The Lambda Variant in Argentina: Analyzing the Evolution and Spread of SARS-CoV-2 Lineage C.37.

The second wave of COVID-19 occurred in South America in early 2021 and was mainly driven by Gamma and Lambda variants. In this study, we aimed to describe the emergence and local genomic diversity of the SARS-CoV-2 Lambda variant in Argentina, from its initial entry into the country until its detection ceased. Molecular surveillance was conducted on 9356 samples from Argentina between October 2020 and April 2022, and sequencing, phylogenetic, and phylogeographic analyses were performed. Our findings revealed that the Lambda variant was first detected in Argentina in January 2021 and steadily increased in frequency until it peaked in April 2021, with continued detection throughout the year. Phylodynamic analyses showed that at least 18 introductions of the Lambda variant into the country occurred, with nine of them having evidence of onward local transmission. The spatial--temporal reconstruction showed that Argentine clades were associated with Lambda sequences from Latin America and suggested an initial diversification in the Metropolitan Area of Buenos Aires before spreading to other regions in Argentina. Genetic analyses of genome sequences allowed us to describe the mutational patterns of the Argentine Lambda sequences and detect the emergence of rare mutations in an immunocompromised patient. Our study highlights the importance of genomic surveillance in identifying the introduction and geographical distribution of the SARS-CoV-2 Lambda variant, as well as in monitoring the emergence of mutations that could be involved in the evolutionary leaps that characterize variants of concern.

Cost-Effective Method to Perform SARS-CoV-2 Variant Surveillance: Detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina.

SARS-CoV-2 variants with concerning characteristics have emerged since the end of 2020. Surveillance of SARS-CoV-2 variants was performed on a total of 4,851 samples from the capital city and 10 provinces of Argentina, during 51 epidemiological weeks (EWs) that covered the end of the first wave and the ongoing second wave of the COVID-19 pandemic in the country (EW 44/2020 to EW 41/2021). The surveillance strategy was mainly based on Sanger sequencing of a Spike coding region that allows the identification of signature mutations associated with variants. In addition, whole-genome sequences were obtained from 637 samples. The main variants found were Gamma and Lambda, and to a lesser extent, Alpha, Zeta, and Epsilon, and more recently, Delta. Whereas, Gamma dominated in different regions of the country, both Gamma and Lambda prevailed in the most populated area, the metropolitan region of Buenos Aires. The lineages that circulated on the first wave were replaced by emergent variants in a term of a few weeks. At the end of the ongoing second wave, Delta began to be detected, replacing Gamma and Lambda. This scenario is consistent with the Latin American variant landscape, so far characterized by a concurrent increase in Delta circulation and a stabilization in the number of cases. The cost-effective surveillance protocol presented here allowed for a rapid response in a resource-limited setting, added information on the expansion of Lambda in South America, and contributed to the implementation of public health measures to control the disease spread in Argentina.

Genetic diversity and phylogeographic analysis of human herpesvirus type 8 (HHV-8) in two distant regions of Argentina: Association with the genetic ancestry of the population.

BACKGROUND: The genetic diversity of persistent infectious agents, such as HHV-8, correlates closely with the migration of modern humans out of East Africa which makes them useful to trace human migrations. However, there is scarce data about the evolutionary history of HHV-8 particularly in multiethnic Latin American populations. OBJECTIVES: The aims of this study were to characterize the genetic diversity and the phylogeography of HHV-8 in two distant geographic regions of Argentina, and to establish potential associations with pathogenic conditions and the genetic ancestry of the population. STUDY DESIGN: A total of 101 HIV-1 infected subjects, 93 Kaposi's Sarcoma (KS) patients and 411 blood donors were recruited in the metropolitan (MET) and north-western regions of Argentina (NWA). HHV-8 DNA was detected by ORF-26 PCR in whole blood, saliva and FFPE tissues. Then, ORF-26 and ORF-K1 were analyzed for subtype assignment. Mitochondrial DNA and Y chromosome haplogroups, as well as autosomal ancestry markers were evaluated in samples in which subtypes could be assigned. Phylogeographic analysis was performed in the ORF-K1 sequences from this study combined with 388 GenBank sequences. RESULTS: HHV-8 was detected in 50.7%, 59.2% and 8% of samples from HIV-1 infected subjects, KS patients and blood donors, respectively. ORF-K1 phylogenetic analyses showed that subtypes A (A1-A5), B1, C (C1-C3) and F were present in 46.9%, 6.25%, 43.75% and 3.1% of cases, respectively. Analyses of ORF-26 fragment revealed that 81.95% of strains were subtypes A/C followed by J, B2, R, and K. The prevalence of subtype J was more commonly observed among KS patients when compared to the other groups. Among KS patients, subtype A/C was more commonly detected in MET whereas subtype J was the most frequent in NWA. Subtypes A/C was significantly associated with Native American maternal haplogroups (p = 0.004), whereas subtype J was related to non-Native American haplogroups (p < 0.0001). Sub-Saharan Africa, Europe and Latin America were the most probable locations from where HHV-8 was introduced to Argentina. CONCLUSIONS: These results give evidence of the geographic circulation of HHV-8 in Argentina, suggest the association of ORF-26 subtype J with KS development and provide new insights about its relationship with ancient and modern human migrations and identify the possible origins of this virus in Argentina.

Phylogenetic analysis of rubella viruses isolated in 2008 outbreak in Argentina.

BACKGROUND: A rubella outbreak was recorded in Buenos Aires during 2008. OBJECTIVES: The objective of this communication is to present the genetic and phylogenetic analyses of wild-type RUBV circulating in Buenos Aires during the 2008 outbreak. STUDY DESIGN: Throat swab samples collected from patients diagnosed with rubella between June 2008 and December 2008 were inoculated in cell culture and 23 isolates were sequenced. RESULTS: Phylogenetic analysis of the WHO-recommended window (nt 8731-9469) of the E1 envelope glycoprotein was performed and all isolates clustered with the 2B genotype. CONCLUSIONS: Genotype 2B seems to be endemically circulating in the Southern cone of Latin America, thus causing recent outbreaks.

Evaluación y experiencia local en la utilización de NAT HCV basado en amplificación por NASBA para el tamizaje de donaciones de sangre / Evaluation and local experience using HCV NAT based on NASBA amplification for screening blood donations

Objetivos: Evaluar un nuevo método de NAT HCV basado en amplificación por NASBA (nucleic acid sequence-based amplification) y presentar los datos de nuestra experiencia en aplicar esta metodología para tamizaje de rutina en banco de sangre. Método: La detección de ARN HCV por NASBA (NASBA-HCV) se realizó con un kit comercial (NucliSens Basic Kit, bioMérieux). Para determinar la sensibilidad por análisis de Probit, se probaron diluciones seriadas de un reactivo de referencia para ARN HCV. La especificidad se evaluó con 100 pooles de plasma normal. El tamizaje de rutina se realizó con pooles conteniendo hasta 48 unidades. Resultados: La sensibilidad de NASBA-HCV fue 95 UI/ml de ARN HCV. El límite de detección calculado para una donación individual en pool de 48 fue 4.560 UI/ml. La especificidad preliminar fue de 98 por ciento. Nuestro laboratorio pudo procesar adecuadamente las muestras para NAT HCV y resolver pooles positivos. No encontramos donaciones NAT HCV positivas/anti-HCV negativas en 27.679 muestras evaluadas. El porcentaje de largadas inválidas y pooles falsos positivos fue de 1,9 y 2.7, respectivamente Conclusiones: El límite de detección de NASBA-HCV para pooles de 48 unidades se encuentra dentro de los lineamientos de sensibilidad recomendados por el centro de referencia Paul Ehrlich Institute. Nuestro laboratorio tuvo la capacidad de implementar NAT HCV y obtener resultados en tiempos adecuados para banco de sangre. El tamizaje por NAT mediante NASBA-HCV es una alternativa viable para mejorar el nivel de seguridad en las transfusiones en nuestro país.

Evaluación y experiencia local en la utilización de NAT HCV basado en amplificación por NASBA para el tamizaje de donaciones de sangre / Evaluation and local experience using HCV NAT based on NASBA amplification for screening blood donations

Objetivos: Evaluar un nuevo método de NAT HCV basado en amplificación por NASBA (nucleic acid sequence-based amplification) y presentar los datos de nuestra experiencia en aplicar esta metodología para tamizaje de rutina en banco de sangre. Método: La detección de ARN HCV por NASBA (NASBA-HCV) se realizó con un kit comercial (NucliSens Basic Kit, bioMérieux). Para determinar la sensibilidad por análisis de Probit, se probaron diluciones seriadas de un reactivo de referencia para ARN HCV. La especificidad se evaluó con 100 pooles de plasma normal. El tamizaje de rutina se realizó con pooles conteniendo hasta 48 unidades. Resultados: La sensibilidad de NASBA-HCV fue 95 UI/ml de ARN HCV. El límite de detección calculado para una donación individual en pool de 48 fue 4.560 UI/ml. La especificidad preliminar fue de 98 por ciento. Nuestro laboratorio pudo procesar adecuadamente las muestras para NAT HCV y resolver pooles positivos. No encontramos donaciones NAT HCV positivas/anti-HCV negativas en 27.679 muestras evaluadas. El porcentaje de largadas inválidas y pooles falsos positivos fue de 1,9 y 2.7, respectivamente Conclusiones: El límite de detección de NASBA-HCV para pooles de 48 unidades se encuentra dentro de los lineamientos de sensibilidad recomendados por el centro de referencia Paul Ehrlich Institute. Nuestro laboratorio tuvo la capacidad de implementar NAT HCV y obtener resultados en tiempos adecuados para banco de sangre. El tamizaje por NAT mediante NASBA-HCV es una alternativa viable para mejorar el nivel de seguridad en las transfusiones en nuestro país. (AU)