Probability of Hospitalization and Death Among Covid-19 Patients With Comorbidity During Outbreaks Occurring in Mexico City

et al. 2022

Viruses

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Omicron is the most mutated SARS-CoV-2 variant—a factor that can affect transmissibility, disease severity, and immune evasiveness. Its genomic surveillance is important in cities with millions of inhabitants and an economic center, such as Mexico City. Results. From 16 November to 31 December 2021, we observed an increase of 88% in Omicron prevalence in Mexico City. We explored the R346K substitution, prevalent in 42% of Omicron variants, known to be associated with immune escape by monoclonal antibodies. In a phylogenetic analysis, we found 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. A haplotype analysis revealed that there was no association between haplotype and vaccination status. Among the 66% of patients who have been vaccinated, no reported comorbidities were associated with Omicron; the presence of odynophagia and the absence of dysgeusia were significant predictor symptoms for Omicron, and the RT-qPCR Ct values were lower for Omicron. Conclusions. Genomic surveillance 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, and can inform public health decisions and detect the spread of any mutation that may affect therapeutic efficacy.

Section: Resultsmentioning

confidence: 89%

Section: Introductionmentioning

confidence: 99%

Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City

et al. 2022

Viruses

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Section: Resultsmentioning

confidence: 89%

“…The logistic regression model showed that none of these comorbidities were associated with a specific variant. These results suggest that risk assessment based on comorbidities and associated clinical risk predictors currently used [4,36] may remain valid for the Omicron variant. In terms of symptomatology, a logistic regression model (see table 2) showed two symptoms as significant to differentiate between the delta and Omicron variants.…”

Section: Epidemiology and Clinical Associationsmentioning

confidence: 84%

“…Mexico City has been heavily affected by the COVID-19 pandemic. Two intense epidemic waves occurred in spring 2020 and winter 2020/2021, during which the heaviest toll of hospitalizations and deaths was observed [4,5]. A vaccination campaign began, starting with frontline healthcare workers and continuing in descending age order, and was completed in fall 2021 (http://vacunacovid.gob.mx/wordpress/calendario-vacunacion/).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

Preprint

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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.

COVID-19 Reinfections in Mexico City: Implications for public health response

et al. 2022

Preprint

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Background: SARS-CoV-2 pandemia continues to be important even when more than 60% of the global population has been vaccinated. As the pandemia evolves the number of reinfection cases will continue to increase as new variants are generated that evade the immune response. Understanding reinfections is important to guide the public health system and to inform decision-makers. Methods: We downloaded clinical outcome and severity of infection data from the SISVER (respiratory disease epidemiological surveillance system) database. We sequenced SARS-CoV-2 samples, identified SARS-CoV-2 lineage and upload this genomic data to GISAID. We analyzed time and lineage between index infection and reinfection. We also analyzed the clinical outcome, severity of infection and vaccination status during reinfections. Findings: In this study we confirmed that each wave of SARS-CoV-2 infections was characterized by a different viral variant showing a prevalence higher that 95%. We found that the fraction of reinfection is not linearly related to the average time of separation between waves with 40% of all the reinfections occurring at wave 5, the only wave with more than one SARS-CoV-2 variant with a prevalence higher than 80%. Regarding type of care 2.63% patients were considered ambulatory during the reinfection even when they were hospitalized during the index infection and only 0.78% presented the opposite behavior. Moreover, 6.74% reinfections transitioned from asymptomatic to mild or severe or from mild to severe; and 8.95% transitioned from severe to mild or asymptomatic or from mild to asymptomatic. The highest number of reinfections have occurred in unvaccinated patients (41.6%), followed shortly by vaccinated patients (31.9%). However, most reinfections occurred after wave 4 when the national vaccination efforts have reached 65% of the general population. Interpretation: The analyzed data suggests a diminished severity of infection during reinfection either if transitions in disease severity or transitions in type of patient care are considered. Finally, we also observed an overrepresentation of unvaccinated patients in reinfections.