Large Scale SARS-CoV-2 Molecular Testing and Genomic Surveillance Reveal Prolonged Infections, Protracted RNA shedding, and Viral Reinfections.

Only 5 of 21(23%) genomes within this timeframe met our quality scores in vaccinated patients compared to 55 of 159(35%) in unvaccinated patients, despite older median age in the vaccinated patients (64 compared to 55, p=0.00065) ( Figure 3B ), and lower median days from the initial test for all samples where sequencing was attempted (17 days vaccinated, 32 days unvaccinated, p=0.0003, Figure 3C ).In general, genomes of repeat positives from vaccinated patients after 20 days from the first positives were very few which caused a notable trend of a decrease in coverage with time when compared to the unvaccinated group ( Figure 3D ).

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