genetic sequencing is solely based on next-generation sequencing where variant calling is by software and not by manual examination of the specific genetic sequence, the scientist said.

When this pattern of COVID-19 infection was discovered

Researchers in Brazil discovered found two people infected with two different types of the mutant Brazilian strain of coronavirus at the same time. This was believed to be the first such detection in the world with respect to COVID-19.

The patients were both in their 30s and infected with the P.2 variant of coronavirus, also known as the B.1.1.28 lineage. They again simultaneously tested positive for another variant of the virus. They had mild symptoms and did not require hospitalisation.

Dr John McCauley, director of the Worldwide Influenza Centre at the Francis Crick Institute in London said the two strains could conceivably meet and swap genetic code - which was unlikely but worrying.

In Belgium, a woman died of COVID-19 in March after contracting two separate COVID variants simultaneously. There was a possibility that the patient may have been infected by the two strains by two different people.

"Both [Alpha and Beta] variants were circulating in Belgium" at the time the woman fell sick," said molecular biologist Anne Vankeerberghen of the OLV Hospital in Aalst on VRT. "It is therefore probable that this woman was infected by two different people with two variants of the virus. Unfortunately, we do not know how this infection happened."

Why getting infected by two different variants simultaneously may be dangerous

"Viruses are masters of evolution, constantly mutating and creating new variants with every cycle of replication. Selective pressures in the host, such as our immune response, also drive these adaptations. Most of these mutations won’t have a significant effect on the virus. But ones that give an advantage to the virus – for example, by increasing its ability to replicate or evade the immune system – are cause for concern and need to be closely monitored," wrote Maitreyi Shivkumar, Senior Lecturer in Molecular Biology, De Montfort University.

The detection of multiple variants in a person could be because of co-infection by different variants or may be due to mutations within the patient after the initial infection. The actual cause may be reached upon by comparing the sequences of the variants circulating in the population with those in the patient.

The 90-year-old woman who died in a hospital in Belgium in March was not vaccinated. She tested positive for COVID-19 and then developed rapidly worsening respiratory symptoms only to pass away five days later. Genome sequencing of samples from the woman confirmed she was infected by the two variants.

What is the role of RNA viruses?

According to Maitreyi, "This co-infection has opened concerns of SARS-CoV-2 acquiring new mutations even more rapidly. This is because coronaviruses can also undergo large changes in their genetic sequence by a process called recombination. When two viruses infect the same cell, they can swap large parts of their genomes with each other and create completely new sequences. This is a known phenomenon in RNA viruses."