Early genomic, epidemiological, and clinical description of the SARS-CoV-2 Omicron variant in Mexico City

Abstract

Background. Omicron is the most mutated SARS-CoV-2 variant that has emerged, resulting in viral phenotype alterations, which can affect transmissibility, disease severity, and immune evasiveness. Genomic surveillance of a highly transmissible variant is important in cities with millions of inhabitants and an economic center such as Mexico City. In this work, we describe the early effects of the Omicron variant in Mexico City, exploring its genomic profile and clinical description. Methodology. We sequenced SARS-CoV-2-positive samples in November and December 2021 using the public database GISAID. Haplotype and phylogenetic analyses were performed to genomically characterize Omicron. We used the Mexican federal database to explore the association with clinical information such as symptoms and vaccination status. Findings. The first case of Omicron was detected on November 16, 2022, and until December 31, 2021, we observed an increase from 88% in sequenced samples. Nineteen nonsynonymous mutations were found in the Omicron RBD, and we further explored the R346K substitution, which was prevalent in 42% of the samples and associated with immune escape by monoclonal antibodies. In the phylogenetic analysis, we found that there were several independent exchanges between Mexico and the world, and there was an event followed by local transmission that gave rise to most of the Omicron diversity in Mexico City. The haplotype analysis allowed us to observe that there was no association between haplotype and vaccination status. Of the patients with clinical data, 66% were vaccinated, none of the reported comorbidities were associated with Omicron, the presence of odynophagia and absence of dysgeusia were significant predictor symptoms for Omicron, and the Ct value on RT-qPCR was lower in Omicron. Conclusions. Genomic surveillance in highly populated and fast-moving urban regions such as Mexico City is key to detecting the emergence and spread of SARS-CoV-2 variants in a timely manner, even weeks before the onset of an infection wave, to detect patterns that can inform public health decisions. It is also necessary to continue sequencing to detect the spread of any mutation that may affect the therapeutic efficacy or guide it.

The relative prevalence of the Omicron variant within SARS-CoV-2 infected cohorts in different countries: A systematic review

“…The studies are ordered based on the earliest date in each study. Omicron Study Country Dates BA.1 BA.2 Omicron Delta (or other variant) Cedro-Tanda et al 38 Mexico November 16, 2021 – November 21, 2021 2% 98% December 13, 2021 – December 19, 2021 65% 35% December 27, 2021 – December 31, 2021 88% 12% Mella-Torres et al 75 Chile November 29, 2021 – January 24, 2022 B.1.1529 (534/588) 90.5% 9.1%(54/588) Alpha (B.1.1.7) 0.2% (1/588) Gamma (P.1) 0.2% (1/588) Carrazco-Montalvo et al 56 Ecuador December 12, 2021 – December 18, 2021 50% (33/66) 50% (33/66) De Souza et al 25 …”

New SARS-CoV-2 Omicron variant — clinical picture, treatment, prevention (literature review)

“…также ниже у животных, инфицированных Омикроном, по сравнению с Дельта-штаммом или диким вариантом в обеих моделях животных. Однако при сравнении больных со штаммами Дельта и Омикрон по возрасту, полу, количеству сопутствующих заболеваний и выраженности симптомов на момент постановки диагноза, значимых различий не выявлено [29,30]. У первых пациентов, у которых в ноябре 2021г в Южной Африке был идентифицирован новый штамм SARS-CoV-2, отмечались очень легкие симптомы без потребности в кислородной поддержке.…”

“…По данным большинства исследователей продолжительность госпитализации в случае заражения вариантом Омикрон (BA.1) значительно короче, чем при Дельта-штамме (B.1.617.2), средняя разница длительности госпитализации составляет 4 сут. [16,30].…”

“…В клинических исследованиях показано достоверное и клинически значимое снижение тяжести течения заболевания при заражении вариантом Омикрон. Это было подтверждено в исследованиях, проводимых в различных странах мира: Шотландии 30 , Великобритании 31,32 , Канаде [52], США [11].…”

“…https://www.research.ed.ac.uk/en/publications/severity-of-omicron-variant-of-concern-and-vaccine-effectiveness (22.12.2021). 30 Israeli Ministry of Health. 31 Brown J, Zhou J, Peacock T, et al 32 WHO Report (2021).…”