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Diagnosis of SARS-CoV-2: Experience with rapid immunochromatography tests and RT-qPCR

JOURNAL OF CLINICAL VIROLOGY PLUS 2025年第2期5卷 100207-100207页

作者： Gaytan, David Alejandro Cabrera Bautista, Porfirio Felipe Hernandez tinoco, clara esperanza santacruz Yaah, Julio Elias Alvarado Hernandez, Yu-Mei Anguiano Miguel, Bernardo Martinez Paras, Alfonso Vallejos Nieto, Lumumba Arriaga Gutierrez, Nancy Sandoval Muniz, Concepcion Grajales Paz, Alejandro Moctezuma Betancourt, Leticia Jaimes Inst Mexicano Seguro Social Coordinac Calidad Insumos & Labs Especializados Ciudad De Mexico Mexico Inst Mexicano Seguro Social Coordinac Vigilancia Epidemiol Ciudad De Mexico Mexico Inst Mexicano Seguro Social Bienestar IMSS BIENEST Organismo Publ Descentralizado Serv Salud Ciudad De Mexico Mexico Inst Mexicano Seguro Social Coordinacio Invest Salud Ciudad De Mexico Mexico Inst Mexicano Seguro Social Unidad Med Familiar 7 Ciudad De Mexico Mexico

Background: Mexico has experienced six waves were experiences between 2019 and 2023 of coronavirus disease 2019 (COVID-19). In the first wave, diagnosis relied on RT-qPCR;rapid tests for SARS-CoV-2 were introduced from the second wave onward. However, the patterns of results with this test in Mexico have not been documented in population-based studies. Objective: To describe the temporal patterns of the results from RT-qPCR and rapid immunochromatography tests for SARS-CoV-2 detection from the second to the sixth epidemic wave in Mexico. Materials and methods: This was a multicenter study at the national level. The operational definition of suspected cases of viral respiratory illness, confirmed cases of SARS-CoV-2 in Mexico, and data for asymptomatic individuals who required rapid testing between 2020 and 2023 were employed;testing was employed for the entirety of the four years. Positivity was estimated per epidemiological week, state, and condition for both tests. Spearman's correlation coefficient, trend chi-square analysis, and odds ratios with 95 % confidence intervals were used. Results: A total of 1749,765 cases had RT-qPCR data recorded from 2020 to 2023, and 8356,903 cases with rapid tests were conducted for virus identification. Compared with the rest of the country, the southeastern region exhibited different patterns. The positivity rate of rapid tests from the epidemiological surveillance system was lower than that of RT-qPCR during interepidemics periods, whereas the positivity rate of rapid tests for symptomatic individuals was higher than that of RT-qPCR tests over two years. Conclusion: Rapid tests for SARS-CoV-2 identification in Mexico were affordable and timely at the local level. These tests revealed differing epidemic wave patterns in the southeastern region of the country.

关键词： RT-qPCR SARS-CoV-2 Rapid antigen test Epidemiological surveillance RdRp gene

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Genetic polymorphisms rs1800871 and rs1800872 of IL-10 gene are associated with dengue infection, especially with serotype 1 and DwoWS in Mexican population

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CYTOKINE 2023年第1期166卷 156194页

作者： Monroy-Munoz, Irma Eloisa Munoz-Medina, Jose Esteban Fragoso, Jose Manuel santacruz-tinoco, clara esperanza Sevilla-Montoya, Rosalba Hidalgo-Bravo, Alberto Montes-Herrera, Daniel Bravo-Flores, Eyerahi Angeles-Martinez, Javier Inst Nacl Perinatol Isidro Espinosa de los Reyes Dept Genet & Genom Humana Ciudad De Mexico 11000 Mexico Inst Mexicano Seguro Social Coordinac Calidad Insumos & Labs Especializados Mexico City DF Mexico Inst Nacl Cardiol Ignacio Chavez Dept Biol Mol Ciudad De Mexico 14080 Mexico Inst Mexicana Seguro Social Div Labs Vigilancia & Invest Epidemiol Ciudad De Mexico 07760 Mexico Inst Nacl Rehabil Luis Guillermo Ibarra Ibarra Dept Med Genom Ciudad De Mexico 14389 Mexico Inst Mexicano Seguro Social Lab Cent Epidemiol Ciudad De Mexico 02990 Mexico

Introduction:Dengue infection is generated by a complex interaction between DENV (Dengue Virus) and the host's immune response. Interleukin-10 is an immunoregulatory cytokine during DENV infection. The objective of this study was to investigate whether genetic variants in IL-10 could be useful as a predictive and susceptibility marker in the prognosis of DENV infection, particularly with serotype 1, and in participants with dengue without warning signs. Material and methods:A study of cases (n = 365) and controls (n = 364) was carried out. Genotyping was performed by real-time PCR using TaqMan probes. Sample size power was calculated using Quanto software Results:This is the first report showing the independent association of the T allele of rs1800871 (P = 0.023) and the A allele of rs1800872 (P = 0.010) with the risk of dengue infection. Statistical analysis established the genotypic association of IL-10 SNPs with DENV infection under different inheritance models. Our results also showed the association of the CC, TC, and CA haplotypes (P = 0.0064, P = 0.0032, and P = 0.0010 respectively) with infection. Furthermore, both polymorphic sites were associated with the risk of DwoWS and serotype 1 (Den-1) under different inheritance models. Finally, under the dominant model, we identified a positive correlation between IL-10 levels vs. IFN-& gamma;and IL-8. Conclusion:Our results show the first independent association of the T and A alleles of the polymorphic sites rs1800871 and rs1800872, with dengue infection, particularly with Den-1, and in participants with DwoWs.

关键词： Dengue Polymorphisms Inflammation IL-10

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In Silico Identification of Highly Conserved Epitopes of Influenza A H1N1, H2N2, H3N2, and H5N1 with Diagnostic and Vaccination Potential

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BIOMED RESEARCH INTERNATIONAL 2015年第0期2015卷 813047-813047页

作者： Esteban Munoz-Medina, Jose Javier Sanchez-Vallejo, Carlos Mendez-Tenorio, Alfonso Elosia Monroy-Munoz, Irma Angeles-Martinez, Javier Santos Coy-Arechavaleta, Andrea esperanza santacruz-tinoco, clara Gonzalez-Ibarra, Joaquin Anguiano-Hernandez, Yu-Mei Raul Gonzalez-Bonilla, Cesar Ramon-Gallegos, Eva Alberto Diaz-Quinonez, Jose Inst Mexicano Seguro Social Ctr Med Nacl Raza Lab Cent Epidemiol Mexico City 02990 DF Mexico Inst Politecn Nacl Escuela Nacl Ciencias Biol Lab Biotecnol Bioinformat & Genomic Mexico City 11340 DF Mexico Inst Nacl Perinatol Isidro Espinosa Reyes Dept Genet Genom & Humana Lab Genom Mexico City 11000 DF Mexico Inst Nacl Cardiol Ignacio Chavez Dept Biol Mol Lab Genom Mexico City 14080 DF Mexico Inst Mexicano Seguro Social Div Lab Vigilancia & Invest Epidemiol Mexico City 03100 DF Mexico Inst Politecn Nacl Escuela Nacl Ciencias Biol Campus Zacatenco Dept Morfol Lab Citopatol Ambiental Mexico City 07738 DF Mexico Inst Diagnost & Referencia Epidemiol Manuel Marti Colonia Unidad Lomas Plateros Mexico City 01480 DF Mexico Univ Nacl Autonoma Mexico Fac Med Colonia Copilco Univ Mexico City 04510 DF Mexico

The unpredictable, evolutionary nature of the influenza A virus (IAV) is the primary problem when generating a vaccine and when designing diagnostic strategies;thus, it is necessary to determine the constant regions in viral proteins. In this study, we completed an in silico analysis of the reported epitopes of the 4 IAV proteins that are antigenically most significant (HA, NA, NP, and M2) in the 3 strains with the greatest world circulation in the last century (H1N1, H2N2, and H3N2) and in one of the main aviary subtypes responsible for zoonosis (H5N1). For this purpose, the HMMER program was used to align 3,016 epitopes reported in the Immune Epitope Database and Analysis Resource (IEDB) and distributed in 34,294 stored sequences in the Pfam database. Eighteen epitopes were identified: 8 in HA, 5 in NA, 3 in NP, and 2 in M2. These epitopes have remained constant since they were first identified (similar to 91 years) and are present in strains that have circulated on 5 continents. These sites could be targets for vaccination design strategies based on epitopes and/or as markers in the implementation of diagnostic techniques.

关键词： INFLUENZA diagnosis INFLUENZA prevention ALGORITHMS ANTIGENS COMPUTER simulation EVOLUTION (Biology) INFLUENZA vaccination INFLUENZA A virus, H3N2 subtype POPULATION geography BIOINFORMATICS INFLUENZA A virus INFLUENZA A virus, H5N1 subtype INFLUENZA A virus, H1N1 subtype DATA analysis software DESCRIPTIVE statistics SEQUENCE analysis

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Longevity and Neutralizing Capacity of IgG Antibodies against SARS-CoV-2 Generated by the Application of BNT162b2, AZD1222, Convidecia, Sputnik V, and CoronaVac Vaccines: a Cohort Study in the Mexican Population

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MICROBIOLOGY SPECTRUM 2023年第1期11卷 e0237622页

作者： Fernandes-Matano, Larissa Gustavo Salas-Lais, Angel Grajales-Muniz, Concepcion Hernandez-Avila, Mauricio Omar Garfias-Becerra, Yonathan Cesar Rodriguez-Sepulveda, Mario Segura-Sanchez, Carlos Montes-Herrera, Daniel Mendoza-Sanchez, Denisse Angeles-Martinez, Javier Santos Coy-Arechavaleta, Andrea Elias Alvarado-Yaah, Julio esperanza santacruz-tinoco, clara Ramon-Gallegos, Eva Esteban Munoz-Medina, Jose Inst Mexicano Seguro Social Coordinac Calidad Insumos & Labs Especializados Mexico City DF Mexico Inst Politecn Nacl Escuela Nacl Ciencias Biol Programa Doctorado Biomed & Biotecnol Mol Mexico City DF Mexico Inst Mexicano Seguro Social Lab Cent Epidemiol Mexico City DF Mexico Oficina Vigilancia Epidemiol Programa IMSS Bienes Mexico City DF Mexico Inst Mexicano Seguro Social Direcc Prestn Econ & Sociales Mexico City DF Mexico Conde De Valenciana Fdn Inst Ophthalmol Res Unit Mexico City DF Mexico Univ Nacl Autonoma Mexico Fac Med Dept Biochem Mexico City DF Mexico Inst Mexicano Seguro Social Div Labs Especializados Mexico City DF Mexico

The WHO has approved the use of several vaccines during the COVID-19 pandemic;experience over the last 2 years has indicated that dose demand can only be covered using more than one design. Therefore, having scientific evidence of the performance of the different vaccines applied in a country is highly relevant. In Mexico, 5 vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were used, allowing a cohort study to analyze the generation of anti-S1/S2 IgG antibodies and anti-RBD antibodies with neutralizing activity at 0, 21, 90, and 180 days after vaccination. Five groups of participants were formed on the basis of the type of vaccine received and were divided on the basis of whether they previously had or did not have COVID-19. After completing the vaccination schedule, the seroprevalence was 95.5, 97.5, 81.0, 95.2, and 90.0% (BNT162b2, AZD1222, Convidecia, Sputnik V, and CoronaVac, respectively). Among the participants without COVID-19 prior to vaccination, the largest amount of antibodies in the 90-day period was observed in the BNT162b2 group, and the amount of antibodies in the Sputnik V group decreased the least over time. Even though the percentages of seroconversion obtained in this study were lower than those currently reported in other parts of the world, the tested vaccines are able, in most cases, to induce a good production of IgG antibodies anti-S1/S2 and neutralizing capacity. The fact that there are people who have not produced antibodies during the study leaves open some questions that must be investigated to avoid the appearance of serious cases of *** Since the start of the vaccination programs against COVID-19 in 2020, it was evident that due to global shortages, the demand for the dose required in Mexico could only be covered by acquiring different vaccines. Therefore, determining the effectiveness of these and the longevity of acquired immunity is extremely important in a scenario where SARS-CoV-2 circul

关键词： longevity antibodies vaccines

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Diversity, composition, and networking of saliva microbiota distinguish the severity of COVID-19 episodes as revealed by an analysis of 16S rRNA variable V1-V3 region sequences

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MSYSTEMS 2023年第4期8卷 e0106222页

作者： Larios Serrato, Violeta Meza, Beatriz Gonzalez-Torres, Carolina Gaytan-Cervantes, Javier Gonzalez Ibarra, Joaquin santacruz tinoco, clara esperanza Anguiano Hernandez, Yu-Mei Martinez Miguel, Bernardo Cazarez Cortazar, Allison Sarquiz Martinez, Brenda Alvarado Yaah, Julio Elias Mendoza Perez, Antonina Reyna Palma Herrera, Juan Jose Garcia Soto, Leticia Margarita Chavez Rojas, Adriana Ines Bravo Mateos, Guillermo Samano Marquez, Gabriel Grajales Muniz, Concepcion Torres, Javier Inst Politecn Nacl Dept Bioquim Escuela Nacl Ciencias Biolog Mexico City Mexico Univ Autonoma Baja California La Paz Baja California Mexico Ctr Invest Biolog Noroeste SC La Paz Baja California Mexico Ctr Med Nacl SXXI IMSS Unidad Invest Med Enfermedades Infecciosa UMAE Pediat Torreon Mexico IMSS Div Desarrollo Invest Lab Secuenciac Torreon Mexico IMSS Coordinac Invest Salud Div Desarrollo Invest Salud Torreon Mexico IMSS Coordinac Calidad Insumos & Lab Especializ Div Lab Especializados Torreon Mexico IMSS Direcc Prestaciones Med Coordinac Vigilancia Epidemiol Torreon Mexico IMSS Hosp Gen Zona 27 Mexico City Mexico OOAD Cd Mexico Coordinadora Informac & Analisis Estrateg Mexico City Mexico IMSS Hosp Gen Zona Med Familiar 8 Cd Mexico City Mexico IMSS Bienestar Dept Vigilancia Epidemiol Mexico City Mexico

SARS-CoV-2 infection is the most severe pandemic of humankind in the last hundred years. The outcome of the infection ranges from asymptomatic or mild to severe and even fatal cases, but reasons for this remain unknown. Microbes normally colonizing the respiratory tract form communities that may mitigate the transmission, symptoms, and severity of viral infections, but very little is known on the role of these microbial communities in the severity of COVID-19. We aimed to characterize the bacterial communities in saliva of patients with different severity of COVID-19 disease, from mild to fatal cases. Our results revealed clear differences in the composition and in the nature of interactions (networking) of the bacterial species present in the different clinical groups and show community-patterns associated with disease severity. Characterization of the microbial communities in saliva may offer important clues to learn ways COVID-19 patients may suffer from different disease severities. Studies on the role of the oral microbiome in SARS-CoV-2 infection and severity of the disease are limited. We aimed to characterize the bacterial communities present in the saliva of patients with varied COVID-19 severity to learn if there are differences in the characteristics of the microbiome among the clinical groups. We included 31 asymptomatic subjects with no previous COVID-19 infection or vaccination;176 patients with mild respiratory symptoms, positive or negative for SARS-CoV-2 infection;57 patients that required hospitalization because of severe COVID-19 with oxygen saturation below 92%, and 18 fatal cases of COVID-19. Saliva samples collected before any treatment were tested for SARS-CoV-2 by PCR. Oral microbiota in saliva was studied by amplification and sequencing of the V1-V3 variable regions of 16S gene using an Illumina MiSeq platform. We found significant changes in diversity, composition, and networking in saliva microbiota of patients with COVID-19, as well as pa

关键词： COVID-19 microbiota microbial networks disease severity viral infections

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The Alpha Variant (B.1.1.7) of SARS-CoV-2 Failed to Become Dominant in Mexico

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MICROBIOLOGY SPECTRUM 2022年第2期10卷 e0224021页

作者： Zarate, Selene Taboada, Blanca Esteban Munoz-Medina, Jose Isa, Pavel Sanchez-Flores, Alejandro Boukadida, Celia Herrera-Estrella, Alfredo Selem Mojica, Nelly Rosales-Rivera, Mauricio Gomez-Gil, Bruno Gustavo Salas-Lais, Angel esperanza santacruz-tinoco, clara Montoya-Fuentes, Hector Elias Alvarado-Yaah, Julio Maria Molina-Salinas, Gloria Elena Espinoza-Ayala, Gloria Antonio Enciso-Moreno, Jose Maria Gutierrez-Rios, Rosa Loza, Antonio Moreno-Contreras, Joaquin Garcia-Lopez, Rodrigo Rivera-Gutierrez, Xaira Comas-Garcia, Andreu Maria Wong-Chew, Rosa Jimenez-Corona, Maria-Eugenia Maria del Angel, Rosa Armando Vazquez-Perez, Joel Matias-Florentino, Margarita Perez-Garcia, Marissa Avila-Rios, Santiago Castelan-Sanchez, Hugo G. Delaye, Luis Martinez-Castilla, Leon P. Escalera-Zamudio, Marina Lopez, Susana Arias, Carlos F. Univ Autonoma Ciudad de Mexico Posgrad Ciencias Genom Ciudad De Mexico Mexico Univ Nacl Autonoma Mexico Inst Biotecnol Dept Genet Desarrollo & Fisiol Mol Cuernavaca Morelos Mexico Inst Mexicano Seguro Social Coordinac Calidad Insumos & Labs Especializados Ciudad De Mexico Mexico Univ Nacl Autonoma Mexico Inst Biotecnol Unidad Univ Secuenciac Mas & Bioinformat Cuernavaca Morelos Mexico Inst Nacl Enfermedades Resp Ismael Cosio Villegas Ctr Invest Enfermedades Infecciosas Ciudad De Mexico Mexico Ctr Invest & Estudios Avanzados IPN Unidad Genom Avanzada Lab Nacl Genom Biodiversidad Irapuato Mexico Univ Nacl Autonoma Mexico Ctr Ciencias Matemat Morelia Michoacan Mexico Univ Autonoma Estado Morelos Ctr Invest Ciencias Inst Invest Ciencias Basicas & Aplicadas Cuernavaca Morelos Mexico Ctr Invest Alimentac & Desarrollo AC Unidad Mazatlam Mazatlan Mexico Inst Mexicano Seguro Social Lab Cent Epidemiol Ciudad De Mexico Mexico Inst Mexicano Seguro Social Div Labs Especializados Ciudad De Mexico Mexico Inst Mexicano Seguro Social Ctr Invest Biomed Occidente Guadalajara Jalisco Mexico Inst Mexicano Seguro Social Unidad Invest Med Yucatan Merida Yucatan Mexico Inst Mexicano Seguro Social Ctr Invest Biomed Noreste Monterrey Mexico Inst Mexicano Seguro Social Unidad Invest Biomed Zacatecas Zacatecas Zacatecas Mexico Univ Nacl Autonoma Mexico Inst Biotecnol Dept Microbiol Mol Cuernavaca Morelos Mexico Univ Autonoma San Luis Potosi Fac Med San Luis Potosi San Luis Potosi Mexico Univ Autonoma San Luis Potosi Ctr Invest Ciencias Salud & Biomed San Luis Potosi San Luis Potosi Mexico Univ Nacl Autonoma Mexico Fac Med Div Invest Lab Invest Enfermedades Infecciosas Ciudad De Mexico Mexico Inst Nacl Cardiol Ignacio Chavez Dept Epidemiol Ciudad De Mexico Mexico CINVESTAV Dept Infectom & Patogenesis Mol Ciudad De Mexico Mexico Lab Biol Mol Enfermedades Emergentes Ciudad De Mexico Mexico EPOC Inst Nacl Enfermedades Resp Ismael Cosio Vil Ciudad De Mexico Mexi

During the coronavirus disease 2019 (COVID-19) pandemic, the emergence and rapid increase of the B.1.1.7 (Alpha) lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first identified in the United Kingdom in September 2020, was well documented in different areas of the world and became a global public health concern because of its increased transmissibility. The B.1.1.7 lineage was first detected in Mexico during December 2020, showing a slow progressive increase in its circulation frequency, which reached its maximum in May 2021 but never became predominant. In this work, we analyzed the patterns of diversity and distribution of this lineage in Mexico using phylogenetic and haplotype network analyses. Despite the reported increase in transmissibility of the B.1.1.7 lineage, in most Mexican states, it did not displace cocirculating lineages, such as B.1.1.519, which dominated the country from February to May 2021. Our results show that the states with the highest prevalence of B.1.1.7 were those at the Mexico-U.S. border. An apparent pattern of dispersion of this lineage from the northern states of Mexico toward the center or the southeast was observed in the largest transmission chains, indicating possible independent introduction events from the United States. However, other entry points cannot be excluded, as shown by multiple introduction events. Local transmission led to a few successful haplotypes with a localized distribution and specific mutations indicating sustained community transmission. IMPORTANCE The emergence and rapid increase of the B.1.1.7 (Alpha) lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) throughout the world were due to its increased transmissibility. However, it did not displace cocirculating lineages in most of Mexico, particularly B.1.1.519, which dominated the country from February to May 2021. In this work, we analyzed the distribution of B.1.1.7 in Mexico using phylogenetic and haplotype netw

关键词： Alpha genomic surveillance Mexico SARS-CoV-2

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