Real-time analysis of a mass vaccination effort confirms the safety of FDA-authorized mRNA vaccines for COVID-19 from Moderna and Pfizer/BioNtech
Authors: McMurry Reid , Lenehan Patrick , Awasthi Samir , Silvert Eli , Puranik Arjun , Pawlowski Colin , Venkatakrishnan AJ , Anand Praveen , Agarwal Vineet , O’Horo John C. , Gores Gregory J. , Williams Amy W. , Badley Andrew D. , Halamka John , Virk Abinash , Swift Melanie D. , Carlson Katie , Doddahonnaiah Deeksha , Metzger Anna , Kayal Nikhil , Berner Gabi , Ramudu Eshwan , Carpenter Corinne , Wagner Tyler , Rajasekharan Ajit , Soundararajan Venky 
Published: February 2021

As the COVID-19 vaccination campaign unfolds as one of the most rapid and widespread in history, it is important to continuously assess the real-world safety of the FDA-authorized vaccines. Curation from large-scale electronic health records (EHRs) allows for near real-time safety evaluations that were not previously possible. Here, we advance context- and sentiment-aware deep neural networks over the multi-state Mayo Clinic enterprise (Minnesota, Arizona, Florida, Wisconsin) for automatically curating the adverse effects mentioned by healthcare providers in over 108,000 EHR clinical notes between December 1st2020 and February 8th2021. We retrospectively compared the clinical notes of 31,029 individuals who received at least one dose of the Pfizer/BioNTech or Moderna mRNA vaccine to those of 30,933 unvaccinated individuals who were propensity matched by demographics, residential location, and history of prior SARS-CoV-2 testing. We find that vaccinated and unvaccinated individuals were seen in the clinic at similar rates within 21 days of the first or second actual or assigned vaccination date (first dose Odds Ratio = 1.14, 95% CI: 1.10-1.18; second dose Odds Ratio = 0.91, 95% CI: 0.86-0.96). Further, the incidence rates of all surveyed adverse effects were similar or lower in vaccinated individuals compared to unvaccinated individuals after either vaccine dose, although myalgia was modestly increased within 7 days of the second dose when considering only pairs of matched individuals who each had at least one clinical note in this time window (Incidence Rate Ratio = 2.5, 95% CI: 1.1-6.7). Finally, the most frequently documented adverse effects within 7 days of each vaccine dose were fatigue (Dose 1: 1.75%, Dose 2: 1.18%), nausea (Dose 1: 1.03%, Dose 2: 0.84%), myalgia (Dose 1: 0.41%; Dose 2: 0.43%), diarrhea (Dose 1: 0.65%; Dose 2: 0.45%), arthralgia (Dose 1: 0.64%; Dose 2: 0.57%), erythema (Dose 1: 0.56%; Dose 2: 0.44%), vomiting (Dose 1: 0.44%, Dose 2: 0.29%) and fever (Dose 1: 0.21%; Dose 2: 0.18%). These frequencies of adverse event documentation in EHR notes are 2.1 times (95% CI: [1.5, 3.0]) to 1500 times (95% CI: [670, 2800]) lower than the frequencies of adverse events recorded via active solicitation during clinical trials or post-marketing surveillance, with headache after second vaccination showing the highest ratio of trial reporting to EHR documentation. This rapid and timely analysis of EHR notes from 31,029 vaccinated individuals highlights the rarity of vaccine-associated adverse effects requiring clinical attention and reaffirms the tolerability of the FDA-authorized COVID-19 vaccines in practice.