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Systematic surveillance of SARS-CoV-2 reveals dynamics of variant mutagenesis and transmission in a large urban population

Aynaud, M.-M.; Caldwell, L.; Al-Zahrani, K.; Barutcu, S.; Chan, K.; Obersterescu, A.; Ogunjimi, A.; jin, m.; Zakoor, K.-R.; Patel, S.; padilla, R.; Jen, M.; Mae, P.; Dewsi, N.; Yonathan, F.; Zhang, L.; Ayson-Fortunato, A.; Aquino, A.; Krzyzanowski, P.; Simpson, J. T.; Bartlett, J.; Lungu, I.; Poutanen, S.; Wouters, B.; Gekas, M.; Rini, J.; Pelletier, L.; Mazzulli, T.; Wrana, J. L.

2024-07-29 infectious diseases
10.1101/2024.07.25.24311007 medRxiv
Show abstract

Highly mutable pathogens generate viral diversity that impacts virulence, transmissibility, treatment, and thwarts acquired immunity. We previously described C19-SPAR-Seq, a high-throughput, next-generation sequencing platform to detect SARS-CoV-2 that we deployed to systematically profile variant dynamics of SARS-CoV-2 for over 3 years in a large, North American urban environment (Toronto, Canada). Sequencing of the ACE2 receptor binding motif and polybasic furin cleavage site of Spike in over 70,000 patients revealed that population sweeps of canonical variants of concern (VOCs) occurred in repeating wavelets. Furthermore, we found that subvariants and putative quasi-species with alterations characteristic of future VOCs and/or predicted to be functionally important arose frequently, but always extinguished. Systematic screening of functionally relevant domains in pathogens could thus provide a powerful tool for monitoring spread and mutational trajectories, particularly those with zoonotic potential.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.