Intra-Host Evolution Provides for Continuous Emergence of SARS-CoV-2 Variants

Variants of concern in SARS-CoV-2 refer to viral genomes that differ significantly from the ancestor virus and that show the potential for higher transmissibility and/or worse clinical progression.  Newly emerging SARS-CoV-2 variants of concern (VOC) have the potential to disrupt ongoing public health measures and vaccine efforts. Yet, little is known regarding how frequently different viral variants emerge and under what circumstances. We report a longitudinal study to determine the degree of SARS-CoV-2 sequence evolution in 94 COVID-19 cases and to estimate the frequency at which highly diverse variants emerge. 2 cases accumulated ≥ 9 single-nucleotide variants (SNVs) over a two-week period and 1 case accumulated 23 SNVs over a three-week period, including three non-synonymous mutations in S (D138H, E554D, D614G). We estimate that in 2% of COVID cases, viral variants with multiple mutations, including in the Spike surface glycoprotein, can become the dominant strains in as little as one month of hospitalization, indicative of persistent virus replication. This suggests the continued local emergence of VOC independent of travel patterns. Surveillance by sequencing for (i) viremic COVID-19 patients, (ii) patients suspected of re-infection, and (iii) patients with diminished immune function may offer broad public health benefits. Funding: This work was supported by funding from the Medical Foundation of North Carolina, the NC Collaboratory, and public health service grants 5UM1CA121947-10 to R.P.M, 2P01CA01901438 to J.D.G, and B.D., and 2-R01-DE018304-10, 1-R01-CA239583-01 to D.P.D. Conflict of Interest: Authors declare no competing interests. Ethical Approval: Sample use was approved under # 20-2448 and # 13-2140 by the Internal Review Board.