Virologic characteristics of SARS-CoV-2 infection across evolving Omicron subvariants

Abstract

BACKGROUNDSARS-CoV-2 has evolved subvariants since the emergence of the Omicron variant in 2021. Whether these changes impact viral shedding and transmissibility is not known.METHODSPOSITIVES is a prospective longitudinal cohort of individuals with mild SARS-CoV-2 infection. Ambulatory, immunocompetent participants who did not receive antivirals self-administered 6 anterior nasal swabs over 15 days. Samples were analyzed by qPCR to quantify viral RNA, semiquantitative viral culture to detect shedding of replication-competent virus, and whole-genome sequencing to classify subvariants. Our predictor of interest was Omicron subvariants: BA.1x, BA.2x, BA.4/5x, XBB.x, and JN.x. Outcomes included RNA levels and duration of shedding replication-competent virus. We additionally explored whether symptoms are a valid marker for ending isolation.RESULTSThe median peak nasal SARS-CoV-2 RNA (6.0-6.3 log10 RNA copies/mL), median days to peak RNA (4-5 days), median days to undetectable viral RNA (12-14 days), and median days to negative viral culture (4-8 days) were similar across Omicron subvariants. Number and duration of symptoms were also similar. For all subvariants, a sizeable percentage (range 27.5%-56.0%) shed replication-competent virus after fever resolution and improvement of symptoms.CONCLUSIONDespite ongoing viral evolution, key aspects of viral dynamics of SARS-CoV-2 infection, including the duration of shedding replication-competent virus, have not substantially changed across Omicron subvariants. Replication-competent shedding of these subvariants is detected for a large proportion of people who meet criteria for ending isolation.FUNDINGNIH (U19 AI110818, R01 AI176287, K24 HL166024), the Massachusetts Consortium on Pathogen Readiness, and the Massachusetts General Hospital Department of Medicine.

Keywords: COVID-19; Clinical Research; Infectious disease.

Figure 1. Phylogenetic tree representing the infecting Omicron subvariants in this study based on spike gene sequences (positions 21,565 to 24,025).

Scale bar represents the number of nucleotide substitutions per site.

Figure 2. Baseline, peak, and clearance rates of SARS-CoV-2 RNA levels among Omicron subvariants.

(A) Baseline viral RNA level (= first study nasal swab) for participants in BA.1x, BA.2x, BA.4/5x, XBB.x, and JN.x groups. P = 0.6371, Kruskal-Wallis test. (B) Peak viral RNA level for each participant in BA.1x, BA.2x, BA.4/5x, XBB.x, and JN.x groups. P = 0.8174, Kruskal-Wallis test. (C) Time to reach peak viral RNA level in days, counted from the day of first positive test or symptoms onset for each participant in BA.1x, BA.2x, BA.4/5x, XBB.x, and JN.x groups. P = 0.4688, Kruskal-Wallis test. (A–C) Dashed lines represent the median value for each group, which is reported above each group. (D) Kaplan-Meier survival curves showing time from initial positive SARS-CoV-2 test result or symptom onset until negative viral PCR for groups BA.1x, BA.2x, BA.4/5x, XBB.x, and JN.x. P = 0.3983, log-rank test.

Figure 3. The duration of shedding live virus for Omicron subvariants.

(A) Kaplan-Meier survival curves showing time from initial positive SARS-CoV-2 test result or symptom onset until negative viral culture on Vero-E6 cells for groups BA.1x, BA.2x, BA.4/5x, and XBB.x. P = 0.5178, log-rank test. (B) Kaplan-Meier survival curves showing time from initial positive SARS-CoV-2 test result or symptom onset until negative viral culture on VeroE6-hACE2-hTMPRSS2 (VAT) cells for groups BA.1x, BA.4/5x, and JN.x. P = 0.2783, Mantel-Cox log-rank test. (C) Logistic regression curves showing the probability (mean ± SEM) of positive viral culture on Vero-E6 cells for a range of viral RNA levels for groups BA.1x, BA.2x, BA.4/5x, and XBB.x. P < 0.001, Wald test; viral RNA level and variant category interaction terms from logistic regression model: BA.1x vs. BA.2x P = 0.004, BA.1x vs. BA.4/5x P = 0.871, BA.1x vs. XBB.x P = 0.018, BA.2x vs. BA.4/5x P = 0.004, XBB.x vs. BA.4/5x P = 0.018, and BA.2x vs. XBB.x P = 0.158 at 5 log₁₀ copies RNA/mL. (D) Logistic regression curves showing the probability (mean ± SEM) of positive viral culture on VeroE6-hACE2-hTMPRSS2 cells for a range of viral RNA levels for groups BA.1x, BA.4/5x, and JN.x. P < 0.001, Wald test; viral RNA level and variant category interaction terms from logistic regression model: BA.1x vs. BA.4/5x P = 0.161, JN.x vs. BA.1x P = 0.051, and JN.x vs. BA.4/5x P = 0.545 at 5 log₁₀ copies RNA/mL, JN.x vs. BA.1x P = 0.029 at 4 log₁₀ copies RNA/mL.

Figure 4. Symptom characteristics among Omicron subvariants.

(A) Peak number of symptoms for each participant in BA.1x, BA.2x, BA.4/5x, XBB.x, and JN.x groups. P = 0.6454, Kruskal-Wallis test. (B) Time to reach peak number of symptoms in days, counted from the day of first positive test or symptoms onset for each participant in BA.1x, BA.2x, BA.4/5x, XBB.x, and JN.x groups. P = 0.2487, Kruskal-Wallis test. (A and B) Median values are reported above each group. (C) Number of symptoms at days 1–3, 4–6, and 7–10 for groups BA.1x, BA.2x, BA.4/5x, XBB.x, and JN.x. P = 0.2428 for days 1–3, P = 0.4658 for days 4–6, P = 0.1178 for days 7–10, Kruskal-Wallis test. (D) Time between end of isolation and conversion to negative viral culture for BA.1x, BA.2x, BA.4/5x, and XBB.x on Vero-E6 cells and for BA.1x, BA.4/5x, and JN.x on VAT cells. P = 0.2382 for Vero-E6, P = 0.6450 for VAT, Kruskal-Wallis test (A–D). Dashed lines represent the median value for each group.