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.

Detection and identification of Kinetoplastids of zoonotic interest by HRM-qPCR analysis in Canis lupus familiaris from Argentinean Mesopotamia.

This work aimed to conduct a first PCR-based approach for differential diagnosis of kinetoplastidean infections in dogs. Diagnosis of Kinetoplastid infections in domestic animals is difficult, since parasitemia is intermittent and signs are nonspecific; it is mainly based on parasitological smears or concentration techniques, which lack sensitivity and depend on operator` expertise. Dogs are relevant reservoirs in transmission of Kinetoplastids; they function as sentinels to detect active transmission cycles before they involve humans. Trypanosoma cruzi, Trypanosoma evansi, and various species of Leishmania genus are multi-host parasites, capable of parasitizing dogs among a vast number of reservoirs. An algorithm based on sequential Real-Time PCR-High Resolution Melting (HRM) (qPCR-HRM) assays directed at 24S alpha ribosomal DNA, ITS1 and Hsp70 designed to distinguish among T. cruzi, T. rangeli, T. evansi and Leishmania spp. was tested in fourteen dogs with suspicion of kinetoplastid diseases. A qPCR control of DNA integrity in the tested sample, targeted to the mammalian interphotoreceptor retinoid-binding protein (IRBP) gene fragment was incorporated to the algorithm. T. evansi was detected in four dogs and L. infantum in one. Two of five qPCR positive cases were smear negative. Smear and T. evansi qPCR positive cases corresponded to animals that died despite being treated, indicating the association of parasitemia with disease severity. This laboratory tool increases the possibility of confirming outbreaks of kinetoplastid diseases with zoonotic potential and identify the etiological agents involved.

HTLV I – II infection in an aboriginal population in Northeast Argentina

In order to estimate the prevalence of HTLV I/II viral infection in people belonging to aboriginal ethnic groups of the province of Chaco (North-East Argentina), 335 adults aged 15-68 were studied. Of those, 122 belong to the tobas ethnic group and 213 to the wichis. Samples were obtained with the assistance of bilingual social workers who explained the purposes of the study and requested consent for sample drawing. Antibodies against HTLV-I/II were studied with gelatin particle agglutination test, employing a 4 sera pool. In reactive pools the reaction was repeated individually and reactive sera were confirmed with Western blot. Total prevalence of HTLV I/II infection was 0.9% (3/335). Three infected subjects were found in tobas group and confirmed with WB, demonstrating HTLV II infection in all three cases, i.e. a 2.46% prevalence for this ethnic group. Of these 3 cases, 2 were women aged 30 to 40, while the other was a 42-year old man, all of them single. No positive cases were found in the wichi population. Results confirm that HTLV II infection among the tobas is endemic and probably of ancestral origins (AU)

A fin de conocer la prevalencia de infección por virus HTLV I -II en las etnias aborígenes dela provincia del Chaco (Noreste de Argentina), se estudiaron 335 personas de 15-68 años de edad, de las cuales 122 pertenecen a la etnia toba y 213 a la etnia wichi. Para la toma demuestras se trabajó con promotores sociales bilingües quienes ilustraron sobre los propósitos del estudio y solicitaron consentimiento para la extracción de sangre. Se investigó Acs contra HTLV-I/II por test de aglutinación de partículas de gelatina, empleando pooles de 4 sueros. En los pooles reactivos se repitió la reacción en forma individual y los sueros reactivos se confirmaron mediante Western blot. La prevalencia total de infección por HTLV I/II resultó del0,9 % (3/335). Se encontraron 3 sujetos infectados entre los 122 de la etnia toba que fueron confirmados como HTLV II en los tres casos, lo que significa una prevalencia del 2,46 % para esta etnia. De estos 3 casos, 2 fueron mujeres de entre 30 y 40 años y el otro fue un hombre de 42 años, todos solteros. No se hallaron positivos entre la población Wichi. Los resultados obtenidos reafirman que la infección por HTLV II en población toba es de carácter endémico y probablemente de origen ancestral (AU)