Protection of Omicron sub-lineage infection against reinfection with another Omicron sub-lineage
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Abstract
There is significant genetic distance between SARS-CoV-2 Omicron (B.1.1.529) variant BA.1 and BA.2 sub-lineages. This study investigates immune protection of infection with one sub-lineage against reinfection with the other sub-lineage in Qatar during a large BA.1 and BA.2 Omicron wave, from December 19, 2021 to March 21, 2022. Two national matched, retrospective cohort studies are conducted to estimate effectiveness of BA.1 infection against reinfection with BA.2 (N = 20,994; BA.1-against-BA.2 study), and effectiveness of BA.2 infection against reinfection with BA.1 (N = 110,315; BA.2-against-BA.1 study). Associations are estimated using Cox proportional-hazards regression models after multiple imputation to assign a sub-lineage status for cases with no sub-lineage status (using probabilities based on the test date). Effectiveness of BA.1 infection against reinfection with BA.2 is estimated at 94.2% (95% CI: 89.2–96.9%). Effectiveness of BA.2 infection against reinfection with BA.1 is estimated at 80.9% (95% CI: 73.1–86.4%). Infection with the BA.1 sub-lineage appears to induce strong, but not full immune protection against reinfection with the BA.2 sub-lineage, and vice versa, for at least several weeks after the initial infection.
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SciScore for 10.1101/2022.02.24.22271440: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Oversight: Hamad Medical Corporation and Weill Cornell Medicine-Qatar Institutional Review Boards approved this retrospective study with a waiver of informed consent.
Consent: Oversight: Hamad Medical Corporation and Weill Cornell Medicine-Qatar Institutional Review Boards approved this retrospective study with a waiver of informed consent.Sex as a biological variable not detected. Randomization A total of 315 random SARS-CoV-2-positive specimens collected between December 19, 2021 and January 22, 2022 were viral whole-genome sequenced. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources The hazard ratio comparing incidence of … SciScore for 10.1101/2022.02.24.22271440: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Oversight: Hamad Medical Corporation and Weill Cornell Medicine-Qatar Institutional Review Boards approved this retrospective study with a waiver of informed consent.
Consent: Oversight: Hamad Medical Corporation and Weill Cornell Medicine-Qatar Institutional Review Boards approved this retrospective study with a waiver of informed consent.Sex as a biological variable not detected. Randomization A total of 315 random SARS-CoV-2-positive specimens collected between December 19, 2021 and January 22, 2022 were viral whole-genome sequenced. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources The hazard ratio comparing incidence of infection in case versus control cohorts and corresponding 95% CI were calculated using Cox regression adjusted for matching factors and COVID-19 vaccination status (unvaccinated, one dose, two doses, or three doses at the start of the follow-up) with the STATA 17.0 stcox STATAsuggested: (Stata, RRID:SCR_012763)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:This study has limitations. Since the Omicron wave was initially dominated with BA.1 (Figure 1), the follow-up in the BA.2- against-BA.1 study was shifted in calendar time to after the follow-up in the BA.1- against-BA.2 study. With the high intensity of infection transmission, followed by rapid decline of the Omicron wave, more of the uninfected-controls in the BA.2- against-BA.1 study may have experienced an undocumented Omicron infection compared to the uninfected-controls in the BA.1- against-BA.2 study. This would bias to a lower value and may explain why was lower than that of . Effectiveness against reinfection was estimated for only few weeks after the primary infection. A longer duration of follow-up may identify differences not yet seen given the recency of the Omicron wave. However, evidence has been consistent that natural immunity, unlike vaccine immunity, wanes slowly with minimal waning for at least several months after primary infection.2,5-9,20-22 BA.1 and BA.2 ascertainment was based on proxy criteria, presence or absence of SGTF using the TaqPath PCR assay, but this method of ascertainment is well established not only for Omicron sub-lineages, but also for other variants such as Alpha.6,19,33 BA.1 and BA.2 ascertainment was not possible for infections diagnosed using RAT or other PCR testing. This limitation was mitigated by basing the main analysis estimate on the distribution of known BA.1 and BA.2 cases for each calendar day, and by providing a sensitivi...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
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- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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