Rapid evolution of SARS-CoV-2 challenges human defenses

Abstract

The race between pathogens and their hosts is a major evolutionary driver, where both reshuffle their genomes to overcome and reorganize the defenses for infection, respectively. Evolutionary theory helps formulate predictions on the future evolutionary dynamics of SARS-CoV-2, which can be monitored through unprecedented real-time tracking of SARS-CoV-2 population genomics at the global scale. Here we quantify the accelerating evolution of SARS-CoV-2 by tracking the SARS-CoV-2 mutation globally, with a focus on the Receptor Binding Domain (RBD) of the spike protein determining infection success. We estimate that the > 820 million people that had been infected by October 5, 2021, produced up to 1021 copies of the virus, with 12 new effective RBD variants appearing, on average, daily. Doubling of the number of RBD variants every 89 days, followed by selection of the most infective variants challenges our defenses and calls for a shift to anticipatory, rather than reactive tactics involving collaborative global sequencing and vaccination.

Global m6A RNA Methylation in SARS-CoV-2 Positive Nasopharyngeal Samples in a Mexican Population: A First Approximation Study

“…Rapid changes of the dominant variants over the sampling period could be due to the crowded environment allowing the virus to spread. In addition, high mutation and recombination rates of RNA viruses, as well as asymptomatic infections, could also contribute to the rapid diversification of SARS-CoV-2 [ 32 ] even among fully vaccinated individuals. Despite the limitations of this study (which can be addressed in future studies), our results suggest that viral variants modulate genome and/or viral m6A levels differentially ( Figure 5 ).…”

Variantes de SARS-CoV-2 y los casos asociados a cuatro olas epidemiológicas en Sinaloa, México

“…Vaccination in Sinaloa started at the beginning of the second wave, on January 12, 2021 for health professionals, and on May 16 for teachers, school workers, and people over 50 years old. During the third wave, a large percent of the adult population had received at least All these vaccines were initially designed to fight the original variant of SARS-CoV-2 (Wuhan strain NC_045512); however, mutation and recombination rates mostly in the receptor-binding domain (RBD) of the Spike protein have posed a challenge for acquired immunity (Duarte et al, 2022). A new generation of vaccines should achieve better recognition of viral variants and boost immunity to cope with subsequent epidemic waves.…”

Structural topological analysis of spike proteins of SARS-CoV-2 variants of concern highlight distinctive amino acid substitution patterns

“…( Ahmad et al, (2022) ; Duarte et al, (2022) ; European Centre for Disease Prevention and Control ECDC (2022) ; Nikolaidis et al, (2022) ; Universal Protein Database (2022) ; Wise (2020) ; World Health Organisation (2022a) ; World Health Organisation (2022b) ; World Health Organisation (2020) ; Yang et al, (2021) ; Yi et al, (2020) ; Yoshimoto et al, (2020) …”