The associations between vaccination status, type, and time since vaccination with lineage identity during the emergence of new SARS-CoV-2 variants

By Pooja Toshniwal PahariaReviewed by Danielle Ellis, B.Sc.Sep 7 2022

In a recent study published in Emerging Infectious Diseases, researchers assessed the association between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains and patient age, coronavirus disease 2019 (COVID-19) vaccination status, vaccine type, and days elapsed since the most recent vaccination among New York residents.

Background

Studies have reported higher transmissibility and immune-evasiveness of novel SARS-CoV-2 strains such as Omicron and Delta compared to previously circulating strains. The increased number of mutations in recent strains greatly enhance the infectivity and attenuate the immune protection conferred by existing COVID-19 vaccines, monoclonal antibodies (mAbs), and convalescent sera transfusions. Factors such as patient age, type, vaccination status, and the duration elapsed since the most recent vaccination may also affect COVID-19 vaccine efficacy.

About the study

In the present case-control study, researchers performed a matched case-control analysis to assess the differences in vaccine effectiveness for SARS-CoV-2 strains such as Delta and Omicron associated with variation in vaccination status, vaccine type, time since vaccination, and patient age among New York residents.

A viral genomic sequence dataset linked with demographic and vaccination data obtained from records of the communicable disease electronic surveillance system and New York state immunization information system, respectively, was used for the analysis. The case patient group comprised individuals infected with the emerging SARS-CoV-2 strain, whereas the control group comprised individuals infected with any other SARS-CoV-2 strain.

Respiratory swabs that were found to be SARS-CoV-2-positive by real-time reverse transcription polymerase chain reaction (RT-PCR) were subjected to whole-genome sequencing (WGS) analysis based on the global initiative on sharing all influenza data (GISAID) database sequences. An individual was regarded unvaccinated if the specimen was obtained before COVID-19 vaccinations, vaccinated if the specimen was obtained >2 weeks post-prime vaccination completion (Janssen vaccine’s initial dose and Moderna or Pfizer vaccine’s subsequent dose), and booster vaccinated if the specimen was obtained any time post-booster dose administration of any type of COVID-19 vaccine.

Omicron emergence was analyzed between 28 November 2021 and 24 January 2022, including 1439 case patients (individuals with Omicron infections) and 728 controls (individuals with Delta variant, B.1.617.2, or AY strain infections). Case patients were matched to controls based on the date of specimen collection (±6 days), location (New York state economic areas), patient sex, and age.

Delta emergence was analyzed between 19 March 2021 and 15 August 2021, with 603 case patients and 1,816 controls, respectively. The control group comprised individuals infected with B.1.1.7 and Q.4 Alpha (62%), B.1.526 Iota (20%), P.1.X Gamma (3.5%), and B.1.351.X Beta (1.0%). Logistic regression modeling was used with models selected based on the Akaike information criterion (AIC) scores, and odds ratios (ORs) were calculated.

The team excluded 261 partially vaccinated individuals (whose specimens were obtained between the first dose and two weeks post-completion of vaccination with Moderna (n=90) and or Pfizer vaccines (n=171). In addition, individuals were excluded if they had received the booster (third) vaccination (e.g., potentially immunosuppressed individuals) due to small sample sizes (58 individuals who received booster doses within 135 days of the second vaccination) and different vaccination histories.

Results

Most of the case-control pair individuals for Omicron infections were aged between 18 years and 69 years and resided in the Mid-Hudson and Capital areas. Among cases and controls, 22% and eight percent of individuals had been administered booster vaccinations, respectively. The corresponding percentages for unvaccinated individuals were 30% and 57%, respectively.

The sample population for Pfizer, Moderna, and Janssen vaccinations comprised 177, 109, and 22, respectively. Omicron infections showed the greatest associations with the status of prime vaccinations and booster vaccinations, with OR values of 3.1 and 6.7, respectively. On removing patient age as a criterion for matching (309 case-control pairs), lower age was predictive of Omicron infections (OR 0.96) and OR values for the status of prime vaccination (OR 4.8) and third (booster) vaccination (OR 39) were greater compared to those obtained previously.

On considering only vaccinated individuals (129 case-control pairs), the odds of Omicron infection reduced with a greater duration of days elapsed post-the most recent vaccination (OR 0.99). A trend toward lower chances of Omicron infections post-Janssen vaccinations was observed with borderline significance [OR 0.4, in relation to any messenger ribonucleic acid (mRNA) vaccination].

Among the case-patient/control pairs for Delta infections (55 case-control pairs), most of the individuals were aged between 18 years and 69 years (75%) and resided in Long Island, Mid-Hudson, and Finger Lakes areas (89%). About 62% and 75% of cases and controls were unvaccinated, respectively. Delta infections showed the greatest associations with vaccination status (OR 2.4).

The vaccine type and days elapsed since the most recent vaccination showed no significant association with the odds of Delta infections. Removing age as a matching criterion showed that the odds of Delta infections were 7.3-fold higher among individuals who received Pfizer vaccinations compared to unvaccinated individuals. The odds were also higher for Moderna vaccines (2.0-fold) and Janssen vaccines (0.5-fold), although not statistically significant individually.

Overall, the study findings showed that novel SARS-CoV-2 strains have greater potential than previously circulating strains to cause vaccine breakthrough infections. Infections among completely vaccinated and booster vaccinated individuals were associated significantly with Omicron. However, the odds of being infected with Omicron in relation to Delta reduced with advancing age. An identical but non-significant trend was noted with vaccination status during Delta predominance.