How months-long COVID infections could seed dangerous new variants

Tracking SARS-CoV-2 evolution during persistent cases provides insight into the origins of Omicron and other global variants. What can scientists do with this knowledge?

Ewen Callaway

Nature | June 15, 2022

These are mutations that accumulated in the spike protein of SARS-CoV-2 during a seven-month-long infection.Illustration by Nik Spencer/Nature; Source: Ref. 1

Virologist Sissy Sonnleitner tracks nearly every COVID-19 case in Austria’s rugged eastern Tyrol region. So, when one woman there kept testing positive for months on end, Sonnleitner was determined to work out what was going on.

Before becoming infected with SARS-CoV-2 in late 2020, the woman, who was in her 60s, had been taking immune-suppressing drugs to treat a lymphoma relapse. The COVID-19 infection lingered for more than seven months, causing relatively mild symptoms, including fatigue and a cough.

Sonnleitner, who is based at a microbiology facility in Außervillgraten, Austria, and her colleagues collected more than two dozen viral samples from the woman over time and found through genetic sequencing that it had picked up about 22 mutations (see ‘Tracking spike’s evolution’). Roughly half of them would be seen again in the heavily mutated Omicron variants of SARS-CoV-2 that surged around the globe months later¹. “When Omicron was found, we had a great moment of surprise,” Sonnleitner says. “We already had those mutations in our variant.”

Kids and COVID: why young immune systems are still on top

Innate immunity might be the key to why children have fared better with the virus. But the Delta variant poses fresh unknowns.

Smriti Mallapaty

Nature | September 07, 2021

After extremely low case rates in New York City early this summer, the number of children testing positive for SARS-CoV-2 has begun to rise. Credit: Spencer Platt/Getty

Early last year, children’s hospitals across New York City had to pivot to deal with a catastrophic COVID-19 outbreak. “We all had to quickly learn — or semi-learn — how to take care of adults,” says Betsy Herold, a paediatric infectious-disease physician who heads a virology laboratory at the Albert Einstein College of Medicine. The reason: while hospitals across the city were bursting with patients, paediatric wards were relatively quiet. Children were somehow protected from the worst of the disease.

Data collected by the US Centers for Disease Control and Prevention from hospitals across the country suggest that people under the age of 18 have accounted for less than 2% of hospitalizations due to COVID-19 — a total of 3,649 children between March 2020 and late August 2021. Some children do get very sick, and more than 420 have died in the United States, but the majority of those with severe illness have been adults — a trend that has been borne out in many parts of the world.

How the Delta variant achieves its ultrafast spread

Sara Reardon

Nature | July 21, 2021

A queue at a hospital in Surabaya, Indonesia, that treats people with COVID-19. Indonesia has been hard hit by the Delta variant.Credit: Juni Kriswanto/AFP/Getty

Since first appearing in India in late 2020, the Delta variant of SARS-CoV-2 has become the predominant strain in much of the world. Researchers might now know why Delta has been so successful: people infected with it produce far more virus than do those infected with the original version of SARS-CoV-2, making it very easy to spread.

According to current estimates, the Delta variant could be more than twice as transmissible as the original strain of SARS-CoV-2. To find out why, epidemiologist Jing Lu at the Guangdong Provincial Center for Disease Control and Prevention in Guangzhou, China, and his colleagues tracked 62 people who were quarantined after exposure to COVID-19 and who were some of the first people in mainland China to become infected with the Delta strain.