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.

Laboratory platform for monitoring SARS-CoV-2 based on surveillance of influenza and other respiratory viruses in Peru. / Plataforma laboratorial para monitorear el SARS-CoV-2 basada en la vigilancia de influenza y otros virus respiratorios en Perú.

In Peru, the COVID-19 pandemic demonstrated the usefulness of having a structured laboratory surveillance system that has been operational for 22 years, based on influenza surveillance; initially in the form of sentinel units, and later strengthened and innovated, with its own resources and with external support, to provide quality information. Biotechnological advances have been implemented for diagnostic confirmation and the capacity of the national laboratory network has been expanded, maintaining efficiency, considering the diverse and complex realities of each region, and overcoming difficulties regarding communication and articulation between institutions. It is necessary to consolidate this system, with collaborative and coordinated work between its components, boosting its effectiveness and timeliness and promoting genomic surveillance of new viruses and variants, as is currently the case with SARS-CoV-2.

En el Perú, la pandemia de la COVID-19 ha evidenciado la utilidad de tener un sistema de vigilancia laboratorial estructurado y en funcionamiento desde hace 22 años, basado en la vigilancia de influenza; inicialmente en modalidad de unidades centinela, y después fortaleciéndose e innovándose, con recursos propios y con apoyo externo, para generar información de calidad. Se han implementado avances biotecnológicos para la confirmación diagnóstica e incrementado las capacidades de la red nacional de laboratorios, manteniendo la eficiencia, considerando las diversas y complejas realidades de los niveles regionales, y superando dificultades de comunicación y articulación entre instituciones. Resulta necesario consolidar este sistema, con trabajo colaborativo y coordinado entre sus componentes, impulsando su eficacia y oportunidad y promoviendo la vigilancia genómica de nuevos virus y variantes, como actualmente ocurre con el SARS-CoV-2.

Confirmed Severe Acute Respiratory Syndrome Coronavirus 2 Reinfections After a Second Wave With Predominance of Lambda in Lima and Callao, Peru.

Background: Coronavirus disease 2019 (COVID-19) infection is a major public health problem in the world and reinfections are becoming more frequent. Our main objective was to describe the epidemiological, clinical, and genomic characteristics of the confirmed cases of reinfection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the capital of Lima and Callao, Peru. Methods: We searched in the Peruvian laboratory information system from April 2020 up to May 2021, looking for cases having 2 positive molecular tests for SARS-CoV-2 with more than 90 days between them. We performed genomic sequencing to the available pairs of samples and described the clinical characteristics, epidemiological impact, and genomic analysis of the confirmed reinfections. Results: There were 1 694 164 people with a positive diagnostic test for SARS-CoV-2 in Lima/Callao during the study period. Of these, 1695 had 2 positive molecular tests with more than 90 days between them. Two hundred eleven had both samples available for genomic analysis according to our selection criteria, and these were retrieved and submitted to sequencing. Thirty cases were confirmed to be SARS-CoV-2 reinfections with 2 different lineages in the 2 episodes. The variant Lambda (C.37) was the most common during the second infection and accounted for 19 (63.3%) of the 30 cases. Conclusions: We report 30 cases of confirmed SARS-CoV-2 reinfections. The Lambda variant was the most common cause of the second infections, in concordance with its predominant circulation during Peru's second wave. This report describes the largest series of confirmed reinfections by SARS-CoV-2 in Latin America.We describe the epidemiological, clinical, and genomic characteristics of the confirmed cases of reinfection by severe acute respiratory syndrome coronavirus 2 in Lima and Callao, durante la segunda ola en Peru. The Lambda variant (C.37) was the most common cause of the second infections.

Plataforma laboratorial para monitorear el SARS-CoV-2 basada en la vigilancia de influenza y otros virus respiratorios en Perú / Laboratory platform for monitoring SARS-CoV-2 based on surveillance of influenza and other respiratory viruses in Peru

RESUMEN En el Perú, la pandemia de la COVID-19 ha evidenciado la utilidad de tener un sistema de vigilancia laboratorial estructurado y en funcionamiento desde hace 22 años, basado en la vigilancia de influenza; inicialmente en modalidad de unidades centinela, y después fortaleciéndose e innovándose, con recursos propios y con apoyo externo, para generar información de calidad. Se han implementado avances biotecnológicos para la confirmación diagnóstica e incrementado las capacidades de la red nacional de laboratorios, manteniendo la eficiencia, considerando las diversas y complejas realidades de los niveles regionales, y superando dificultades de comunicación y articulación entre instituciones. Resulta necesario consolidar este sistema, con trabajo colaborativo y coordinado entre sus componentes, impulsando su eficacia y oportunidad y promoviendo la vigilancia genómica de nuevos virus y variantes, como actualmente ocurre con el SARS-CoV-2.

ABSTRACT In Peru, the COVID-19 pandemic demonstrated the usefulness of having a structured laboratory surveillance system that has been operational for 22 years, based on influenza surveillance; initially in the form of sentinel units, and later strengthened and innovated, with its own resources and with external support, to provide quality information. Biotechnological advances have been implemented for diagnostic confirmation and the capacity of the national laboratory network has been expanded, maintaining efficiency, considering the diverse and complex realities of each region, and overcoming difficulties regarding communication and articulation between institutions. It is necessary to consolidate this system, with collaborative and coordinated work between its components, boosting its effectiveness and timeliness and promoting genomic surveillance of new viruses and variants, as is currently the case with SARS-CoV-2.

Validación y evaluación de una prueba de RT-PCR en tiempo real in house para la detección de SARS-CoV-2 usando un gen específico RdRp y control endógeno GAPDH / Validation and evaluation of RT-PCR real time in house test to detection of SARS-CoV-2 using specific RdRp gene and GAPDH endogen control

RESUMEN Se validó y evaluó un método de RT-PCR en tiempo real usando cebadores y sondas específicas para los genes RdRP de SARS-CoV-2 y GAPDH de humanos; este último fue usado como control endógeno. Se evaluó la especificidad y sensibilidad; además, se evaluó otros parámetros como la robustez, la repetibilidad, reproducibilidad, comparabilidad y el límite de detección. La sensibilidad, especificidad, los valores predictivos positivo y negativo, la robustez, comparabilidad y la repetibilidad-reproducibilidad de la prueba de RT-PCR en tiempo real dúplex fue de 100%, con un límite de detección de 100 copias/µL, de acuerdo con los criterios de aceptación establecidos para validación del protocolo. Esta prueba estandarizada es una buena alternativa para el diagnóstico de COVID-19; además, la prueba fue aplicada de manera exitosa en personas sospechosas de la enfermedad permitiendo controlar el número de falsos negativos.

ABSTRACT The present work validated and evaluated a duplex real-time RT-PCR using specific primers and probes for genes RdRp from SARS-CoV-2 and GAPDH from humans; the latter was used as an endogenous control in all reactions. We evaluated the specificity, the sensitivity, the robustness, the reproducibility, the repeatability, the comparability, and the limit of detection. The predictive positive and negative values (PPV and PNV, respectively) and all the parameters evaluated using our duplex real-time RT-PCR was 100%. The detection limit was 100 copies/µL according to the acceptance criteria established for the validation of this protocol. Our duplex real-time RT-PCR demonstrated to be a good alternative for the diagnosis of COVID-19; in addition, this PCR was used adequately in suspicion of COVID-19, allowing it to control the number of false-negatives.

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.

Validation and evaluation of RT-PCR real time in house test to detection of SARS-CoV-2 using specific RdRp gene and GAPDH endogen control. / Validación y evaluación de una prueba de RT-PCR en tiempo real in house para la detección de SARS-CoV-2 usando un gen específico RdRp y control endógeno GAPDH.

The present work validated and evaluated a duplex real-time RT-PCR using specific primers and probes for genes RdRp from SARS-CoV-2 and GAPDH from humans; the latter was used as an endogenous control in all reactions. We evaluated the specificity, the sensitivity, the robustness, the reproducibility, the repeatability, the comparability, and the limit of detection. The predictive positive and negative values (PPV and PNV, respectively) and all the parameters evaluated using our duplex real-time RT-PCR was 100%. The detection limit was 100 copies/µL according to the acceptance criteria established for the validation of this protocol. Our duplex real-time RT-PCR demonstrated to be a good alternative for the diagnosis of COVID-19; in addition, this PCR was used adequately in suspicion of COVID-19, allowing it to control the number of false-negatives.

Se validó y evaluó un método de RT-PCR en tiempo real usando cebadores y sondas específicas para los genes RdRP de SARS-CoV-2 y GAPDH de humanos; este último fue usado como control endógeno. Se evaluó la especificidad y sensibilidad; además, se evaluó otros parámetros como la robustez, la repetibilidad, reproducibilidad, comparabilidad y el límite de detección. La sensibilidad, especificidad, los valores predictivos positivo y negativo, la robustez, comparabilidad y la repetibilidad-reproducibilidad de la prueba de RT-PCR en tiempo real dúplex fue de 100%, con un límite de detección de 100 copias/µL, de acuerdo con los criterios de aceptación establecidos para validación del protocolo. Esta prueba estandarizada es una buena alternativa para el diagnóstico de COVID-19; además, la prueba fue aplicada de manera exitosa en personas sospechosas de la enfermedad permitiendo controlar el número de falsos negativos.

Near-Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Causing a COVID-19 Case in Peru.

A near-complete genome sequence was obtained for a novel coronavirus (SARS-CoV-2) strain obtained from an oropharyngeal swab from a Peruvian patient with coronavirus syndrome (COVID-19) who had contact with an individual who had returned to Peru from travel to Italy.