Diversity and selection of SARS-CoV-2 minority variants in the early New York City outbreak

High error rates of viral RNA-dependent RNA polymerases lead to diverse intra-host viral populations during infection. Errors made during replication that are not strongly deleterious to the virus can lead to the generation of minority variants. Here we analyzed minority variants within the SARS-CoV-2 data in 12 samples from the early outbreak in New York City, using replicate sequencing for reliable identification. While most minority variants were unique to a single sample, we found several instances of shared variants. We provide evidence that some higher-frequency minority variants may be transmitted between patients or across short transmission chains, while other lower-frequency, more widely shared variants arise independently. Further, our data indicate that even with a small transmission bottleneck, the heterogeneity of intra-host viral populations is enhanced by minority variants present in transmission samples. Our data suggest that analysis of shared minority variants could help identify regions of the SARS-CoV-2 genome that are under increased selective pressure, as well as inform transmission chains and give insight into variant strain emergence. IMPORTANCEWhen viruses replicate inside a host, the virus replication machinery makes mistakes. Over time, these mistakes create mutations that result in a diverse population of viruses inside the host. Mutations that are neither lethal to the virus, nor strongly beneficial, can lead to minority variants. In this study, we analyzed the minority variants in SARS-CoV-2 patient samples from New York City during the early outbreak. We found common minority variants between samples that were closely related and showed that these minority variants may be transmitted from one patient to another. We show that in general, transmission events between individuals likely contain genetically diverse viral particles, and we find signatures of selection governing intra-host evolution. We conclude that the analysis of shared minority variants can help to identify transmission events and give insight into emergence of new viral variants.