From ISET to InDRE. IV. Institute of Epidemiological Diagnosis and Reference: new orientation, 1990-2012.

From 1990 to 2012, the Sanitary and Tropical Diseases Institute experienced the most important changes. In 1989, its name and orientation were modified to become the National Institute of Epidemiological Diagnosis and Reference. Shortly before, it had been formalized as the apex of the National Network of Public Health Laboratories and had incorporated laboratories for preventive programs such as exfoliative cytology and rabies, malaria and tuberculosis diagnosis; subsequently, it would incorporate other networks that emerged as part of the response to major epidemic outbreaks and to the new epidemiological outlook. In this period, 27 priority diagnostic algorithms were defined, organized in 18 networks, some of which began to collaborate with global networks. In 2001, the Institute started working with pathogens related to bioterrorism. By then, space restrictions of the headquarter's building were evident; in 2008, starting the construction of new facilities was decided. The Institute and its diagnostic networks constitute a milestone in Latin American public health of the 21st century.

De 1990 a 2012, el Instituto de Salubridad y Enfermedades Tropicales experimentó los cambios más importantes desde su origen. En 1989 modificó su nombre y orientación a Instituto Nacional de Diagnóstico y Referencia Epidemiológicos. Poco antes se había formalizado como cúspide de la organización piramidal denominada Red Nacional de Laboratorios en Salud Pública y había incorporado los laboratorios de programas preventivos como el de citología exfoliativa y los de diagnóstico de rabia, paludismo, tuberculosis; posteriormente incorporaría otras redes que surgieron como parte de la respuesta a brotes epidémicos importantes (cólera, VIH-sida, sarampión, influenza) y al nuevo panorama epidemiológico (dengue, Chagas, rotavirus). En este periodo se definieron 27 algoritmos diagnósticos prioritarios organizados en 18 redes, algunas de las cuales comenzaron a colaborar con redes globales. En 2001, en el Instituto se empezó a trabajar con patógenos relacionados con el bioterrorismo. Para entonces, las severas restricciones de espacio del edificio construido en 1935 fueron evidentes; en 2008, las autoridades decidieron iniciar el diseño y construcción de las nuevas instalaciones. En conjunto, el InDRE y sus redes diagnósticas constituyen un hito en la salud pública latinoamericana del siglo XXI.

From the handling of an outbreak by an unknown pathogen in Wuhan to the preparedness and response in the face of the emergence of Covid-19 in Mexico.

On December 31, 2019, the Chinese health authorities informed the international community, through the mechanisms established by the World Health Organization (WHO), of a pneumonia epidemic of unknown etiology in Wuhan, Hubei Province. The first cases were reported early in that month and were linked to a history of having visited a market where food and live animals are sold. On January 7, 2020, isolation and identification of the culprit pathogen was achieved using next-generation sequencing, while the number of affected subjects continued to rise. The publication of full-genomes of the newly identified coronavirus (initially called 2019-nCoV, now called SARS-CoV2) in public and private databases, of standardized diagnostic protocols and of the clinical-epidemiological information generated will allow addressing the Public Health Emergency of International Concern (PHEIC), declared on January 30 by the WHO. With this document, we intend to contribute to the characterization of the pneumonia epidemic, now designated coronavirus disease (Covid-19) review the strengths Mexico has in the global health concert and invite health professionals to join the preparedness and response activities in the face of this emergency.

El 31 de diciembre de 2019, las autoridades chinas de salud informaron a la comunidad internacional, a través de los mecanismos establecidos por la Organización Mundial de la Salud (OMS), de una epidemia de neumonía con etiología desconocida en Wuhan, provincia de Hubei. Los primeros casos se notificaron a inicios de ese mes y se vincularon al antecedente de visitar un mercado de comida y animales vivos. El 7 de enero de 2020 se logró el aislamiento y reconocimiento del patógeno responsable mediante secuenciación de siguiente generación, mientras el número de afectados continuaba en ascenso. La publicación de genomas completos del nuevo coronavirus identificado (inicialmente denominado 2019-nCoV, ahora designado SARS-CoV2) en bases de datos públicas y privadas, de protocolos diagnósticos estandarizados y de la información clínica epidemiológica generada permitirá atender la Emergencia de Salud Pública de Importancia Internacional (ESPII) declarada el 30 de enero por la OMS. Con este documento pretendemos aportar a la caracterización de la epidemia de neumonía, ahora llamada enfermedad por coronavirus (Covid-19), revisar las fortalezas que tiene México en el concierto de la salud global e invitar a los profesionales de la salud a incorporarse a las actividades de preparación y respuesta ante esta emergencia.

From ISET to InDRE. V. Institute of Epidemiological Diagnosis and Reference. Global strategic position, 2012-2019.

This document describes the changes at the Institute of Epidemiological Diagnosis and Reference (InDRE) from 2012 to 2019, the administrative and equipment modifications, the new headquarters and the National System of Epidemiological Surveillance legal modifications. The process of relocation is mentioned, especially the careful transfer of the biological material protected by the Institute, and the new way of studying epidemic outbreaks, endemic diseases and the negative network is analyzed. At the international level, the promotion of links with global networks of the Pan American Health Organization, the World Health Organization (WHO) and other international organizations is described. The assignation to InDRE of four WHO collaborating centres is also mentioned. The Global Health Security Initiative Laboratory Network acknowledged InDRE's leadership, which co-chaired the working group during the study period.

En este documento se describen los cambios en el Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) de 2012 a 2019, las modificaciones administrativas y de equipamiento, la nueva sede y las modificaciones jurídicas al Sistema Nacional de Vigilancia Epidemiológica. Se menciona el proceso de mudanza, en especial el cuidadoso traslado del material biológico que resguarda el Instituto y se analiza la nueva forma de estudiar los brotes epidémicos, los padecimientos endémicos y la red negativa. Respecto al ámbito internacional, se describe el fomento de la vinculación con redes globales de la Organización Panamericana de la Salud, la Organización Mundial de la Salud (OMS) y otros organismos internacionales. También se menciona la designación en el InDRE de cuatro centros colaboradores de la OMS. La Red de Laboratorios de la Iniciativa Global para la Seguridad en Salud reconoció el liderazgo del InDRE, cuyo director ocupó la copresidencia del grupo de trabajo en el periodo de estudio.

Public Veterinary Medicine: Public Health Rabies virus variants identified in Nuevo Leon State, Mexico, from 2008 to 2015.

OBJECTIVE: To identify rabies virus variants (RVVs) isolated from bats and terrestrial mammals in Nuevo Leon between 2008 and 2015 and Coahuila in 2006. SAMPLE: RVVs isolated from 15 bats and terrestrial mammals in Nuevo Leon and from a cow (Bos taurus) in Coahuila, along with 46 reference rabies virus sequences. PROCEDURES: Antigenic characterization of the 16 isolates was performed with an indirect fluorescent antibody technique. Genomic sequencing of the nucleoprotein gene in the 16 isolates was performed with a reverse transcription PCR assay. Phylogenetic reconstruction of the 62 sequences was performed by means of Bayesian inference. RESULTS: 9 isolates from bats and 1 isolate from a domestic cat that became infected as a result of contact with a Mexican free-tailed bat all clustered in the lineage associated with Lasiurus spp in the Americas or the lineage associated with Tadarida brasiliensis mexicana. An isolate from a domestic dog was identified as a variant associated with the dog-coyote lineage. The RVV isolated from a fox clustered in an Arizona fox lineage. The 3 RVVs from skunks (Mephitis macroura) were placed in a lineage with variants isolated from spotted skunks (Spilogale putorius). The RVV isolated from the cow was clustered in a lineage associated with foxes in Texas and separate from the lineage for the fox from Nuevo Leon. CONCLUSIONS AND CLINICAL RELEVANCE: Results reinforced the need for Mexico to implement rabies surveillance and monitoring programs for bats and wild-living terrestrial carnivores.

Field Performance of Two Methods for Detection of Poliovirus in Wastewater Samples, Mexico 2016-2017.

To enhance our ability to monitor poliovirus circulation and certify eradication, we evaluated the performance of the bag-mediated filtration system (BMFS) against the two-phase separation (TPS) method for concentrating wastewater samples for poliovirus detection. Sequential samples were collected at two sites in Mexico; one L was collected by grab and ~ 5 L were collected and filtered in situ with the BMFS. In the laboratory, 500 mL collected by grab were concentrated using TPS and the sample contained in the filter of the BMFS was eluted without secondary concentration. Concentrates were tested for the presence of poliovirus and non-poliovirus enterovirus (NPEV) using Global Poliovirus Laboratory Network standard procedures. Between February 16, 2016, and April 18, 2017, 125 pairs of samples were obtained. Collectors spent an average (± standard deviation) of 4.3 ± 2.2 min collecting the TPS sample versus 73.5 ± 30.5 min collecting and filtering the BMFS sample. Laboratory processing required an estimated 5 h for concentration by TPS and 3.5 h for elution. Sabin 1 poliovirus was detected in 37 [30%] samples with the TPS versus 24 [19%] samples with the BMFS (McNemar's mid p value = 0.004). Sabin 3 poliovirus was detected in 59 [47%] versus 49 (39%) samples (p = 0.043), and NPEV was detected in 67 [54%] versus 40 [32%] samples (p < 0.001). The BMFS method without secondary concentration did not perform as well as the TPS method for detecting Sabin poliovirus and NPEV. Further studies are needed to guide the selection of cost-effective environmental surveillance methods for the polio endgame.

The burden of influenza A and B in Mexico from the year 2010 to 2013: An observational, retrospective, database study, on records from the Directorate General of Epidemiology database.

Despite vaccination programs, influenza still represents a significant disease burden in Mexico. We conducted an observational, retrospective analysis to better understand the epidemiological situation of the influenza virus in Mexico. Analysis of the seasonal patterns of influenza A and B were based on the Directorate General of Epidemiology dataset of influenza-like illness(ILI), and severe acute respiratory infection(SARI) that were recorded between January 2010 and December 2013. Our objectives were 1) to describe influenza A and B activity, by age group, and subtype and, 2) to analyze the number of laboratory-confirmed cases presenting with ILI by influenza type, the regional distribution of influenza, and its clinical features. Three periods of influenza activity were captured: August 2010-January 2011, December 2011-March 2012, and October 2012-March 2013. Cases were reported throughout Mexico, with 50.3% (n = 10,320) of cases found in 18-49 year olds. Over the entire capture period, a total of 76,085 ILI/SARI episodes had swab samples analyzed for influenza, 27% were positive. During the same period, influenza A cases were higher in the 18-49 years old, and influenza B cases in both 5-17 and 18-49 age groups. Peak activity occurred in January 2012 (n = 4,159) and December 2012 (n = 348) for influenza A and B respectively. This analysis confirms that influenza is an important respiratory pathogen for children and adults in Mexico despite vaccination recommendations. School-age children and adolescents were more prone to influenza B infection; while younger adults were susceptible to both influenza A and B viruses. Over the seasons, influenza A and B co-circulated.

Desde el ISET al InDRE. IV. Instituto de Diagnóstico y Referencia Epidemiológicos: nueva orientación, 1990-2012 / From ISET to InDRE. IV. Institute of Epidemiological Diagnosis and Reference: new orientation, 1990-2012

Resumen De 1990 a 2012, el Instituto de Salubridad y Enfermedades Tropicales experimentó los cambios más importantes. En 1989 modificó su nombre y orientación a Instituto Nacional de Diagnóstico y Referencia Epidemiológicos. Poco antes se había formalizado como cúspide de la Red Nacional de Laboratorios en Salud Pública y había incorporado los laboratorios de programas preventivos como el de citología exfoliativa y los de diagnóstico de rabia, paludismo, tuberculosis; posteriormente incorporaría otras redes que surgieron como parte de la respuesta a brotes epidémicos y al nuevo panorama epidemiológico. En este periodo, 27 algoritmos diagnósticos se definieron y organizaron en 18 redes, algunas de las cuales comenzaron a colaborar con redes globales. En 2001, en el Instituto se empezó a trabajar con patógenos relacionados con el bioterrorismo. Para entonces, las restricciones del edificio sede fueron evidentes; en 2008, se decidió construir nuevas instalaciones. El Instituto y sus redes diagnósticas constituyen un hito en la salud pública latinoamericana del siglo XXI.

Abstract From 1990 to 2012, the Sanitary and Tropical Diseases Institute experienced the most important changes. In 1989, its name and orientation were modified to become the National Institute of Epidemiological Diagnosis and Reference (InDRE). Shortly before, it had been formalized as the apex of the National Network of Public Health Laboratories and had incorporated laboratories for preventive programs such as exfoliative cytology and rabies, malaria and tuberculosis diagnosis; subsequently, it would incorporate other networks that emerged as part of the response to major epidemic outbreaks and to the new epidemiological outlook. In this period, 27 priority diagnostic algorithms were defined and organized in 18 networks, some of which began to collaborate with global networks. In 2001, the Institute started working with pathogens related to bioterrorism. By then, space restrictions of the headquarters’ building were evident; in 2008, starting the construction of new facilities was decided. The institute and its diagnostic networks constitute a milestone in Latin American public health of the 21st century.

De la atención de un brote por un patógeno desconocido en Wuhan hasta la preparación y respuesta ante la emergencia de Covid-19 en México / From the handling of an outbreak by an unknown pathogen in Wuhan to the preparedness and response in the face of the emergence of Covid-19 in Mexico

Resumen El 31 de diciembre de 2019, las autoridades chinas de salud informaron a la comunidad internacional, a través de los mecanismos establecidos por la Organización Mundial de la Salud (OMS), de una epidemia de neumonía con etiología desconocida en Wuhan, provincia de Hubei. Los primeros casos se notificaron a inicios de ese mes y se vincularon al antecedente de visitar un mercado de comida y animales vivos. El 7 de enero de 2020 se logró el aislamiento y reconocimiento del patógeno responsable mediante secuenciación de siguiente generación, mientras el número de afectados continuaba en ascenso. La publicación de genomas completos del nuevo coronavirus identificado (inicialmente denominado 2019-nCoV, ahora designado SARS-CoV2) en bases de datos públicas y privadas, de protocolos diagnósticos estandarizados y de la información clínica epidemiológica generada permitirá atender la Emergencia de Salud Pública de Importancia Internacional (ESPII) declarada el 30 de enero por la OMS. Con este documento pretendemos aportar a la caracterización de la epidemia de neumonía, ahora llamada enfermedad por coronavirus (Covid-19), revisar las fortalezas que tiene México en el concierto de la salud global e invitar a los profesionales de la salud a incorporarse a las actividades de preparación y respuesta ante esta emergencia.

Abstract On December 31, 2019, the Chinese health authorities informed the international community, through the mechanisms established by the World Health Organization (WHO), of a pneumonia epidemic of unknown etiology in Wuhan, Hubei Province. The first cases were reported early in that month and were linked to a history of having visited a market where food and live animals are sold. On January 7, 2020, isolation and identification of the culprit pathogen was achieved using next-generation sequencing, while the number of affected subjects continued to rise. The publication of full-genomes of the newly identified coronavirus (initially called 2019-nCoV, now designated SARS-CoV2) in public and private databases, of standardized diagnostic protocols and of the clinical-epidemiological information generated will allow addressing the Public Health Emergency of International Concern (PHEIC), declared on January 30 by the WHO. With this document, we intend to contribute to the characterization of the pneumonia epidemic, now called Corona virus disease (Covid-19) review the strengths Mexico has in the global health concert and invite health professionals to join the preparedness and response activities in the face of this emergency.

Del ISET al InDRE. V. Instituto de Diagnóstico y Referencia Epidemiológicos. Posición estratégica global, 2012-2019 / From ISET to InDRE. V. Institute of Epidemiological Diagnosis and Reference. Global strategic position, 2012-2019

Resumen En este documento se describen los cambios en el Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) de 2012 a 2019, las modificaciones administrativas y de equipamiento, la nueva sede y las modificaciones jurídicas al Sistema Nacional de Vigilancia Epidemiológica. Se menciona el proceso de mudanza, en especial el cuidadoso traslado del material biológico que resguarda el Instituto y se analiza la nueva forma de estudiar los brotes epidémicos, los padecimientos endémicos y la red negativa. Respecto al ámbito internacional, se describe el fomento de la vinculación con redes globales de la Organización Panamericana de la Salud, la Organización Mundial de la Salud (OMS) y otros organismos internacionales. También se menciona la designación en el InDRE de cuatro centros colaboradores de la OMS. La Red de Laboratorios de la Iniciativa Global para la Seguridad en Salud reconoció el liderazgo del InDRE, cuyo director ocupó la copresidencia del grupo de trabajo en el periodo de estudio.

Abstract This document describes the changes at the Institute of Epidemiological Diagnosis and Reference (InDRE) from 2012 to 2019, the administrative and equipment modifications, the new headquarters and the National System of Epidemiological Surveillance legal modifications. The process of relocation is mentioned, especially the careful transfer of the biological material protected by the Institute, and the new way of studying epidemic outbreaks, endemic diseases and the negative network is analyzed. At the international level, the promotion of links with global networks of the Pan American Health Organization, the World Health Organization (WHO) and other international organizations is described. The designation of four WHO collaborating centres granted to InDRE is also mentioned. The Global Health Security Initiative Laboratory Network acknowledged InDRE's leadership, which co-chaired the working group during the study period.

Epidemiological characterization of a fourth wave of pandemic A/H1N1 influenza in Mexico, winter 2011-2012: age shift and severity.

BACKGROUND AND AIMS: A substantial recrudescent wave of pandemic influenza A/H1N1 affected the Mexican population from December 1, 2011-March 20, 2012 following a 2-year period of sporadic transmission. METHODS: We analyzed demographic and geographic data on all hospitalizations with severe acute respiratory infection (SARI) and laboratory-confirmed A/H1N1 influenza, and inpatient deaths, from a large prospective surveillance system maintained by a Mexican social security medical system during April 1, 2009-March 20, 2012. We also estimated the reproduction number (R) based on the growth rate of the daily case incidence by date of symptoms onset. RESULTS: A total of 7569 SARI hospitalizations and 443 in-patient deaths (5.9%) were reported between December 1, 2011, and March 20, 2012 (1115 A/H1N1-positive inpatients and 154 A/H1N1-positive deaths). The proportion of laboratory-confirmed A/H1N1 hospitalizations and deaths was higher among subjects ≥60 years of age (χ(2) test, p <0.0001) and lower among younger age groups (χ(2) test, p <0.04) for the 2011-2012 pandemic wave compared to the earlier waves in 2009. The reproduction number of the winter 2011-2012 wave in central Mexico was estimated at 1.2-1.3, similar to that reported for the fall 2009 wave, but lower than that of spring 2009. CONCLUSIONS: We documented a substantial increase in the number of SARI hospitalizations during the period December 2011-March 2012 and an older age distribution of laboratory-confirmed A/H1N1 influenza hospitalizations and deaths relative to 2009 A/H1N1 pandemic patterns. The gradual change in the age distribution of A/H1N1 infections in the post-pandemic period is consistent with a build-up of immunity among younger populations.