In the ongoing COVID-19 pandemic, it didn’t take long to spot which countries had a solid response and which ones, well, totally flubbed it. Months later, though, advances in scientists’ understanding of the virus and its transmission patterns have helped shape more effective public health policies. At a recent precision health conference, experts shared their stories about what worked and what didn’t.
Before the SARS-CoV-2 virus emerged in humans, most countries had a pandemic plan. Unfortunately, says Jemma Geoghegan, a virologist at the University of Otago in New Zealand, those plans were typically modeled on the flu. In that case, flattening the curve — by taking enough measures to ensure that hospitals aren’t overwhelmed — makes sense. But the COVID-19 pandemic wasn’t comparable to the flu. “Early on it became really clear that [flattening the curve] wasn’t going to work,” Geoghegan says. The ease of transmissibility and severity of the disease caused by the virus called for a different approach.
Countries that beat back SARS-CoV-2 most effectively instead used a pandemic plan based on the original SARS outbreak, which aimed for total elimination of the pathogen rather than simply reducing its spread. This calls for a carefully choreographed mix of lockdown or at least mask-wearing and social distancing, rigorous and frequent testing, and rapid isolation and tracing of any new cases. In New Zealand, a strict month-long lockdown and meticulous monitoring stopped infections in their tracks and led to 100 days of zero spread. For the most part, new cases detected since then have been caught at the country’s airports, where incoming travelers spend two weeks in quarantine.
While tracing the global spread of a pandemic doesn’t do much to affect the outcome of any particular infected individual, it’s one of the best tools scientists have to make public health policies that can make a big difference at the community or national level.
With tens of thousands of SARS-CoV-2 virus genomes now sequenced, researchers have a remarkable view of how the pandemic spread around the world. In New Zealand, for instance, there were many separate introductions of the virus from lots of sources, although early on it was most commonly brought in by travelers from North America.
In the UK, scientists used genome data to trace more than 1,000 lineages of the virus, each triggered by a separate introduction to the country, reports infectious disease expert Oliver Pybus at the University of Oxford. Statistical analyses indicate that the first transmissions came from China, followed by Italy, Spain, and France. By combining that lineage data with information about travelers — before lockdown, some 250,000 people were traveling to the UK every day — scientists were able to estimate the time it took from when an infected person entered the country to the start of a new COVID-19 transmission chain.
While New Zealand and the UK saw varying degrees of success in their public health response, the U.S. quickly became “the country that has taught us the most important lesson of all, which is how not to do it,” says Kristian Andersen, director of infectious disease genomics at Scripps Research.
In addition to having “the most disappointing response of any country in the world,” the U.S. is large enough to be fighting “not one epidemic [but] a set of outbreaks and epidemics rolling all across the country,” he adds. An analysis of belatedly collected data from New Orleans, for instance, shows that the city’s population was seeded with the pathogen from many lineages already thriving in other states. “[The virus] was already here, we just weren’t looking for it,” Andersen says, pointing to the abysmal testing rates that have been a hallmark of the American response to COVID-19. In the U.S. some leaders, most notably the president, have been reluctant or unwilling to emphasize testing.
In New York state, where leaders “prioritized testing and tracing,” according to Commissioner of Health Howard Zucker, the outcome has been measurably better. “Our positivity rate is steadily below 1%,” he adds. Based on the success of the state’s data-first approach, he calls recent guidance from the U.S. Centers for Disease Control and Prevention not to test asymptomatic people “indefensible.”
As the cost of genome sequencing fell in recent years before the pandemic, scientists in countries around the world launched mega-scale efforts to sequence huge swaths of their populations. These large studies were critical for a public health understanding of COVID-19: researchers turned to the people already enrolled in these studies, using surveys and other tools to gather important information. As a participant in the American “All of Us” research program, for example, I answered monthly questionnaires about my mental health and behavior this spring and summer. It has been a huge advantage for public health officials to be able to activate these groups of people and gather data that could help them understand how society was responding to the pandemic.
One reliable view of a post-COVID world comes from infectious disease experts like Geoghegan, from a country with very effective responses to the pandemic: New Zealand. This pandemic was not a once-in-a-lifetime event. As human populations squeeze into areas historically reserved for wildlife, new infectious disease outbreaks will become more common, she says. SARS-CoV-2 is the seventh documented coronavirus that has made the leap into humans, according to Geoghegan, and five of those emerged in the last 20 years. Preventing future pandemics will depend on better controlling human exposure to wildlife and establishing routine genomic surveillance in the places where virus crossover is most likely to occur. Once an outbreak has started, rapid testing and isolation are key. In New Zealand, after 100 disease-free days, four new community cases arose in Auckland. “We had no idea where they came from,” Geoghegan says. But fast genome sequencing and an immediate reinstatement of lockdown for that region helped shed light on the new lineage and prevent broader spread.
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