Jessica Manning had no experience with coronaviruses. The infectious disease researcher had lived and worked in Cambodia off and on since 2013, studying the mosquitoes of the Mekong Delta and how their saliva helps spread disease in humans. But in January, the country flagged its first Covid-19 patient, and the lab that delivered the diagnosis wanted to send samples from the patient and his family to Manning for further testing.
Manning works at the National Institute of Allergy and Infectious Diseases’ Laboratory of Malaria and Vector Research in Phnom Penh, which is part of a decades-old collaboration between NIAID and the Cambodian National Center for Parasitology, Entomology, and Malaria Control. In September, her team had booted up a white machine, small enough to fit in an airplane’s overhead compartment and designed to read out DNA letters one by one. For the past few months they’d been using that new sequencer to figure out which microbes, other than the dengue virus, are behind so many high fevers in Cambodia. Now, they were going to ask it to piece together the coronavirus that had just arrived on their shore. And they were going to do it with the help of something called IDSeq.