Genomic Sequences and Analysis of Five SARS-CoV-2 Variants Obtained from Patients in Lambayeque, Peru

Aguilar–Gamboa, Franklin Rómulo; Salcedo-Mejía, Luis Alberto; Serquén-López, Luis Miguel; Llontop, Marco E. Mechan; Tullume-Vergara, Percy Omar; Bonifacio-Briceño, Juan José; Asencios, Rámses Salas; Silva-Díaz, Heber; Cárdenas, Juan Pablo

doi:10.1128/mra.01267-20

Cited by 3 publications

(4 citation statements)

References 10 publications

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“…The predominant lineage in this sampling period was lineage C.14 in 76.7% (n = 23) belonging to clade 20D, which also detected the circulation of lineages C.33, B.1.1.485, B.1.1, B.1.1.1, and B.1.111 in a percentage ranging between 3.3% and 6.7%, respectively, distributed between clades 20B and 20A. The results agreed with those reported by [ 4 ], who sequenced five genomes obtained from patients from the Lambayeque region at the end of April 2020, reporting the circulation of lineage B.1.1.1, which was classified according to Nextclade of Nextstrain in clade 20B. Also, our results agree with what was described by [ 3 ].…”

Section: Discussionsupporting

confidence: 91%

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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: Discussionsupporting

confidence: 91%

“…This mutation had already spread widely in Europe at that time. However, other uncommon mutations demonstrate the virus’s rapid evolutionary processes and adaptive capabilities [ 4 ]. Subsequent investigations corroborated the presence of a variant endemic to the region, which was designated the Lambda variant [ 5 ].…”

Section: Introductionmentioning

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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“…Phylogeny was inferred using IQTREE (version 2.0.3) [20] with setting –ufboot 1000 -m GTR + F + I + G4. Phylogenetic tree visualization and annotation was performed using iTOL (version 5.6.3) [21] .…”

Section: Sars-cov-2 Wgs 2020mentioning

confidence: 99%

SARS-CoV-2 whole-genome sequencing using reverse complement PCR: For easy, fast and accurate outbreak and variant analysis.

Coolen

Wolters

Tostmann

et al. 2021

Journal of Clinical Virology

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During the course of the SARS-CoV-2 pandemic reports of mutations with effects on spreading and vaccine effectiveness emerged. Large scale mutation analysis using rapid SARS-CoV-2 Whole Genome Sequencing (WGS) is often unavailable but could support public health organizations and hospitals in monitoring transmission and rising levels of mutant strains. Here we report a novel WGS technique for SARS-CoV-2, the EasySeq™ RC-PCR SARS-CoV-2 WGS kit. By applying a reverse complement polymerase chain reaction (RC-PCR), an Illumina library preparation is obtained in a single PCR, thereby saving time, resources and facilitating high-throughput screening. Using this WGS technique, we evaluated SARS-CoV-2 diversity and possible transmission within a group of 173 patients and healthcare workers (HCW) of the Radboud university medical center during 2020. Due to the emergence of variants of concern, we screened SARS-CoV-2 positive samples in 2021 for identification of mutations and lineages. With use of EasySeq™ RC-PCR SARS-CoV-2 WGS kit we were able to obtain reliable results to confirm outbreak clusters and additionally identify new previously unassociated links in a considerably easier workaround compared to current methods. Furthermore, various SARS-CoV-2 variants of interest were detected among samples and validated against an Oxford Nanopore sequencing amplicon strategy which illustrates this technique is suitable for surveillance and monitoring current circulating variants.

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“…In view of this scenario, we described the circulation of an underestimated SARS‐CoV‐2 Lambda VOI (C.37/GR/452Q.V1/21G lineage) in the Sao Paulo State, providing a primary overview of its transmission dynamics. This VOI has been largely disseminated in many South American countries, including Chile, Peru, Argentina, Ecuador, and Colombia 2–6 but there is a unique report considering Brazil 7 . In total, we detected seven Lambda VOI isolates in a total of approximately 8000 sequenced SARS‐CoV‐2 genomes and therefore we describe their molecular epidemiology and mutational profile in the Sao Paulo State.…”

Section: Introductionmentioning

confidence: 99%

Introduction of SARS‐CoV‐2 C.37 (WHO VOI lambda) in the Sao Paulo State, Southeast Brazil

Kashima

Slavov

Giovanetti

et al. 2021

Journal of Medical Virology

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Genomic Sequences and Analysis of Five SARS-CoV-2 Variants Obtained from Patients in Lambayeque, Peru

Abstract: Here, we report the genomic sequences of five severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains obtained from nasopharyngeal samples from five tested COVID-19-infected patients from the Lambayeque region in Peru during early April 2020.

Cited by 3 publications

References 10 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

SARS-CoV-2 whole-genome sequencing using reverse complement PCR: For easy, fast and accurate outbreak and variant analysis.

Introduction of SARS‐CoV‐2 C.37 (WHO VOI lambda) in the Sao Paulo State, Southeast Brazil

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