Secuenciación del SARS-CoV-2: la iniciativa tecnológica para fortalecer los sistemas de alerta temprana ante emergencias de salud pública en Latinoamérica y el Caribe

Álvarez-Díaz, Diego A.; Laiton‐Donato, Katherine; Franco-Muñoz, Carlos; Mercado, Marcela

doi:10.7705/biomedica.5841

Cited by 7 publications

(2 citation statements)

References 36 publications

(26 reference statements)

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“…Still, it is common in other viruses, including those causing the common cold and in the human genome. By inserting this fragment into itself, Omicron could mimic the host and better evade the human immune system response, contributing to its transmissibility and the possibility of causing mild or asymptomatic disease [ 27 ].…”

Section: Discussionmentioning

confidence: 99%

Genomic and Phylogenetic Characterisation of SARS-CoV-2 Genomes Isolated in Patients from Lambayeque Region, Peru

Aguilar-Martinez,

Sandoval-Peña,

Molina-Mora

et al. 2024

TropicalMed

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Objective: this study aims to identify and characterise genomic and phylogenetically isolated SARS-CoV-2 viral isolates in patients from Lambayeque, Peru. Methods: Nasopharyngeal swabs were taken from patients from the Almanzor Aguinaga Asenjo Hospital, Chiclayo, Lambayeque, Peru, which had been considered mild, moderate, and severe cases of COVID-19. Patients had to have tested positive for COVID-19, using a positive RT-PCR for SARS-CoV-2. Subsequently, the SARS-CoV-2 complete viral genome sequencing was carried out using Illumina MiSeq®. The sequences obtained from the sequence were analysed in Nextclade V1.10.0 to assign the corresponding clades, identify mutations in the SARS-CoV-2 genes and perform quality control of the sequences obtained. All sequences were aligned using MAFFT v7.471. The SARS-CoV-2 isolate Wuhan NC 045512.2 was used as a reference sequence to analyse mutations at the amino acid level. The construction of the phylogenetic tree model was achieved with IQ-TREE v1.6.12. Results: It was determined that during the period from December 2020 to January 2021, the lineages s C.14, C.33, B.1.1.485, B.1.1, B.1.1.1, and B.1.111 circulated, with lineage C.14 being the most predominant at 76.7% (n = 23/30). These lineages were classified in clade 20D mainly and also within clades 20B and 20A. On the contrary, the variants found in the second batch of samples of the period from September to October 2021 were Delta (72.7%), Gamma (13.6%), Mu (4.6%), and Lambda (9.1%), distributed between clades 20J, 21G, 21H, 21J, and 21I. Conclusions: This study reveals updated information on the viral genomics of SARS-CoV-2 in the Lambayeque region, Peru, which is crucial to understanding the origins and dispersion of the virus and provides information on viral pathogenicity, transmission and epidemiology.

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Section: Discussionmentioning

confidence: 99%

Genomic and Phylogenetic Characterisation of SARS-CoV-2 Genomes Isolated in Patients from Lambayeque Region, Peru

Aguilar-Martinez,

Sandoval-Peña,

Molina-Mora

et al. 2024

TropicalMed

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“…However, sharing sequencing results in the GISAID database is crucial for almost real-time genomic surveillance worldwide, providing a better understanding of the transmission and viral evolution dynamics of SARS-CoV-2. (26,27) Although this study provides valuable information, it has some limitations related mainly to the sample size and the lack of clinical data. Thus, only 74 viral sequences were analysed in two groups, which may limit the ability to detect some low-frequency circulating variants.…”

Section: Discussionmentioning

confidence: 99%

Genomic and Phylogenetic Characterisation of SARS-CoV-2 Genomes Isolated in Patients from Lambayeque Region, Peru

Aguilar-Martinez,

Sandoval-Peña,

Molina-Mora

et al. 2023

Preprint

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Objective: To identify and characterise genomic and phylogenetically isolated SARS-CoV-2 viral isolates in patients from Lambayeque, Peru. Methods: nasopharyngeal swabs were taken from patients from the Almanzor Aguinaga Asenjo Hospital, Chiclayo, Lambayeque, Peru, which have been considered mild, moderate and severe cases of COVID-19. Patients had to have tested positive for COVID-19, using a positive RT-PCR for SARS-CoV-2. Subsequently, the SARS-CoV-2 complete viral genome sequencing was carried out using Illumina MiSeq®. The sequences obtained from the sequence were analysed in Nextclade V1.10.0 to assign the corresponding clades, identify mutations in the SARS-CoV-2 genes and perform quality control of the sequences obtained. All sequences were aligned using MAFFT v7.471. The SARS-CoV-2 isolate Wuhan NC 045512.2 was used as a reference sequence to analyse mutations at the amino acid level. The construction of the phylogenetic tree model was achieved with IQ-TREE v1.6.12. Results: it was determined that during the period December 2020 and January 2021, the lineages s C.14, C.33, B.1.1.485, B.1.1, B.1.1.1, B.1.111 circulated, lineage C.14 the most predominant with 76.7% (n=23/30), these lineages were classified in clade 20D mainly and also within clade 20B and 20A. On the contrary, the variants found in the second batch of samples of the period September – October 2021 were Delta Variant (72.7%), Gamma (13.6%), Mu (4.6%), Lambda (9.1%), distributed between clades 20J, 21G, 21H, 21J and 21I. Conclusions: This study reveals updated information on the viral genomics of SARS-CoV-2 in the Lambayeque region, Peru, which is crucial to understanding the origins and dispersion of the virus and provides information on viral pathogenicity, transmission and epidemiology.

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Anthropological genetic insights on Caribbean population history

Nieves-Colón

2022

Evolutionary Anthropology

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As the last American region settled by humans, yet the first to experience European colonization, the Caribbean islands have a complex history characterized by continuous migration, admixture, and demographic change. In the last 20 years, genetics research has transformed our understanding of Caribbean population history and revisited major debates in Caribbean anthropology, such as those surrounding the first peopling of the Antilles and the relationship between ancient Indigenous communities and present‐day islanders. Genetics studies have also contributed novel perspectives for understanding pivotal events in Caribbean post‐contact history such as European colonization, the Atlantic Slave Trade, and the Asian Indenture system. Here, I discuss the last 20 years of Caribbean genetics research and emphasize the importance of integrating genetics with interdisciplinary historic, archaeological, and anthropological approaches. Such interdisciplinary research is essential for investigating the dynamic history of the Caribbean and characterizing its impact on the biocultural diversity of present‐day Caribbean peoples.

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Secuenciación del SARS-CoV-2: la iniciativa tecnológica para fortalecer los sistemas de alerta temprana ante emergencias de salud pública en Latinoamérica y el Caribe

Cited by 7 publications

References 36 publications

Genomic and Phylogenetic Characterisation of SARS-CoV-2 Genomes Isolated in Patients from Lambayeque Region, Peru

Genomic and Phylogenetic Characterisation of SARS-CoV-2 Genomes Isolated in Patients from Lambayeque Region, Peru

Genomic and Phylogenetic Characterisation of SARS-CoV-2 Genomes Isolated in Patients from Lambayeque Region, Peru

Anthropological genetic insights on Caribbean population history

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