Quantitative RT-PCR revealed fluctuating SARS-CoV-2 viral loads in nasal swab specimens collected throughout the patient’s prolonged hospitalization (Fig.
1C). Cycle threshold (Ct) values were low on days 4 and 13 of illness, which indicated a high viral load at the onset of the infection. Viral Ct values increased in subsequent specimens up to a peak value of 36 on day 27, indicating a steady decrease in viral load. However, viral Ct values rebounded on day 31 and remained low through day 41. This rebound in viral load corresponded to a decline in the patient’s clinical status as indicated by worsening hypotension and increasing serum lactate levels (Fig.
1B). Viral load at day 51 was below the level of detection for the assay, suggesting clearance of the infection.
We performed whole-genome sequencing of SARS-CoV-2 from seven residual diagnostic specimens with sufficient viral load for sequencing (Ct values < 30), corresponding to days 4, 13, 18, 22, 31, 36, and 41 post-symptom onset. Phylogenetic analysis of the consensus sequences clustered the specimens into two groups (Fig.
2A). Specimens collected on days 4, 13, 31, 36, and 41 all belonged to Pango lineage AY.118, a Delta lineage, whereas specimens collected on days 18 and 22 were both identified as Pango lineage BA.1, an Omicron lineage. To confirm these results, independent nucleic acid extractions, library preparations, and sequencing runs were performed from separate aliquots of five specimens (Table
S1), yielding identical lineage assignments. The consensus sequences obtained from independent runs align well, with most instances showing near-identical matches. However, in three specific samples (D18, D22, and D31) very minor variations (often one or two substitutions) were observed between the consensus sequences from the two runs (Table
S1). All consensus sequences of Delta genomes (those runs we used in the study and deposited to GISAID) were found to be identical. The only differences detected between the consensus sequence of Day 41 having two additional nucleotide substitutions, C19955T and A20055G, with the first resulting in a missense mutation (nsp15 T112I). Among the omicron consensus sequences, the sequence from D18 included four additional nucleotide substitutions [C27807T, G28881A, G28882A, and G28883C (N:RG203KR)] compared to the D22 consensus sequence. While D22 included three additional nucleotide substitutions [C27874T (ORF7b:T40I), G28202A, G28881T (N:R203M)] compared to the D18 consensus sequence. No known remdesivir resistance-associated mutations were present in any isolate sequence. To confirm contemporaneous co-circulation of both these Delta and Omicron lineages in the region, we assessed the daily distribution of the most common lineages from publicly available sequences in the GISAID database from Chicago and surrounding Cook County over the dates of the patient’s infection (Fig.
2B and Fig.
2C). At the time of symptom onset, the proportion of new COVID-19 infections in Cook County caused by the Delta VOC was approximately 3–4%, which decreased to less than 1% by day 31 when Delta resurged in the patient (Fig.
2B). By day 18, when Omicron BA.1 was first detected in the patient, Omicron BA.1* lineages were causing greater than 98% of new COVID-19 infections in Cook County. Phylogenetic analysis of the consensus sequences with publicly available sequences in GISAID of isolates collected in Chicago and Cook County during the same time period confirmed that the patient isolates from days 4, 13, 31, 36, and 41 clustered with other contemporaneous Delta lineage sequences whereas the day 18 and 22 isolates clustered with other contemporaneous Omicron lineage sequences (Fig.
2D).
The above deep sequencing results suggested that the patient was initially infected with the SARS-CoV-2 Delta variant followed by a transient superinfection with the Omicron variant. However, these results were based on short-read deep sequencing, which does not capture mutational linkage and may not be reliable for capturing low-frequency variants due to the inherent error rate. Therefore, to better understand when the Omicron superinfection started and if any recombinants arose intra-host, we performed Sanger sequencing of individual 1.5 kilobase (kb) Spike amplicons from 4 specimens at days 4, 13, 18, and 31 (Fig.
3A). 60 individual clones were sequenced for each timepoint plus an additional 60 clones from day 4. Sequences that did not span the entire amplicon or that yielded conflicting forward and reverse sequencing results were discarded (total of 109, 56, 52, and 58 sequences from days 4, 13, 18, and 31, respectively).
Phylogenetic analysis of the individual Spike amplicons revealed close clustering of sequences from days 4, 13, and 31 (Delta variant sequences) and a distinct clustering of Spike amplicons from day 18 (Omicron variant sequences) (Fig.
3B). All amplicons from days 4, 13, and 31 were consistent with a Delta variant infection, while nearly all amplicons from day 18 were consistent with an Omicron variant infection with the exception of a single Delta amplicon. These data suggest that the Omicron superinfection started sometime after day 13 with both variants present at day 18 prior to clearance of the Omicron superinfection by day 31. Notably, Ct values steadily increased over the first 22 days of infection, signifying that the superinfection was not associated with an increase in viral load. Shortly thereafter, a very high Ct value specimen at day 27 preluded the resurgence of the Delta variant at day 31, suggesting that the patient may have been close to clearing the infection in the nasopharynx before re-establishment or reseeding of the viral population by Delta.