Tracking SARS-CoV-2 evolution one infection at a time

From the Bloom Lab, Basic Sciences Divisions, and the Greninger and Jerome Labs, Vaccine and Infectious Disease Division

In the later stages of the COVID-19 pandemic, public attention has shifted largely to the topic of viral evolution – when will the next variant arrive? How well will it evade immunity? How large an infectious wave will it cause? Such discussions have focused on large scale evolutionary dynamics, as viral surveillance efforts record sweeps of new variants through state, national, and global communities. But the emergence of every new variant begins at the small scale, with one virus in one person mutating, expanding, and infecting a new host. There is much we still don’t know about SARS-CoV-2 evolution on this scale, in part because observing these early stages is much more difficult than tracking large-scale changes in variant frequency. In a new research article published in Virus Evolution, Dr. Jesse Bloom’s lab in Fred Hutch’s Basic Sciences Division, in collaboration with the labs of Drs. Alex Greninger and Keith Jerome in the Vaccine and Infectious Disease Division, make use of a natural experiment to examine the very earliest stages of SARS-CoV-2 evolution.

“One interest of our lab is how evolutionary dynamics acting in individual infections contribute to viral evolution on a global level. Two key factors influencing the connection between viral evolution on these different scales are the amount of viral diversity that accumulates within an infected person and how bottlenecked that viral population becomes during transmission,” says Will Hannon, Bloom lab graduate student and lead author on the study. The size of a bottleneck corresponds to how many viruses are transferred between individuals to initiate a new infection. “If there is a wide transmission bottleneck [aka many viruses transmitted],” he explains, “then mutations can gradually increase in frequency as a virus transmits from one host to another. However, a narrow transmission bottleneck [aka one or few viruses transmitted] means that low-frequency mutations present in a donor host will typically be either lost or fixed in a recipient host.” Hannon notes that previous studies have suggested that SARS-CoV-2 spread is subject to a narrow bottleneck. However, he explains, “none of these studies looked at superspreading events, which are a significant factor in the global spread of SARS-CoV-2.” Due to their extreme contagiousness, there was reason to suspect that superspreaders may not follow the standard rules of transmission.

To understand the small scale dynamics of viral evolution during a superspreader event, the authors investigated the case of an isolated outbreak that occurred over the course of 16 days on a fishing boat in 2020. During this time, over 80% of the ship’s 122 crew members were infected with the virus, a rate of transmission consistent with a superspreader event. Shortly after the sailors returned to shore, the researchers collected and performed deep sequencing of nasal swab samples. Sequence data from 13 individuals ultimately passed stringent quality control metrics and were used for further analysis.

The group first used their viral sequence data to examine intra-host variability, a representation of the extent to which the virus was mutating within an infected individual. They found little within-host viral diversity; an average of only 3 variants were identified per individual, and these were present mostly at low frequencies. They then also considered inter-host variability to build a phylogenetic tree representing the likely evolutionary path of the virus as it was transmitted between crewmembers. This phylogeny, the authors note, was also suggestive of a superspreading event in which few transmission events separated the initial infected individual from the rest of those infected. Finally, the authors attempted to determine whether inter-host diversity was more consistent with a narrow bottleneck or a wide bottleneck. “If the transmission bottleneck is narrow, most non-fixed variants would be private to single individuals, and at sites with fixed variants, the mutations will generally be present at ~0 percent or ~100 percent frequency. If transmission bottlenecks were wide on the boat, variants would be observed in multiple individuals at intermediate frequency,” they wrote. The data they observed, was clearly consistent with the narrow transmission model. As Hannon summarized, “we found that even in circumstances that are highly conducive to transmission like a superspreading event, SARS-CoV-2 exhibits limited within-host diversity that is rarely transmitted between individuals.” From humble beginnings great things come.

Hannon was eager to note the importance of the cross-divisional collaboration in the success of this work. “[Jerome lab member] Dr. Pavitra Roychoudhury…spearheaded the sequencing effort and was instrumental to this study. We couldn’t have done it without her!”

Top: Schematized timeline of fishing boat outbreak and sample collection. Bottom: phylogeny of SARS-CoV-2 genomes from the boat. Nodes/numbers represent 1 (small), 4 (medium), or 26 (large) crew members.

This work was supported by the National Institutes of Health, the Washington/Fred Hutch Center for AIDS Research, and the Howard Hughes Medical Institute.

Fred Hutch/UW Cancer Consortium member Keith Jerome contributed to this work.

Hannon WW, Roychoudhury P, Xie H, Shrestha L, Addetia A, Jerome KR, Greninger AL, Bloom JD. Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat. Virus Evol. 2022 Jun 16;8(2):veac052. doi: 10.1093/ve/veac052. PMID: 35799885; PMCID: PMC9257191.