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

BackgroundSARS-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. MethodsWe 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. FindingsIn 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. InterpretationThe 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.

Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico

Up to November 2021, over 200 different SARS-CoV-2 lineages circulated in Mexico. To investigate lineage replacement dynamics, we applied a phylodynamic approach to explore the evolutionary trajectories of five dominant lineages that circulated during the first year of the local epidemic. For most lineages, peaks in sampling frequencies coincided with different epidemiological waves of infection in the country. Lineages B.1.1.222 and B.1.1.519 showed comparable dynamics, represented by clades likely originating in Mexico and persisting for over a year. Lineages B.1.1.7, P.1 and B.1.617.2 also displayed similar dynamics, characterized by multiple introduction events leading to a few successful extended local transmission chains that persisted for several months. We further explored viral movements across the country, applied within the largest clades identified (belonging to lineage B.1.617.2). Many clades were located within the south region of the country, suggesting that this area played a key role in the spread of SARS-CoV-2 in Mexico.

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

BackgroundOmicron 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. MethodologyWe sequenced SARS-CoV-2-positive samples in November and December 2021 and we using the public database GISAID. Haplotype and phylogenetic analyses were performed to genomically characterize Omicron. We used the Mexican federal database toexplore the association with clinical information such as symptoms and vaccination status. FindingsThe 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. ConclusionsGenomic 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.

PROBABILITY OF HOSPITALIZATION AND DEATH AMONG COVID-19 PATIENTS WITH COMORBIDITY DURING OUTBREAKS OCCURRING IN MEXICO CITY.

BackgroundWorldwide, it has been observed that there is a strong association between the severity of COVID-19 and with being over 40 years of age, having diabetes mellitus (DM), hypertension and/or obesity. ObjectiveTo compare the probability of death caused by COVID-19 in patients with comorbidities during three periods defined for this study as follows: first wave (March 23 to July 12, 2020), interwave period (July 13 to October 25, 2020), and the second wave (October 26, 2020, to March 29, 2021) using the different fatality rates observed in Mexico City. MethodsThe cohort studied included individuals over 20 years of age. During the first wave (symptomatic), the interwave period, and the second wave (symptomatic and asymptomatic), participants were diagnosed using nasopharyngeal swabs taken in kiosks. Symptomatic individuals with risk factors for serious disease or death were referred to hospital. SARS-CoV-2 infection was defined by real time polymerase chain reaction in all hospitalized patients. All data from hospitalized patients and outpatients were added to the SISVER database. ResultsThe total cohort size for this study was 2,260,156 persons (having a mean age of 43.1 years). Of these, 8.6% suffered from DM, 11.6% from hypertension, and 9.7% from obesity. Of the total of 2,260,156 persons, 666,694 tested positive (29.5%) to SARS CoV-2, (with a mean age of 45). During the first wave, 82,489 tested positive; in the interwave period, 112,115; and during the second wave, 472,090. That is, a considerable increase in the number of cases of infection was observed in all age groups between the first and second waves (an increase of +472% on the first wave). Of the infected persons, a total of 85,587 (12.8%) were hospitalized: 24,023 in the first wave (29.1% of those who tested positive in this period); 16,935 (15.1%) during the interwave period, and 44,629 (9.5%) in the second wave, which represents an increase of 85.77% on the first wave. Of the hospitalized patients, there were 42,979 deaths (50.2% of those hospitalized), in the first wave, 11,964 (49.8% of those hospitalized in this period), during the interwave period, 6,794 (40.1%), and in the second wave 24,221 (54.3%), an increase of +102.4% between the first wave and the second. While within the general population, the probability of a patient dying having both COVID-19 and one of the specified comorbidities (DM, obesity, or arterial hypertension) showed a systematic reduction across all age groups, the probability of death for a hospitalized patient with comorbidities increased across all age groups during the second wave. When comparing the fatality rate of hospitalized COVID-19 patients in the second wave with those of the first wave and the interwave period, a significant increase was observed across all age groups, even in individuals without comorbidities. ConclusionThe data from this study show a considerable increase in the number of detected cases of infection in all age groups between the first and second waves. In addition, 12.8% of those infected were hospitalized for severe COVID-19, representing an increase of +85.9% from the first wave to the second. A high mortality rate was observed among hospitalized patients (>50%), as was a higher probability of death in hospitalized COVID-19 patients with comorbidities for all age groups during the second wave, although there had been a slight decrease during the interwave period. SUMMARY BOXO_ST_ABSWhat is already known?C_ST_ABSWorldwide the resurging of COVID-19 cases in waves has been observed. In Mexico, like in the rest of the world, we have observed surges of SARS CoV-2 infections, COVID-19 hospitalizations and fatal outcomes followed by decreases leading to local minima. Pre-existing health conditions such as being older, having diabetes mellitus (DM), hypertension and/or obesity has been observed to be associated with an increase in the severity of COVID-19. What are the new findings?O_LIBetween the first and second waves, considerable increases were observed in the number of detected cases of infection (+472%), in the number of hospitalized subjects (+85.9%), and the number of hospitalized subjects and deaths (+102.4%) in all age groups. C_LIO_LIWhen analysing only hospitalized individuals, with or without comorbidities, the Case Fatality Rate was high (50.2%), the probability of death increased considerably in all age groups between the first and second waves. This increase was more noticeable in those individuals with previously identified comorbidities (DM, hypertension, or obesity). C_LIO_LIAn increased probability of death among individuals without comorbidities was observed between the first and second waves. C_LI What do the new findings imply?During the second wave, demand for hospitalization increased, magnifying the impact of age and comorbidities as risk factors. This situation highlights the importance of decreasing the prevalence of comorbidities among the population.

Machine Learning in the analysis of lethality and evolution of infection by the SARS-CoV-2 virus (COVID-19) in workers of the Mexico City Metro

In terms of the number of fatalities, Mexico has been one of the countries most affected worldwide by the pandemic. Using different Machine Learning techniques, some of the first cases of the infection registered in Mexico City (CDMX), the geographical and political center of the country, are analyzed in order to determine the causes of lethality and evolution of infection by the SARS-CoV-2 virus, from April 1 to September 27, 2020 in workers of the Capital Metro.

The evolutionary landscape of SARS-CoV-2 variant B.1.1.519 and its clinical impact in Mexico City

The SARS-CoV-2 pandemic is one of the most concerning health problems around the globe. We report the emergence of SARS-CoV-2 variant B.1.1.519 in Mexico City. This variant represented up to 90% of sequenced cases in February 2021. It is characterized by three amino acid changes in the spike protein: T478K, P681H, and T732A. We report the effective reproduction number of B.1.1.519 and present evidence of its geographical origin based on phylogenetic analysis. We also studied its evolution via haplotype analysis and identified the most recurrent haplotypes. Finally, we studied the clinical impact of B.1.1.519: patients infected with variant B.1.1.519 showed a highly significant adjusted odds ratio (aOR) increase of 1.85 over non-B.1.1.519 patients for developing a severe/critical outcome (P = 0.000296, 1.33-2.6 95% CI) and a 2.35-fold increase for hospitalization (P = 0.005, 1.32-4.34 95% CI). The continuous monitoring of this and other variants will be required to control the ongoing pandemic as it evolves.