Time-varying effectiveness of the mRNA-1273, BNT162b2 and Ad26.COV2.S vaccines against SARS-CoV-2 infections and COVID-19 hospitalizations and deaths: an analysis based on observational data from Puerto Rico

Robles-Fontan, M. M.; Nieves, E. G.; Cardona-Gerena, I.; Irizarry, R. A.

Background We collected hospitalization, death, and vaccination status data for all 86,488 laboratory- confirmed SARS-CoV-2 infections in Puerto Rico since the first COVID-19 vaccine was administered starting on December 15, 2020 and ending September 24, 2021. Using these data we estimated real-world time-varying effectiveness of the mRNA-1273 (Moderna), BNT162b2 (Pfizer), and Ad26.COV2.S (J & J) COVID-19 vaccines to quantify the public health benefits of Puerto Rico's immunization campaign. Furthermore, we compared the effectiveness of the COVID-19 vaccines before and after the dominance of the Delta variant. As of this writing, Puerto Rico had a higher vaccination rate and lower SARS-CoV-2 infection rate than all 50 States in the USA. Methods We used data obtained from the integration of the Puerto Rico Department of Health databases holding vaccination status, SARS-CoV-2 test results, and COVID-19 hospitalizations, and deaths. We estimated time-varying vaccine effectiveness against SARS-CoV-2 infections by fitting a statistical model that adjusts for time-varying incidence rates, age, gender, and day of the week. We also used this model to estimate the relative risk of hospitalization and deaths comparing vaccinated to unvaccinated individuals. Code and data are provided to reproduce the analysis here: https://github.com/rafalab/vax-eff-pr Results All vaccines were effective at reducing risks for all outcomes across all age groups. At the peak of their protection, mRNA-1273, BNT162b2, and Ad26.COV2.S had an effectiveness of 87% (85% - 89%), 85% (82% - 87%), and 65% (58% - 70%), with Ad26.COV2.S reaching this peak 32 days after the being considered fully vaccinated. After four months, effectiveness waned to about 73%, 58%, and 32% for mRNA-1273, BNT162b2, and Ad26.COV2.S, respectively. All vaccines had a lower effectiveness for those over 85 years, with the decrease in effectiveness particularly low for the Ad26.COV2.S vaccine. We found no clear evidence that effectiveness was different after the Delta variant became dominant. For those infected, the vaccines provided further protection against hospitalization and deaths across all age groups, although the protection was less for those above 85 years. Using the rates observed for the unvaccinated we would have observed 6,109 and 2,071 hospitalizations and deaths among the vaccinated population but we instead observed 728 and 164, respectively. Conclusions The mRNA-1273 and BNT162b2 vaccines where highly effective across all age groups. They were still effective after four months although the protection did wain. The Ad26.COV2.S vaccine was effective but to a lesser degree, especially for the older age groups, and with the protection waning substantially sooner in comparison to the other two vaccines.