How our pandemic toolkit fought the many viruses of 2022

COVID-19 caused headlines again this year, but it was matched by a slew of other newsworthy viruses: the adenoviruses suspected to be behind the rise in hepatitis cases in early spring, the outbreak of mpox—formerly known as monkeypox—in the summer, an early surge in respiratory syncytial virus (RSV), and a peak in influenza cases following the Thanksgiving holiday season. Each of these viruses has tested clinicians, epidemiologists, and virologists. But these experts have responded by employing some of the tools that were built during the COVID pandemic.

The beginning of 2022 brought the first trial run for our toolkit: huge numbers of COVID cases, caused by the emergence of the highly transmissible Omicron variant. Virologists had to re-enact the early days of the pandemic: identifying the strain, testing its disease severity, and understanding its ability to escape the immune system. The available COVID vaccines were pitted against Omicron, and thankfully, showed good efficacy. By now, these studies were familiar, and early results were shared quickly to inform how public health officials around the world acted to protect populations.

After the initial surge of cases, in spring of 2022, many jurisdictions began to reduce COVID testing and tracing. The Centers for Disease Control and Prevention (CDC) changed its guidance on face coverings, so fewer people wore masks out and about. Still, researchers continued to track Omicron and its subvariants, and those who’d worked at speed to understand the latest strain would get little respite—2022 had more pathogens to throw at them yet.

Genome sequencing predicts viral spread

Monitoring mutations is a virus-fighting tool that had been employed early in the pandemic, because it’d been proven to help many times before. Since 2008, researchers sequencing all types of viruses have been able to upload whole genomes to GISAID, a science surveillance initiative. Their work had allowed for quick research at the start of the H1N1 flu pandemic in 2009 and during the 2013 bird flu epidemic. 

“When the unknown coronavirus emerged in January 2020, GISAID had already played a key role in influenza surveillance for 12 years,” says Sebastian Maurer-Stroh, executive director of the Bioinformatics Institute in Singapore and a collaborator with GISAID. The collaborative’s array of tools, though designed for tracking flu viruses, had been built in connection with the research community and large organizations like the World Health Organization (WHO). These tools were relatively easy to adapt to track the spread of COVID, Maurer-Stroh says. 

[Related: The World Health Organization officially renamed monkeypox to mpox]

GISAID’s database of SARS-CoV-2 genomes has helped research into the pathogen’s spike protein, the area on the virus that affects how it enters our cells and causes infection. It’s also meant that countries can monitor the rise and fall of different strains in their populations and make changes to guidelines accordingly. Though submissions of new SARS-CoV-2 genomes started to trail off in early 2022, GISAID and the WHO are still tracking Omicron and the emergence of subvariants. 

But in May 2022, GISAID researchers noticed a new genome being uploaded. The hMpxV virus and the disease it caused, mpox, was already endemic in countries in Africa, but rarely caused infections outside the continent. GISAID surveillance showed that there were new lineages spreading rapidly, and by July the virus was present in 75 countries. That month, the WHO declared the outbreak to be a public health emergency. Cases have been steadily dropping since then, though the WHO reports that seven countries are still seeing new cases. As of December 15, there have been more than 80,000 mpox cases worldwide.

Wastewater provide breadcrumbs for disease outbreaks

At the same time as GISAID was monitoring DNA sequences of the mpox virus, researchers were employing another surveillance tool used during the pandemic. Wastewater taken from July to October in  New York showed that poliovirus was circulating in six of 13 sampled counties.

Wastewater sampling had detected COVID in sewers back in April 2020; in September of that year, the CDC launched the National Wastewater Surveillance System (NWSS) to monitor virus levels. Compared to mass-scale PCR testing, testing wastewater offered an easy and unobtrusive way to find out where there were hotspots of virus activity. 

“You can track a lot of viruses in the wastewater, and what we’re seeing with COVID is that it may be an easier way of doing epidemiology, at least on a bigger picture scale,” says virologist Michael Teng, of the University of South Florida Department of Molecular Medicine. Wastewater surveillance can’t pinpoint individuals, so it won’t help identify potential “superspreaders” before they infect others. But it’s a great tool for virologists to see general geographical trends in virus levels.

[Related: Polio is officially circulating in the US again]

The poliovirus spread in the state was “silent,” but posed a real threat. Cases of polio had been basically non-existent in the US since the introduction of the polio vaccine, which has an average uptake of 92 percent in kids across the country—though some counties’ rates of vaccination are as low as 37 percent.

Vaccines fight viruses in and across individuals

As evidenced by the pandemic, vaccine uptake is one of the–if not the–best tools for stopping the spread of a virus. COVID vaccines protect against infection, and if you do get the disease, you’re less likely to have severe illness if you’ve been vaccinated.

So when researchers predicted a tripledemic of COVID, the flu, and RSV heading towards the US, the message was clear: Get your flu shot and COVID booster. But with no RSV vaccine available, case numbers quickly rose in young children and elderly population.

“We had a COVID vaccine within about 11 months of when the first virus sequence came out well, but RSV was first identified in 1957, and since then we have not really had good vaccines,” says Teng, whose focus is on the respiratory pathogen. “But one of the really exciting stories for this year is that Pfizer [who developed one of the COVID vaccines] along with GSK have had really good results in tests for an RSV vaccine for the elderly.”

[Related: Fighting RSV in babies starts with a mother’s antibodies]

Teng says the purchase of COVID vaccines led to an infusion of capital in companies like Pfizer and Moderna, the latter of which has been able to invest into research it began long before the pandemic. This money meant Moderna could move forward with several vaccines in development, according to Teng, including one for HIV.

These important elements of tackling viruses in 2022—genomic monitoring, wastewater surveillance, and vaccine development—are just part of the huge fight against infectious diseases. There is, of course, still a lot we don’t know about COVID and other viruses, and we cannot predict what 2023 will bring. But researchers are armed with more information about the spread of viruses than ever before, and they’ve already begun putting the pandemic’s teachings into practice.