Novel B2 mitogenomes from Continental southern Patagonia's Late Holocene: New insights into the peopling of the Southern Cone.

OBJECTIVES: The main aim of this study is to discuss the migratory processes and peopling dynamics that shaped the genetic variability of populations during the settlement of the Southern Cone, through the analysis of complete mitogenomes of individuals from southern Patagonia. MATERIALS AND METHODS: Complete mitogenomes were sequenced through massively parallel sequencing from two late Holocene individuals (SAC 1-1-3 and SAC 1-1-4) buried in the same chenque at Salitroso Lake Basin (Santa Cruz province, Argentina). To evaluate matrilineal phylogenetic affinities with other haplotypes, maximum likelihood and Bayesian phylogenetic reconstructions were performed, as well as a haplotype median-joining network. RESULTS: The mitogenomes were assigned to haplogroups B2 and B2b, exhibiting an average depth of 54X and 89X (≥1X coverage of 98.6% and 100%), and a high number of nucleotide differences among them. The phylogenetic analyses showed a relatively close relationship between the haplotype found in SAC 1-1-4 and those retrieved from a Middle Holocene individual from Laguna Chica (Buenos Aires province), and from a group of individuals from the Peruvian coast. For the SAC 1-1-3, no clear affiliations to any other haplotype were established. DISCUSSION: The large divergence between the haplotypes presented in this study suggests either a highly variable founder gene pool, or a later enrichment by frequent biological contact with other populations. Our results underline the persistence of genetic signals related to the first waves of peopling in South America, suggesting that the regional settlement of the southern end of the continent has been much more complex than initially thought.

OBJETIVOS: El objetivo principal de este estudio es discutir los procesos migratorios y la dinámica de poblamiento que moldearon la variabilidad genética de las poblaciones durante el poblamiento del Cono Sur, a través del análisis de mitogenomas completos de individuos del sur de Patagonia. MATERIALES Y MÉTODOS: Se obtuvieron mitogenomas completos mediante secuenciación masiva de dos individuos del Holoceno tardío (SAC 1-1-3 y SAC 1-1-4) enterrados en el mismo chenque en la Cuenca del Lago Salitroso (provincia de Santa Cruz, Argentina). Para evaluar las afinidades matrilineales con otros haplotipos, se realizaron reconstrucciones filogenéticas de máxima verosimilitud y bayesianas, así como una red mediana de haplotipos. RESULTADOS: Los mitogenomas fueron asignados a los haplogrupos B2 y B2b, exhibiendo una profundidad de secuenciación promedio de 54X y 89X (cobertura ≥1X de 98,6% y 100%), y un elevado número de diferencias nucleotídicas entre ellos. Los análisis filogenéticos mostraron una relación relativamente estrecha entre el haplotipo encontrado en el SAC 1-1-4 y los recuperados de un individuo del Holoceno Medio de Laguna Chica (provincia de Buenos Aires), y de un grupo de individuos de la costa peruana. Para el SAC 1-1-3, no se establecieron relaciones claras con ningún otro haplotipo. DISCUSIÓN: La gran divergencia entre los haplotipos presentados en este estudio sugiere gran variabilidad en el acervo genético fundador, o bien un enriquecimiento posterior por contacto biológico frecuente con otras poblaciones. Nuestros resultados destacan la persistencia de señales genéticas relacionadas con las primeras oleadas de poblamiento de Sudamérica, lo que sugiere que el poblamiento regional del extremo sur del continente ha sido mucho más complejo de lo que se pensaba inicialmente.

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.

Microsatellite isolation and characterization in sunflower (Helianthus annuus L.).

Development of microsatellite markers for sunflower (Helianthus annuus L.) was performed to estimate their frequency, nature (structure), levels of polymorphism, usefulness for genotype identification, and calculation of genetic relationships between inbred lines representing the species diversity. Isolation was performed from a small-insert genomic library followed by hybridization screening using oligonucleotide probes containing different nucleotide arrays. In this work, 503 unique microsatellite clones were sequenced and 271 PCR primer sequences bordering the microsatellite repeat were designed. For polymorphism assessment, 16 H. annuus germplasm accessions were checked and 170 of the primers tested were shown to be polymorphic for the selected lines. The polymorphic microsatellites produced an average of 3.5 alleles/locus and an average polymorphism information content (PIC) of 0.55. The most frequently found motifs within polymorphic simple-sequence repeats (SSRs) were: (GA)n, (GT)n, (AT)n, followed by trinucleotides (ATT)n, (TGG)n, and (ATC)n, and the tetranucleotide (CATA)n. Most of the 170 SSRs obtained showed important differences in the 16 reference inbred lines used for their characterization. In this work, 20 of the most informative SSRs destined to sunflower genotyping and legal fingerprinting purposes are fully described.