Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: A retrospective cohort study
- Harvard TH Chan School of Public Health, United States
- Yale School of Public Health, United States
- University of Nebraska Medical Center, United States
- IQVIA, Real World Solutions, United States
- Duke Center for Antimicrobial Stewardship and Infection Prevention, United States
- Tempus Labs, United States
- Vagelos College of Physicians and Surgeons, Columbia University, United States
- Hospital for Special Surgery, United States
- National Basketball Association, United States
Figures
Figure 1
PCR Ct value trajectories for confirmed and suspected infections.
(A) PCR Ct value trajectories for each acute Delta (red), Omicron BA.1 (blue), and other (black) infection. Individuals are grouped by the gap between detection and their most recent negative or …
Figure 2
Posterior estimates from a generalized linear model predicting probability of Ct value <30 with spline terms for the interaction between days since detection with age group and the interaction between days since detection with vaccination status and variant.
Shown are the marginal effects of (A) vaccination status and (B) age group on the proportion of individuals with Ct <30 on each day post detection after conditioning on being an Omicron BA.1 …
Figure 3
Effect of booster status, antibody titer against the founder SARS-CoV-2 strain and age group on the probability of Ct value <30 over days post detection.
(A) Proportion of Omicron BA.1 infections with Ct value <30 on each day post detection, stratified by age group and the interaction of booster status at the time of infection and antibody titer …
Figure 4
Estimated viral trajectories by variant and titer.
Points depict measured Ct values, lines depict the estimated population mean viral trajectories, and shaded regions depict the 95% credible intervals for the estimated population viral trajectories. …
Appendix 1—figure 1
Summary of cohort.
Top row describes cohort demographics and data on immune histories. Middle row describes infection data. Bottom row provides additional information on the infection data.
Appendix 1—figure 2
Summary of all infection and vaccination events over time, in addition to serum sample collection dates, included in the dataset.
(A) Histogram showing the distribution of vaccination dates (note that most first doses were administered prior to 2021-06-25), showing when in time the majority of individuals were vaccinated. (B) …
Appendix 1—figure 3
Frequency and proportion of SARS-CoV-2 variant detections.
(A) Frequency of sequenced and unsequenced detected infections over time by week. Vertical dashed lines and shaded backgrounds demarcate periods of variant dominance.
Appendix 1—figure 4
Correlation between authentic virus neutralization assay (ID50) and the Diasorin antibody titer against (A) wildtype and (B) Delta.
Horizontal yellow bar shows an ID50 titer of 50 and 100 respectively, Diagonal lines and shaded regions show mean and 95% confidence intervals (CI) for a linear regression between the Diason …
Appendix 1—figure 5
Distribution of delays from detection to symptom onset among individuals with known symptom status.
Dashed lines mark the median delay between detection and symptom onset. Solid lines mark the day of detection (0).
Appendix 1—figure 6
Distribution of delays from symptom onset to peak Ct values among individuals with known symptom status.
Dashed lines mark the median delay between detection and symptom onset. Solid lines mark the day of symptom onset (0).
Appendix 1—figure 7
Proportion of infections with Ct <30 on each day post detection stratified by detection speed.
Solid colored lines and shaded ribbons show posterior means and 95% credible intervals from a generalized linear model predicting probability of Ct <30 as a function of days since detection. Dashed …
Appendix 1—figure 8
All viral trajectories classified as rebound shown in Figure 1B.
Subplots are colored by the most stringent definition for rebound. To be included here, individuals must have 2+consecutive days of Ct ≥30 after an initial Ct <30. The vertical red dotted line marks …
Appendix 1—figure 9
Proportion of infections with Ct <30 on each day post detection by confirmed or suspected variant, vaccination status and detection group, conditional on being in the <30 years age group.
Solid colored lines and shaded ribbons are posterior estimates from a generalized linear model predicting probability of Ct <30 as a function of days since detection and vaccination status, showing …
Appendix 1—figure 10
Identical to Appendix 1—figure 9, but after excluding data from all players.
Appendix 1—figure 11
Proportion of Omicron BA.1 infections, stratified by symptom status, with Ct <30 on each day post detection by booster status and detection group.
Solid colored lines and shaded ribbons are posterior estimates from a generalized linear model predicting probability of Ct <30 as a function of days since detection, variant (only BA.1 results …
Appendix 1—figure 12
Proportion of Omicron BA.1 infections with Ct <30 on each day post detection stratified by vaccination status, age group and detection group.
Solid colored lines and shaded ribbons are posterior estimates from a generalized linear model predicting probability of Ct <30 as a function of days since detection, vaccination status and variant, …
Appendix 1—figure 13
Individual antibody titers to the ancestral SARS-CoV-2 spike over time.
(A) Measured antibody titers by date of sample collection. Lines show longitudinal samples from the same individual, colored by the most recent exposure at the time of sample collection. Lines going …
Appendix 1—figure 14
Histogram of time between (A) second vaccine dose and antibody titer measurement and (B) booster dose and antibody titer measurement.
Dashed line marks the median lag (162 days). 1 individual was infected between receiving their second vaccine dose and having a titer measurement taken (Delta infection). 42 individuals were …
Appendix 1—figure 15
Distribution of antibody titers among Omicron BA.1-infected individuals (colored points) stratified by age group and vaccination status at the time of infection.
Shown are mean titers (large black point) and bootstrapped 95% confidence intervals for the mean (black bars). Note that stratification is by infection and not individual, and that antibody titers …
Appendix 1—figure 16
Proportion of BA.1 Omicron infections with Ct <30 on each day post detection stratified by the interaction of booster status at the time of infection and antibody titer group (note, not stratified by age group here due to small subgroup size).
Shown are posterior estimates from a generalized linear model predicting probability of Ct <30 with a spline term on days since detection, conditional on titer/vaccination status category. Solid …
Appendix 1—figure 17
Schematic diagram of the likelihood function for viral kinetic inference.
The plot depicts the likelihood as a function of ΔCt, the difference between the observed Ct value and the limit of detection, so that ΔCt = 0 (the origin) represents observations at the limit of …
Tables
Table 1
Characteristics of the documented infections.
Counts (N) correspond to numbers of infections.
| Variable | Category | N | Percent |
|---|---|---|---|
| Total | – | 1280 | 100 |
| Variant | Delta | 180 | 14.1 |
| Omicron BA.1 | 878 | 68.6 | |
| Other | 222 | 17.3 | |
| Vaccination Status | Unvaccinated | 228 | 17.8 |
| First dose | 6 | 0.5 | |
| Second dose | 420 | 32.8 | |
| Boosted | 626 | 48.9 | |
| Antibody Titer | 13–250 | 473 | 37.0 |
| 250–800 | 504 | 39.4 | |
| Unknown | 303 | 23.7 | |
| Symptomatic | No | 257 | 20.1 |
| Yes | 664 | 51.9 | |
| Unknown | 359 | 28 | |
| Detection Speed | Delayed detection | 877 | 68.5 |
| Frequent testing | 403 | 31.5 | |
| Age Group | 0–30 | 556 | 43.4 |
| 31–50 | 568 | 44.4 | |
| 50+ | 155 | 12.1 | |
| Unknown | 1 | 0.1 | |
| Cumulative Infection Number | 1 | 1128 | 88.1 |
| 2 | 149 | 11.6 | |
| 3 | 2 | 0.2 | |
| 4 | 1 | 0.1 | |
| Days Since Previous Exposure | Naïve (no prior exposure) | 220 | 17.2 |
| <1 month | 273 | 21.3 | |
| 1–3 months | 403 | 31.5 | |
| >3 months | 384 | 30.0 |
Table 2
Number of rebound infections classified under different definitions for initial clearance and subsequent rebound.
| Initial clearance duration (consecutive days with Ct ≥30) | Rebound duration (days above Ct value threshold) | Ct value threshold of rebound | Rebounds | Total | Percentage |
|---|---|---|---|---|---|
| ≥4 | ≥4 | Ct <30 | 0 | 749 | 0.00% |
| ≥4 | ≥3 | Ct <30 | 1 | 749 | 0.13% |
| ≥4 | ≥2 | Ct <30 | 4 | 749 | 0.53% |
| ≥3 | ≥4 | Ct <30 | 2 | 999 | 0.20% |
| ≥3 | ≥3 | Ct <30 | 7 | 999 | 0.70% |
| ≥3 | ≥2 | Ct <30 | 16 | 999 | 1.60% |
| ≥2 | ≥4 | Ct <30 | 7 | 1334 | 0.53% |
| ≥2 | ≥3 | Ct <30 | 18 | 1334 | 1.35% |
| ≥2 | ≥2 | Ct <30 | 40 | 1334 | 3.00% |
| ≥4 | ≥4 | Ct <25 | 0 | 749 | 0.00% |
| ≥4 | ≥3 | Ct <25 | 0 | 749 | 0.00% |
| ≥4 | ≥2 | Ct <25 | 0 | 749 | 0.00% |
| ≥3 | ≥4 | Ct <25 | 1 | 999 | 0.10% |
| ≥3 | ≥3 | Ct <25 | 1 | 999 | 0.10% |
| ≥3 | ≥2 | Ct <25 | 2 | 999 | 0.20% |
| ≥2 | ≥4 | Ct <25 | 1 | 1334 | 0.08% |
| ≥2 | ≥3 | Ct <25 | 2 | 1334 | 0.15% |
| ≥2 | ≥2 | Ct <25 | 5 | 1334 | 0.38% |
Appendix 1—table 1
Number of identified rebounds stratified by variant, either confirmed through sequencing or assumed based on detection date.
Rebounds are defined here as any trajectory with an initial Ct <30, followed by a sequence of two or more consecutive negative tests or tests with Ct ≥30, and subsequently followed by two or more …
| Variant | Rebounds | Total infections | Percentage rebounded |
|---|---|---|---|
| Omicron | 36 | 877 | 4.10% |
| Delta | 1 | 178 | 0.562% |
| Other | 3 | 279 | 1.08% |
Appendix 1—table 2
Number of identified rebounds stratified by vaccination status.
Rebounds are defined here as any trajectory with an initial Ct <30, followed by a sequence of two or more consecutive negative tests or tests with Ct ≥30, and subsequently followed by two or more …
| Vaccination status | Rebounds | Total infections | Percentage rebounded |
|---|---|---|---|
| Boosted | 32 | 494 | 6.48% |
| No record | 5 | 398 | 1.26% |
| Second dose | 3 | 323 | 0.929% |
| Unvaccinated | 2 | 159 | 1.26% |
Appendix 1—table 3
Comparison of linear logistic regression models predicting probability of Ct <30 on each day since detection among individuals in the frequent testing group.
Models are ranked based on their expected log pointwise predictive density (ELPD), where a lower ELPD implies better predictive accuracy. Model weight refers to the weight of each model in a …
| Model | ELPD difference | SE difference | Weight | AUC | Classification accuracy | Accuracy (≥30) | Accuracy (<30) |
|---|---|---|---|---|---|---|---|
| Cumulative number of exposures, variant and age | 0.000 | 0.000 | 0.157 | 0.897 | 0.828 | 0.890 | 0.647 |
| Days since previous exposure, variant and age | –1.813 | 10.011 | 0.299 | 0.896 | 0.823 | 0.878 | 0.664 |
| Vaccination status, variant and age | –7.440 | 9.828 | 0.089 | 0.896 | 0.824 | 0.881 | 0.656 |
| Cumulative number of exposures and age | –27.935 | 8.823 | 0.104 | 0.894 | 0.823 | 0.887 | 0.637 |
| Cumulative number of exposures and variant | –31.536 | 9.428 | 0.000 | 0.894 | 0.824 | 0.891 | 0.630 |
| Vaccination status and age | –33.933 | 12.389 | 0.000 | 0.893 | 0.822 | 0.882 | 0.646 |
| Vaccination status and variant | –35.274 | 13.693 | 0.156 | 0.893 | 0.824 | 0.886 | 0.645 |
| Days since previous exposure and variant | –39.750 | 14.206 | 0.000 | 0.891 | 0.822 | 0.883 | 0.644 |
| Days since previous exposure and age | –40.929 | 12.503 | 0.000 | 0.892 | 0.820 | 0.877 | 0.654 |
| Variant and age | –52.437 | 11.681 | 0.000 | 0.890 | 0.817 | 0.884 | 0.624 |
| Cumulative number of exposures | –53.661 | 12.344 | 0.143 | 0.892 | 0.822 | 0.895 | 0.610 |
| Vaccination status | –58.503 | 15.162 | 0.000 | 0.890 | 0.822 | 0.888 | 0.632 |
| Age | –60.160 | 12.688 | 0.000 | 0.890 | 0.818 | 0.882 | 0.632 |
| Days since previous exposure | –69.842 | 15.547 | 0.045 | 0.888 | 0.817 | 0.884 | 0.624 |
| Variant | –87.427 | 15.554 | 0.007 | 0.887 | 0.818 | 0.889 | 0.611 |
| Baseline | –93.087 | 15.843 | 0.000 | 0.886 | 0.817 | 0.890 | 0.606 |
Appendix 1—table 4
Comparison of linear logistic regression models predicting probability of Ct <30 on each day since detection among individuals in the delayed testing group.
Models are ranked based on their expected log pointwise predictive density (ELPD), where a lower ELPD implies better predictive accuracy. Model weight refers to the weight of each model in a …
| Model | ELPD difference | SE difference | Weight | AUC | Classification accuracy | Accuracy (≥30) | Accuracy (<30) |
|---|---|---|---|---|---|---|---|
| Cumulative number of exposures, variant and age | 0.000 | 0.000 | 0.154 | 0.914 | 0.850 | 0.893 | 0.712 |
| Vaccination status, variant and age | –1.817 | 7.807 | 0.000 | 0.913 | 0.849 | 0.890 | 0.720 |
| Vaccination status and age | –6.061 | 8.899 | 0.134 | 0.913 | 0.849 | 0.888 | 0.724 |
| Cumulative number of exposures and age | –7.900 | 4.710 | 0.007 | 0.913 | 0.849 | 0.893 | 0.712 |
| Days since previous exposure, variant and age | –8.046 | 8.929 | 0.288 | 0.913 | 0.849 | 0.890 | 0.721 |
| Days since previous exposure and age | –20.190 | 9.360 | 0.000 | 0.912 | 0.850 | 0.890 | 0.725 |
| Variant and age | –22.457 | 8.628 | 0.081 | 0.912 | 0.850 | 0.888 | 0.728 |
| Vaccination status and variant | –59.936 | 14.986 | 0.162 | 0.909 | 0.847 | 0.888 | 0.717 |
| Cumulative number of exposures and variant | –60.139 | 12.098 | 0.007 | 0.910 | 0.846 | 0.891 | 0.703 |
| Age | –63.495 | 12.834 | 0.052 | 0.910 | 0.849 | 0.882 | 0.743 |
| Cumulative number of exposures | –65.893 | 12.851 | 0.114 | 0.910 | 0.846 | 0.891 | 0.707 |
| Vaccination status | –67.520 | 15.418 | 0.000 | 0.909 | 0.847 | 0.888 | 0.717 |
| Days since previous exposure and variant | –82.798 | 15.986 | 0.000 | 0.909 | 0.846 | 0.888 | 0.714 |
| Days since previous exposure | –93.537 | 16.058 | 0.000 | 0.909 | 0.846 | 0.887 | 0.718 |
| Variant | –107.362 | 15.800 | 0.000 | 0.907 | 0.845 | 0.883 | 0.723 |
| Baseline | –148.350 | 18.608 | 0.000 | 0.905 | 0.842 | 0.880 | 0.722 |
Appendix 1—table 5
Posterior estimates of viral trajectory attributes by variant and vaccination status.
Estimates are posterior means with 95% credible intervals.
| Trajectory value | Variant/vaccination status | Estimate |
|---|---|---|
| Peak viral load (Ct) | Other: Unvaccinated | 25.0 (24.2, 25.9) |
| Delta: 1–2 doses | 22.4 (21.4, 23.5) | |
| Omicron: 1–2 doses | 25.6 (25.0, 26.2) | |
| Omicron: Boosted | 25.7 (25.4, 26.1) | |
| Peak viral load (log10 copies/ml) | Other: Unvaccinated | 6.8 (6.6, 7.0) |
| Delta: 1–2 doses | 7.5 (7.2, 7.8) | |
| Omicron: 1–2 doses | 6.6 (6.5, 6.8) | |
| Omicron: Boosted | 6.6 (6.5, 6.7) | |
| Proliferation time (days) | Other: Unvaccinated | 3.5 (3.1, 3.9) |
| Delta: 1–2 doses | 3.6 (3.1, 4.1) | |
| Omicron: 1–2 doses | 3.6 (3.3, 4.0) | |
| Omicron: Boosted | 4.0 (3.8, 4.3) | |
| Clearance time (days) | Other: Unvaccinated | 9.9 (9.2, 10.6) |
| Delta: 1–2 doses | 7.6 (7.0, 8.3) | |
| Omicron: 1–2 doses | 6.2 (5.8, 6.6) | |
| Omicron: Boosted | 8.4 (8.0, 8.7) |
Appendix 1—table 6
Posterior estimates of viral trajectory attributes by variant and antibody titer.
Estimates are posterior means with 95% credible intervals.
| Trajectory attribute | Variant/immune status | Estimate |
|---|---|---|
| Peak viral load (Ct) | Other: Unexposed | 24.8 (24.0, 25.6) |
| Delta: Exposed,≤250 AU | 22.1 (20.6, 23.4) | |
| Delta: Exposed,>250 AU | 24.4 (22.7, 26.1) | |
| Omicron: Exposed,≤250 AU | 25.2 (24.7, 25.6) | |
| Omicron: Exposed,>250 AU | 26.2 (25.7, 26.6) | |
| Peak viral load (log10 copies/ml) | Other: Unexposed | 6.9 (6.6, 7.1) |
| Delta: Exposed,≤250 AU | 7.6 (7.3, 8.0) | |
| Delta: Exposed,>250 AU | 7.0 (6.5, 7.4) | |
| Omicron: Exposed,≤250 AU | 6.8 (6.7, 6.9) | |
| Omicron: Exposed,>250 AU | 6.5 (6.4, 6.6) | |
| Proliferation time (days) | Other: Unexposed | 3.5 (3.2, 3.9) |
| Delta: Exposed,≤250 AU | 3.6 (2.8, 4.5) | |
| Delta: Exposed,>250 AU | 4.2 (3.3, 5.3) | |
| Omicron: Exposed,≤250 AU | 3.9 (3.6, 4.2) | |
| Omicron: Exposed,>250 AU | 3.7 (3.5, 4.0) | |
| Clearance time (days) | Other: Unexposed | 9.8 (9.1, 10.6) |
| Delta: Exposed,≤250 AU | 7.7 (6.9, 8.7) | |
| Delta: Exposed,>250 AU | 7.6 (6.4, 8.8) | |
| Omicron: Exposed,≤250 AU | 8.4 (8.0, 8.8) | |
| Omicron: Exposed,>250 AU | 6.9 (6.6, 7.3) |
Appendix 1—table 7
Posterior estimates of Omicron BA.1 viral trajectory attributes by symptom and vaccination status.
Estimates are posterior means with 95% credible intervals.
| Trajectory attribute | Variant/immune status | Estimate |
|---|---|---|
| Peak viral load (Ct) | Omicron: 1–2 doses, no symptoms | 26.7 (25.7, 27.7) |
| Omicron: 1–2 doses, symptoms | 25.3 (24.5, 26.1) | |
| Omicron: boosted, no symptoms | 26.3 (25.7, 27) | |
| Omicron: boosted, symptoms | 25.4 (25, 25.8) | |
| Peak viral load (log10 copies/ml) | Omicron: 1–2 doses, no symptoms | 6.3 (6.1, 6.6) |
| Omicron: 1–2 doses, symptoms | 6.7 (6.5, 6.9) | |
| Omicron: boosted, no symptoms | 6.4 (6.3, 6.6) | |
| Omicron: boosted, symptoms | 6.7 (6.6, 6.8) | |
| Proliferation time (days) | Omicron: 1–2 doses, no symptoms | 3.7 (3.2, 4.2) |
| Omicron: 1–2 doses, symptoms | 3.7 (3.2, 4.2) | |
| Omicron: boosted, no symptoms | 4.3 (3.9, 4.8) | |
| Omicron: boosted, symptoms | 3.8 (3.5, 4.1) | |
| Clearance time (days) | Omicron: 1–2 doses, no symptoms | 5.9 (5.2, 6.6) |
| Omicron: 1–2 doses, symptoms | 6.3 (5.8, 6.8) | |
| Omicron: boosted, no symptoms | 7.4 (6.8, 8.0) | |
| Omicron: boosted, symptoms | 8.7 (8.3, 9.1) |
Appendix 1—table 8
Posterior estimates of Omicron BA.1 viral trajectory attributes by symptom and antibody titer.
Estimates are posterior means with 95% credible intervals.
| Trajectory attribute | Variant/immune status | Estimate |
|---|---|---|
| Peak viral load (Ct) | Omicron: Low titer, no symptoms | 26.1 (25.2, 26.9) |
| Omicron: Low titer, symptoms | 24.8 (24.3, 25.4) | |
| Omicron: High titer, no symptoms | 26.7 (25.9, 27.5) | |
| Omicron: High titer, symptoms | 25.9 (25.4, 26.5) | |
| Peak viral load (log10 copies/ml) | Omicron: Low titer, no symptoms | 6.5 (6.3, 6.8) |
| Omicron: Low titer, symptoms | 6.9 (6.7, 7.0) | |
| Omicron: High titer, no symptoms | 6.3 (6.1, 6.6) | |
| Omicron: High titer, symptoms | 6.6 (6.4, 6.7) | |
| Proliferation time (days) | Omicron: Low titer, no symptoms | 4.3 (3.8, 4.9) |
| Omicron: Low titer, symptoms | 3.6 (3.3, 4.0) | |
| Omicron: High titer, no symptoms | 3.8 (3.4, 4.3) | |
| Omicron: High titer, symptoms | 3.8 (3.4, 4.2) | |
| Clearance time (days) | Omicron: Low titer, no symptoms | 7.4 (6.7, 8.1) |
| Omicron: Low titer, symptoms | 8.7 (8.2, 9.3) | |
| Omicron: High titer, no symptoms | 6.4 (5.8, 7.1) | |
| Omicron: High titer, symptoms | 7.1 (6.6, 7.5) |
Appendix 1—table 9
Posterior estimates of Omicron BA.1 viral RNA clearance times by age and vaccination status.
Estimates are posterior means with 95% credible intervals. Low titer is ≤250 AU, high titer is >250 AU.
| Trajectory attribute | Variant/immune status | Estimate |
|---|---|---|
| Peak viral load (Ct) | Omicron:<30, unboosted | 25.6 (25, 26.3) |
| Omicron:<30, boosted | 25.8 (25.1, 26.4) | |
| Omicron: 30–50, unboosted | 25.3 (24.2, 26.5) | |
| Omicron: 30–50, boosted | 25.7 (25.2, 26.2) | |
| Omicron: 50+, unboosted | 25.5 (22.8, 27.9) | |
| Omicron: 50+, boosted | 25.5 (24.6, 26.3) | |
| Peak viral load (log10 copies/ml) | Omicron:<30, unboosted | 6.6 (6.4, 6.8) |
| Omicron:<30, boosted | 6.6 (6.4, 6.8) | |
| Omicron: 30–50, unboosted | 6.7 (6.4, 7) | |
| Omicron: 30–50, boosted | 6.6 (6.5, 6.7) | |
| Omicron: 50+, unboosted | 6.7 (6, 7.4) | |
| Omicron: 50+, boosted | 6.7 (6.5, 6.9) | |
| Proliferation time (days) | Omicron:<30, unboosted | 3.7 (3.4, 4.1) |
| Omicron:<30, boosted | 4.2 (3.8, 4.7) | |
| Omicron: 30–50, unboosted | 3.6 (3, 4.4) | |
| Omicron: 30–50, boosted | 4 (3.6, 4.3) | |
| Omicron: 50+, unboosted | 4.4 (3, 6.3) | |
| Omicron: 50+, boosted | 3.9 (3.4, 4.4) | |
| Clearance time (days) | Omicron:<30, unboosted | 6 (5.6, 6.5) |
| Omicron:<30, boosted | 7.2 (6.7, 7.7) | |
| Omicron: 30–50, unboosted | 6.4 (5.7, 7.2) | |
| Omicron: 30–50, boosted | 8.6 (8.1, 9.1) | |
| Omicron: 50+, unboosted | 8.7 (6.6, 11.2) | |
| Omicron: 50+, boosted | 9.6 (8.8, 10.6) |
Appendix 1—table 10
Posterior estimates of Omicron BA.1 viral RNA clearance times by age and titer.
Estimates are posterior means with 95% credible intervals. Low titer is ≤250 AU, high titer is >250 AU.
| Trajectory attribute | Variant/immune status | Estimate |
|---|---|---|
| Peak viral load (Ct) | Omicron:<30, low titer | 24.8 (24, 25.5) |
| Omicron:<30, high titer | 26.2 (25.6, 26.8) | |
| Omicron: 30–50, low titer | 25.4 (24.8, 26) | |
| Omicron: 30–50, high titer | 26.1 (25.4, 26.8) | |
| Omicron: 50+, low titer | 24.9 (23.8, 25.9) | |
| Omicron: 50+, high titer | 26.3 (24.8, 27.6) | |
| Peak viral load (log10 copies/ml) | Omicron:<30, low titer | 6.9 (6.7, 7.1) |
| Omicron:<30, high titer | 6.5 (6.3, 6.7) | |
| Omicron: 30–50, low titer | 6.7 (6.5, 6.9) | |
| Omicron: 30–50, high titer | 6.5 (6.3, 6.7) | |
| Omicron: 50+, low titer | 6.8 (6.6, 7.1) | |
| Omicron: 50+, high titer | 6.5 (6.1, 6.9) | |
| Proliferation time (days) | Omicron:<30, low titer | 3.9 (3.4, 4.3) |
| Omicron:<30, high titer | 4 (3.6, 4.4) | |
| Omicron: 30–50, low titer | 4 (3.6, 4.4) | |
| Omicron: 30–50, high titer | 3.6 (3.2, 4) | |
| Omicron: 50+, low titer | 3.8 (3.2, 4.5) | |
| Omicron: 50+, high titer | 3.7 (2.9, 4.7) | |
| Clearance time (days) | Omicron:<30, low titer | 7.2 (6.7, 7.8) |
| Omicron:<30, high titer | 6.2 (5.8, 6.7) | |
| Omicron: 30–50, low titer | 8.7 (8.1, 9.3) | |
| Omicron: 30–50, high titer | 7.4 (6.8, 8) | |
| Omicron: 50+, low titer | 9.9 (8.7, 11.1) | |
| Omicron: 50+, high titer | 9.5 (8, 11.1) |
