Two Years of Evolutionary Dynamics of SARS-CoV-2 in Mexico, With Emphasis on the Variants of Concern

Flores-Alanis, Alejandro; Delgado, Gabriela; Espinosa-Camacho, Luis F.; Rodríguez‐Gómez, Flor; Cruz-Rangel, Armando; Sandner-Miranda, Luisa; Cravioto, Alejandro; Morales-Espinosa, Rosario

doi:10.3389/fmicb.2022.886585

Cited by 3 publications

(2 citation statements)

References 40 publications

(42 reference statements)

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“…In Mexico, SARS-CoV-2 VOCs were introduced mainly from the U.S.A. and Europe, and they were responsible for the four waves described in this study [ 26 ]. In 2020, the most prevalent SARS-CoV-2 lineages were B.1 and B.1.222.…”

Section: Discussionmentioning

confidence: 99%

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Clinical Characteristics of Coronavirus Disease (COVID-19) in Mexican Children and Adolescents

Flores-Alanis

Saldaña-Ahuactzi

Parra-Ortega

et al. 2022

Viruses

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Background: We analyzed the demographic, clinical, and diagnostic data of children and adolescents in Mexico, from the first case of coronavirus disease (COVID-19) to 28 February 2022. Methods: Using the open databases of the Ministry of Health and a tertiary pediatric hospital, we obtained demographic and clinical data from the beginning of the COVID-19 pandemic until 28 February 2022. In addition, quantitative reverse-transcription polymerase chain reaction outputs were used to determine the viral load, and structural protein-based serology was performed to evaluate IgG antibody levels. Results: Of the total 437,832 children and adolescents with COVID-19, 1187 died. Of these patients, 1349 were admitted to the Hospital Infantil de Mexico Federico Gómez, and 11 died. Obesity, asthma, and immunosuppression were the main comorbidities, and fever, cough, and headache were the main symptoms. In this population, many patients have a low viral load and IgG antibody levels. Conclusion: During the first 2 years of the COVID-19 pandemic in Mexico, children and adolescents had low incidence and mortality. They are a heterogeneous population, but many patients had comorbidities such as obesity, asthma, and immunosuppression; symptoms such as fever, cough, and headache; and low viral load and IgG antibodies.

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Section: Discussionmentioning

confidence: 99%

“…In 2020, the most prevalent SARS-CoV-2 lineages were B.1 and B.1.222. These variants were likely the cause of the high mortality rate in the first wave [ 26 ]. Mexico City had the highest number of cases and deaths, and the HIMFG is a tertiary-care pediatric hospital located in Mexico City.…”

Section: Discussionmentioning

confidence: 99%

Clinical Characteristics of Coronavirus Disease (COVID-19) in Mexican Children and Adolescents

Flores-Alanis

Saldaña-Ahuactzi

Parra-Ortega

et al. 2022

Viruses

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Frequency of respiratory virus-associated infection among children and adolescents from a tertiary-care hospital in Mexico City

Nieto-Rivera,

Saldaña-Ahuactzi,

Parra-Ortega

et al. 2023

Sci Rep

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Acute respiratory infections (ARIs) are a major cause of morbidity and mortality among children. The causative pathogens show geographic and seasonal variations. We retrospectively evaluated the frequency and seasonality of respiratory pathogens in children and adolescents (age: 0–19 years) with ARIs treated between January 1, 2021, and March 31, 2022, at a single center in Mexico. Out of 2400 patients, 1,603 were diagnosed with SARS-CoV-2 infection and 797 were diagnosed with other common respiratory pathogens (CRPs). Of the 797 patients, 632 were infected with one CRP and 165 with > 2 CRPs. Deaths occurred only in SARS-CoV-2-infected patients. Rhinovirus/Enterovirus, respiratory syncytial virus B, and parainfluenza virus 3 were the most prevalent in cases with single and multiple infections. CRP showed a high frequency between autumn and winter of 2021, with higher incidence of hospitalization compared to COVID-19. The main comorbidities were immunosuppression, cardiovascular disease (CD), and asthma. The frequency of CRPs showed a downward trend throughout the first half of 2021. CRPs increased in single- and co-infection cases between the fourth and fifth waves of COVID-19, probably due to decreased nonpharmaceutical interventions and changes in diagnostic tests. Age, cyanosis (symptom), and immunosuppression (comorbidity) were found to differentiate between SARS-CoV-2 infection and CRP infection.

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Rural populations facilitated early SARS-CoV-2 evolution and transmission in Missouri, USA

Tang,

Li,

Haynes

et al. 2023

npj Viruses

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In the United States, rural populations comprise 60 million individuals and suffered from high COVID-19 disease burdens. Despite this, surveillance efforts are biased toward urban centers. Consequently, how rurally circulating SARS-CoV-2 viruses contribute toward emerging variants remains poorly understood. In this study, we aim to investigate the role of rural communities in the evolution and transmission of SARS-CoV-2 during the early pandemic. We collected 544 urban and 435 rural COVID-19-positive respiratory specimens from an overall vaccine-naïve population in Southwest Missouri between July and December 2020. Genomic analyses revealed 53 SARS-CoV-2 Pango lineages in our study samples, with 14 of these lineages identified only in rural samples. Phylodynamic analyses showed that frequent bi-directional diffusions occurred between rural and urban communities in Southwest Missouri, and that four out of seven Missouri rural-origin lineages spread globally. Further analyses revealed that the nucleocapsid protein (N):R203K/G204R paired substitutions, which were detected disproportionately across multiple Pango lineages, were more associated with urban than rural sequences. Positive selection was detected at N:204 among rural samples but was not evident in urban samples, suggesting that viruses may encounter distinct selection pressures in rural versus urban communities. This study demonstrates that rural communities may be a crucial source of SARS-CoV-2 evolution and transmission, highlighting the need to expand surveillance and resources to rural populations for COVID-19 mitigation.

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Two Years of Evolutionary Dynamics of SARS-CoV-2 in Mexico, With Emphasis on the Variants of Concern

Cited by 3 publications

References 40 publications

Clinical Characteristics of Coronavirus Disease (COVID-19) in Mexican Children and Adolescents

Clinical Characteristics of Coronavirus Disease (COVID-19) in Mexican Children and Adolescents

Frequency of respiratory virus-associated infection among children and adolescents from a tertiary-care hospital in Mexico City

Rural populations facilitated early SARS-CoV-2 evolution and transmission in Missouri, USA

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