Genomic surveillance of the Lambda SARS-CoV-2 variant in a global phylogenetic context.

The massive sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and global genomic surveillance strategies allowed the detection of many variants of concern and interest. The variant of interest Lambda (C.37), which originated in South America, has been the most prevalent in Peru and Chile, but its dispersion in other continents still remains unknown. The current study aims to determine the phylogenetic relationship among C.37 isolates worldwide, focusing on spike mutations to understand the spread of Lambda in pandemics. A total of 7441 sequences identified as C.37 were downloaded from the GISAID database; local analysis was carried out to identify spike mutations and phylogenetic analysis was carried out to determine the rate of spread of the virus. Our results showed some spike mutations of Lambda that allowed us to detect small local outbreaks in different countries that occurred in the past and identify several clades that have not yet been designated. Although the lineage C.37 is not epidemiologically relevant in Europe or North America, the endemic behavior of this variant in Peru had a major impact on the second SARS-CoV-2 wave.

Genomic analysis reveals a rapid spread and predominance of lambda (C.37) SARS-COV-2 lineage in Peru despite circulation of variants of concern.

The pandemic generated by SARS-Cov-2 has caused a large number of cases and deaths in the world, but South America has been one of the continents that were most hard hit. The appearance of new variants causes concern because of the possibility that they may evade the protection generated by vaccination campaigns, their greater capacity to be transmitted, or their higher virulence. We analyzed the circulating variants in Peru after improving our Genomic Surveillance program. The results indicate a steep increase of the lambda lineage (C.37) until becoming predominant between January and April 2021, despite the cocirculation of other variants of concern or interest. Lambda lineage deserves close monitoring and could probably become a variant of concern in the near future.

Genetic identification of newborns in Peru: A pilot study. / Identificación genética de recién nacidos en Perú: Un estudio piloto.

OBJECTIVE: To determine the feasibility of genetic identification in a group of newborns from a public hospital in Lima, Peru. MATERIAL AND METHOD: Descriptive cross-sectional study, carried out by the National Registry of Identification and Civil Status of Peru, on live newborns and their mothers, from the Carlos Lanfranco La Hoz Hospital (Puente Piedra, Lima) during January. 2015. The samples were collected in FTA (Fast Technology for Analysis of nucleic acids) cards that allowed a direct analysis by PCR (Polymerase Chain Reaction) and capillary electrophoresis of 21 STR markers (Short Tandem Repeats), including the amelogenin marker for gender determination. RESULTS: 44 mothers and 45 newborns were included (there was a twin birth). The probability of maternity was higher than 99.9% in all cases. There were no difficulties in the sampling or in transporting the material. The obtained biological material was enough to collect DNA to identify the newborn. CONCLUSIONS: The genetic identification procedure was possible to perform in this hospital. Stages of the process that could be improved were identified for the eventual application of this procedure on a larger scale in Peru.

Neutralization of SARS-CoV-2 (lineage B.1.1) by hyperimmune llama (Lama glama) serum in vero cell culture. / Neutralización del virus SARS-CoV-2 (linaje B.1.1) por suero hiperinmune de llama (Lama glama) en cultivo de células Vero.

OBJECTIVE.: To evaluate the serological antibody response of a llama (Lama glama) to SARS-CoV-2 (B.1.1 lineage) immunization and the neutralizing capacity of hyperimmune llama serum against SARS-CoV-2 virus (B.1.1 lineage) in Vero cells. MATERIALS AND METHODS.: A llama was immunized with inactivated SARS-CoV-2 (B.1.1 lineage). Serum samples were analyzed to evaluate the level of antibodies by ELISA, as well as reactivity to SARS-CoV-2 antigens by Western Blot. In addition, viral neutralization in cell cultures was assessed by the Plate Reduction Neutralization Test (PRNT). RESULTS: . Seroreactivity increased in the immunized llama from week 4 onwards. Antibody titers were the highest after the seventh immunization booster. Western blot results confirmed the positive ELISA findings, and immune serum antibodies recognized several viral proteins. The neutralization assay (PRNT) showed visible viral neutralization, which was in accordance with the ELISA and Western Blot results. CONCLUSIONS.: The findings suggest that hyperimmune llama serum could constitute a source of therapeutic antibodies against SARS-CoV-2 infections (lineage B.1.1), and should be studied in further research.

OBJETIVO.: Evaluar la respuesta serológica de anticuerpos de una llama (Lama glama) a la inmunización del virus SARS-CoV-2 (linaje B.1.1) y la capacidad neutralizante del suero de llama hiperinmune frente al virus SARS-CoV-2 (linaje B.1.1) en células Vero. MATERIALES Y MÉTODOS.: Se inmunizó una llama con el virus SARS-CoV-2 inactivado (Linaje B.1.1) y se analizaron muestras de suero para evaluar el nivel de anticuerpos mediante ELISA, así como la reactividad a antígenos de SARS-CoV-2 mediante Western Blot. Además, se evaluó la neutralización viral en cultivos celulares por la Prueba de Neutralización por Reducción de Placas (PRNT, por sus siglas en inglés). RESULTADOS.: Se observó un aumento en la serorreactividad en la llama inmunizada desde la semana 4 en adelante. Los títulos de anticuerpos fueron más elevados en el séptimo refuerzo de inmunización. Los resultados de Western Blot confirmaron los hallazgos positivos del ELISA, y los anticuerpos del suero inmune reconocieron varias proteínas virales. El ensayo de neutralización (PRNT) mostró una neutralización viral visible, concordante con los resultados de ELISA y Western Blot. CONCLUSIONES.: Los hallazgos sugieren que el suero hiperinmune de llama podría constituir una fuente de anticuerpos terapéuticos contra las infecciones por el virus SARS-CoV-2 (linaje B.1.1) y que deberá ser evaluado en estudios posteriores.

Cloning, expression and seroreactivity of the recombinant lipopolysaccharide assembly protein - D (LptD) from Bartonella bacilliformis. / Clonamiento, expresión y seroreactividad de la proteína recombinante de ensamblaje de lipopolisacáridos - D (LptD) de Bartonella bacilliformis.

OBJECTIVE.: To evaluate in silico and at the serological level the antigenic potential of the recombinant extracellular domain of the lipopolysaccharide assembly protein - D (LptD) of Bartonella bacilliformis (dexr_LptD). MATERIALS AND METHODS.: Through in silico analysis, we selected a B. bacilliformis protein with antigenic and immunogenic potential. The selected protein gene was cloned into Escherichia coli TOP10 and expressed in Escherichia coli BL21 (DE3) pLysS. Recombinant protein was expressed using isopropyl-ß-D-1-thiogalactopyranoside (IPTG) and induction conditions were optimized. Finally, it was purified with Ni-IDA resin (His60 Ni Superflow) and a Western Blot assay was conducted. RESULTS.: In silico, the selected protein was LptD because it is located in the outer membrane and is antigenic and immunogenic. Optimized conditions for dexr_LptD induction were 0.5 mM IPTG, 16 hours, TB (Terrific Broth) medium, 3% (v/v) ethanol, 28 ºC, OD600: 1-1.5 and 200 rpm. Purification was carried out under denaturating conditions on a small scale and we obtained 2.6 µg/mL of partially purified dexr_LptD. The Western Blot assay showed a positive reaction between the sera from patients with Carrión's Disease and dexr_LptD, which shows the antigenicity of dexr_LptD. CONCLUSIONS.: The dexr_LptD shows antigenicity both in silico and at the serological level, these results are the basis for further studies on vaccine candidates against Carrion's Disease.

OBJETIVO.: Evaluar in silico y a nivel serológico el potencial antigénico del dominio extracelular recombinante de la proteína de ensamblaje de lipopolisacáridos - D (LptD) de Bartonella bacilliformis (dexr_LptD). MATERIALES Y MÉTODOS.: Mediante el análisis in silico se realizó la selección de una proteína de B. bacilliformis con potencial antigénico e inmunogénico. El gen de la proteína seleccionada se clonó en Escherichia coli TOP10 y se expresó en Escherichia coli BL21 (DE3) pLysS. La proteína recombinante fue expresada usando isopropil-ß-D-1-tiogalactopiranósido (IPTG) y se optimizaron las condiciones de inducción. Por último, se purificó con resina Ni-IDA (His60 Ni Superflow) y se realizó un ensayo de Western Blot. RESULTADOS.: In silico, la proteína seleccionada fue LptD por estar localizada en la membrana externa y ser antigénica e inmunogénica. Las condiciones optimizadas para la inducción del dexr_LptD fueron 0,5 mM IPTG, 16 h, medio TB (Terrific Broth), etanol al 3% (v/v), 28 ºC, OD600: 1-1,5 y 200 r.p.m. La purificación se realizó en condiciones denaturantes a pequeña escala y se obtuvo 2,6 µg/mL de dexr_LptD parcialmente purificada. El ensayo de Western Blot mostró una reacción positiva entre los sueros provenientes de pacientes con la enfermedad de Carrión y dexr_LptD, ello evidencia la antigenicidad del dexr_LptD. CONCLUSIONES.: El dexr_LptD muestra antigenicidad in silico y a nivel serológico, estos resultados son base para posteriores estudios sobre candidatos vacunales contra la enfermedad de Carrión.

Identificación genética de recién nacidos en Perú: un estudio piloto / Genetic identification of newborns in Peru: a pilot study

OBJETIVO: Determinar la factibilidad de la identificación genética a un grupo de recién nacidos prove nientes de un hospital público de Lima-Perú. MATERIAL Y MÉTODO: Estudio descriptivo de corte trans versal, realizado por Registro de Identificación y Estado Civil de Perú, en recién nacidos vivos y sus respectivas madres, provenientes del Hospital Carlos Lanfranco La Hoz (Puente Piedra-Lima) du rante el mes de enero del 2015. Las muestras fueron colectadas en tarjetas FTA (Fast Technology for Analysis of nucleic acids) que permitieron un análisis directo por PCR (Polymerase Chain Reaction) y electroforesis capilar de 21 marcadores genéticos de tipo STR (Short Tandem Repeats), incluyendo el marcador amelogenina para la determinación del sexo. RESULTADOS: Se incluyeron un total de 44 madres y 45 recién nacidos (existió un parto gemelar). La probabilidad de maternidad fue mayor al 99.9% en todos los casos. No se encontraron dificultades en la toma de muestra, ni en el transporte del material. El material biológico obtenido fue suficiente para la obtención de ADN para realizar la identificación del recién nacido. CONCLUSIONES: El procedimiento de identificación genética fue factible de realizar en este hospital. Se identificaron etapas del proceso que podrían mejorarse para la posible aplicación de este procedimiento a una mayor escala en el Perú.

OBJECTIVE: To determine the feasibility of genetic identification in a group of newborns from a public hospital in Lima, Peru. MATERIAL AND METHOD: Descriptive cross-sectional study, carried out by the National Registry of Identification and Civil Status of Peru, on live newborns and their mothers, from the Carlos Lanfranco La Hoz Hospital (Puente Piedra, Lima) during January. 2015. The samples were collected in FTA (Fast Technology for Analysis of nucleic acids) cards that allowed a direct analysis by PCR (Polymerase Chain Reaction) and capillary electrophoresis of 21 STR markers (Short Tandem Repeats), including the amelogenin marker for gender determination. RESULTS: 44 mothers and 45 newborns were included (there was a twin birth). The probability of maternity was higher than 99.9% in all cases. There were no difficulties in the sampling or in transporting the material. The obtained biological material was enough to collect DNA to identify the newborn. CONCLUSIONS: The genetic identification procedure was possible to perform in this hospital. Stages of the process that could be improved were identified for the eventual application of this procedure on a larger scale in Peru.

[Experiences in the epidemiological surveillance of foodborne pathogens by pulsed field gel electrophoresis (PFGE) in Peru]. / Experiencias en la vigilancia epidemiológica de agentes patógenos transmitidos por alimentos a través de electroforesis en campo pulsado (PFGE) en el Perú

Foodborne diseases and other enteric infections often occur as outbreaks and cause morbidity and mortality all over the world. In Perú, they represent a serious public health problem, and are caused by a great variety of infectious agents. For epidemiological research, a wide array of typification methods are used. One of the most important tools for the molecular subtyping of bacterial pathogens is the Pulsed Field Gel Electrophoresis (PFGE), which is a highly precise method that allows the discrimination between different bacterial isolates which are epidemiologically related. The Instituto Nacional de Salud del Perú (INS) is part of the WHO Global Foodborne Infections Network (WHO-GFN) and of the PulseNet Latin American and Caribbean Net (PN-AL & C), with whom it shares the genetic profiles of the isolated pathogenic strains, so that it is possible to compare de genotypes of similar strains found in different countries and to identify the occurrence of epidemic outbreaks in the region, strengthening the regional system of epidemiological surveillance and generating a rapid, coordinated response between the countries. We present the two last years experience including the advances in the use of these strategic tools that have allowed us to characterize genotype patterns implicated in foodborne diseases from isolates recovered in the laboratory network of Peru.

Caracterización molecular de cepas de Klebsiella pneumoniae productoras de BLEE causantes de infección intrahospitalaria en el servicio de neonatología de un hospital de Lima, Perú / Molecular characterization of extended-spectrum beta-lactamase-producing (ESBL) strains of Klebsiella pneumoniae causing nosocomial infections in a neonatal unit in Lima, Peru

Objetivo: Caracterizar por métodos de microbiología y biología molecular siete cepas de Klebsiella pneumoniae productoras de BLEE, de pacientes con bacteremia y sospechosos de pertenecer a un brote de infección intrahospitalaria en el servicio de neonatología de un hospital de Lima-Perú. Material y métodos: Se realizó la genotipificación de los aislamientos por Eric-PCR, Rep-PCR y Electroforesis en Gel de Campo Pulsado (PFGE) con el fin de determinar la relación clonal. El análisis de susceptibilidad antimicrobiana por el método de Difusión de Doble Disco (DDD) mostró que los siete aislamientos eran portadores de a-lactamasas de Espectro extendido (BLEE). Resultados: Los tres métodos de genotipificación, Eric-PCR, PCR-Rep y el método estándar de oro PFGE demostraron relación clonal entre cinco de los aislamientos, revelando que todas pertenecían a una única cepa o clona de K. pneumoniae; mientras que los dos aislamientos restantes también provenían de una misma cepa, pero muy diferente genéticamente a la cepa inicial de 5 aislamientos. Conclusiones: Este estudio revela la transmisión clonal de algunas cepas de K. pneumoniae portadoras de BLEE en el servicio de neonatología de un hospital de Lima-Perú, y pone de manifiesto la utilidad de las técnicas de biología molecular para la investigación de brotes hospitalarios y para la vigilancia epidemiológica. Este es el primer reporte de aplicación del análisis de genotipificación por PFGE a la investigación de brotes hospitalarios de Klebsiella pnuemoniae en un hospital peruano.

Objective: To characterize the molecular features of seven extended-spectrum betalactamase-producing (ESBL) strains of Klebsiella pneumoniae in patients with bacteremia during a nosocomial outbreak in a neonatal unit in Lima, Peru. Methods: Genotyping was performed using Eric-PCR, Rep-PCR and pulsed field gel electrophoresis (PFGE) to evaluate clonality. Disk diffusion test showed that all seven strains were ESBL producing strains. Results:The three-genotyping methods showed that five out of seven strains were genetically related to a single clone. Conclusions: The study represents the first attempt to apply genotyping methods to study nosocomial outbreaks in neonatal units in Lima, and reveals clonal transmission of ESBL producing strains of K. pneumonia.

Experiencias en la vigilancia epidemiológica de agentes patógenos transmitidos por alimentos a través de electroforesis en campo pulsado (PFGE) en el Perú / Experiences in the epidemiological surveillance of foodborne pathogens by pulsed field gel electrophoresis (PFGE) in Peru

Las enfermedades transmitidas por alimentos (ETA) y otras enfermedades entéricas infecciosas ocurren a menudo como brotes y son causa de morbilidad y mortalidad en todo el mundo. En el Perú, son un importante problema de salud pública y son causados por una gran variedad de agentes infecciosos. Para la investigación epidemiológica se utiliza una variedad de métodos de tipificación. Una de las herramientas más importantes en la subtipificación molecular de patógenos bacterianos es la técnica de la electroforesis en campo pulsado (PFGE), que es un método altamente resolutivo que permite la discriminación entre diferentes aislamientos bacterianos epidemiológicamente relacionados. El Instituto Nacional de Salud (INS) del Perú integra las redes WHO Global Foodborne Infections Network y la Red PulseNet América Latina y Caribe, con quienes comparte los perfiles genéticos de las cepas patógenas aisladas, permitiendo comparar los genotipos de cepas semejantes halladas en diferentes países y reconocer la ocurrencia de brotes epidémicos en la región, fortaleciendo el sistema de vigilancia epidemiológica regional y generando una rápida respuesta conjunta entre países. Se presenta la experiencia de los dos últimos años sobre los avances en la utilización de estas herramientas estratégicas que nos ha permitido caracterizar patrones de genotipo de principales patógenos implicados en ETA a partir de aislamientos recuperados de la red de laboratorios del Perú.

Foodborne diseases and other enteric infections often occur as outbreaks and cause morbidity and mortality all over the world. In Perú, they represent a serious public health problem, and are caused by a great variety of infectious agents. For epidemiological research, a wide array of typification methods are used. One of the most important tools for the molecular subtyping of bacterial pathogens is the Pulsed Field Gel Electrophoresis (PFGE), which is a highly precise method that allows the discrimination between different bacterial isolates which are epidemiologically related. The Instituto Nacional de Salud del Perú (INS) is part of the WHO Global Foodborne Infections Network (WHO-GFN) and of the PulseNet Latin American and Caribbean Net (PN-AL & C), with whom it shares the genetic profiles of the isolated pathogenic strains, so that it is possible to compare de genotypes of similar strains found in different countries and to identify the occurrence of epidemic outbreaks in the region, strengthening the regional system of epidemiological surveillance and generating a rapid, coordinated response between the countries. We present the two last years´ experience including the advances in the use of these strategic tools that have allowed us to characterize genotype patterns implicated in foodborne diseases from isolates recovered in the laboratory network of Peru.