Comparative complete scheme and booster effectiveness of COVID-19 vaccines in preventing SARS-CoV-2 infections with SARS-CoV-2 Omicron (BA.1) and Delta (B.1.617.2) variants

  1. Irina Kislaya
  2. André Peralta-Santos
  3. Vítor Borges
  4. Luís Vieira
  5. Carlos Sousa
  6. Bibiana Ferreira
  7. Ana Pelerito
  8. João Paulo Gomes
  9. Pedro Pinto Leite
  10. Baltazar Nunes

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Abstract

Introduction

Information on vaccine effectiveness and viral loads in a context of novel variants of concern (VOC) emergence is of key importance to inform public health policies. This study aimed to estimate a measure of comparative vaccine effectiveness between Omicron (BA.1) and Delta (B.1.617.2 and sub-lineages) VOC according to vaccination exposure (primary or booster) and time since primary vaccination and to compare cycle threshold (Ct) values between Omicron and Delta VOC infections according to the vaccination status as an indirect measure of viral load.

Methods

We developed a case-case study using data on RT-PCR SARS-CoV-2 positive cases notified in Portugal during weeks 49-51 2021. The odds of vaccination in Omicron cases were compared to Delta using logistic regression adjusted for age group, sex, region and week of diagnosis and laboratory of origin. RT-PCR Ct values were compared by vaccination status and variant using linear regression model.

Results

Higher odds of vaccination were observed in cases infected by Omicron (BA.1) VOC compared to Delta (B.1.617.2) VOC cases for both complete primary vaccination (OR=2.1; CI 95% :1.8 to 2.4) and booster dose (OR= 5.2; CI 95%: 3.1 to 8.8), indicating vaccine effectiveness reduction against Omicron. No differences in distribution of Ct-values between these two VOC were observed for any vaccination exposure categories.

Conclusion

Consistent lower VE was observed against Omicron infection. Complete primary vaccination may not be protective against SARS-CoV-2 infection in regions where Omicron variant is dominant, but a massive rollout of booster vaccination campaign can contribute to reduce SARS-CoV-2 incidence in the population.

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  1. ScreenIT

    SciScore for 10.1101/2022.01.31.22270200: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Variant classification: SARS-CoV-2 variants were classified by viral whole-genome sequencing (WGS) or inferred for non-sequenced samples based on data on S-gene amplification using the TaqPath™ Covid 19 CE IVD RT-PCR Kit (Thermo Scientific™) assay, as follows: no S-gene amplification (Omicron BA.1) and S-gene amplification (Delta).
    WGS
    suggested: None

    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:
    Our study has several limitations. First, we were unable to differentiate between symptomatic and asymptomatic infections. Second, our study was based on RT-PCR tests, so rapid antigen test widely used in Portugal for SARS-CoV-2 diagnosis(26) were not covered by our data. Although study included cases samples from National SARS-CoV-2 Genomic Surveillance Network and three major clinical pathology laboratories, we cannot exclude that cases included in our study might not be representative of the overall infections detected in Portugal during week 49-51 2021. Hence, we compared age group, sex and region of study sample and the overall cases notified with infection in the same period. We found no significant differences in the sex and age group distribution between the universe of identified cases through rapid or RT-PCR testing and notified to SINAVE and the study sample. However, the north region tends to be overrepresented in our study sample. Third, incentives for testing had changed during the study period, negative tests regardless vaccination status became required to go to restaurants, hotels and to participate cultural events(27). This change may affect study results. However, selection of cases to the study sample was independent from the VOC type and from vaccination status. Fourth, this study did not collected data on comorbidities, considered relevant confounding variables in vaccines effectiveness research. So, we were not able to adjust for comorbidities in our mo...

    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.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

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  2. Version published to 10.1101/2022.01.31.22270200 on medRxiv