SARS-CoV-2 Next Generation Sequencing (NGS) data from clinical isolates from the East Texas Region of the United States

Carpenter, Rob E.; Tamrakar, Vaibhav K; Almas, Sadia; Sharma, Archana; Sharma, Rahul

doi:10.1016/j.dib.2023.109312

Cited by 5 publications

(5 citation statements)

References 7 publications

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“…But, very rapidly, as in most countries in the world, a PCR-based approach was introduced as gold standard to accurately detect viral RNA [ 14 ]. However, following the emergence of SARS-CoV-2 variants of concern associated with severe clinical signs and symptoms, whole genome sequencing using NGS technique has become the method of choice to timely detect the emergence and spread of new variants with novel mutations and understand the transmission dynamics of the virus worldwide, including in Mauritania [ 16 , 17 , 41 ]. To document COVID-19 dynamics in Mauritania, a set of SARS-CoV-2 clinical isolates collected from Mauritanian COVID-19-positive patients were analyzed for their genomic profile during the period from September to November 2021, corresponding to the third wave of the COVID-19 epidemic in most West African countries [ 42 ].…”

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Genomic Characterization of SARS-CoV-2 Variants from Clinical Isolates during the COVID-19 Epidemic in Mauritania

Deida,

Papa Mze,

Beye

et al. 2024

Genes

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The rapid genetic evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the coronavirus disease 2019 (COVID-19) pandemic has greatly challenged public health authorities worldwide, including in Mauritania. Despite the presence of the virus in Mauritania, only one study described its genomic variation during the course of the epidemic. The purpose of the present study was to document the genomic pattern of SARS-CoV-2 variants from clinical isolates during the COVID-19 outbreak in Mauritania, from September to November 2021. The whole genomes from 54 SARS-CoV-2 strains detected in nasopharyngeal swabs with a cycle threshold value ≤ 30 were successfully sequenced using next-generation sequencing (NGS) and the Illumina protocol. The mean genome coverage (±standard deviation) was 96.8% (±3.7). The most commonly identified clade was 21J (57.4%), followed by 21D (16.7%), 20A (11.1%), and 20B (9.2%). At the level of lineages, the majority of the samples were Delta variants with the sub-lineage AY.34 (or B.1.617.2.34). Among the 54 SARS-CoV-2 isolates that were successfully sequenced, 33 (61.1%) came from vaccinated individuals, and 21 (38.9%) were from unvaccinated individuals. Several SARS-CoV-2 variants were present in Mauritania between September and November 2021. As Mauritania, like many West African countries, is resource-limited regarding viral genome sequencing facilities, establishment of mutualized sub-regional sequencing platforms will be necessary to ensure continuous monitoring of mutations in viral genomes and track potential reduction in COVID-19 vaccine efficacy, increased transmissibility, and disease severity.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Genomic Characterization of SARS-CoV-2 Variants from Clinical Isolates during the COVID-19 Epidemic in Mauritania

Deida,

Papa Mze,

Beye

et al. 2024

Genes

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“…The resulting amplified fragments were used to construct a library for Illumina deep sequencing, utilizing the Nextera XT DNA Library Preparation and Index kits (Illumina, San Diego, CA, USA). Sequencing was performed with a pair end approach on the Illumina MiSeq platform using the MiSeq Reagent Kit v3 [35].…”

Section: Sars-cov-2 Ngs Sequencingmentioning

confidence: 99%

“…The obtained sequence data were subjected to analysis using the Illumina ® DRAGEN COVID Lineage App [35]. Briefly, following base calling and quality scoring, the resulting sequence reads underwent adapter removal and trimming of ends with low-quality scores.…”

Section: Sars-cov-2 Ngs Sequencingmentioning

confidence: 99%

“…The remaining high-quality reads were then mapped and aligned to the Wuhan-hu-1 reference sequence (Accession Number MN908947.3). Sequence variants were identified using the DRAGEN Somatic caller and the high confident ones incorporated into the reference genome to generate a consensus genome for the sequences based on the selected reference [35]. The first lineage/clade analysis on the consensus genomes was run using Pangolin [36] and/or NextClade [37].…”

Section: Sars-cov-2 Ngs Sequencingmentioning

confidence: 99%

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Characterization of SARS-CoV-2 Variants in Military and Civilian Personnel of an Air Force Airport during Three Pandemic Waves in Italy

Equestre,

Marcantonio,

Marascio

et al. 2023

Microorganisms

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We investigated SARS-CoV-2 variants circulating, from November 2020 to March 2022, among military and civilian personnel at an Air Force airport in Italy in order to classify viral isolates in a potential hotspot for virus spread. Positive samples were subjected to Next-Generation Sequencing (NGS) of the whole viral genome and Sanger sequencing of the spike coding region. Phylogenetic analysis classified viral isolates and traced their evolutionary relationships. Clusters were identified using 70% cut-off. Sequencing methods yielded comparable results in terms of variant classification. In 2020 and 2021, we identified several variants, including B.1.258 (4/67), B.1.177 (9/67), Alpha (B.1.1.7, 9/67), Gamma (P.1.1, 4/67), and Delta (4/67). In 2022, only Omicron and its sub-lineage variants were observed (37/67). SARS-CoV-2 isolates were screened to detect naturally occurring resistance in genomic regions, the target of new therapies, comparing them to the Wuhan Hu-1 reference strain. Interestingly, 2/30 non-Omicron isolates carried the G15S 3CLpro substitution responsible for reduced susceptibility to protease inhibitors. On the other hand, Omicron isolates carried unusual substitutions A1803V, D1809N, and A949T on PLpro, and the D216N on 3CLpro. Finally, the P323L substitution on RdRp coding regions was not associated with the mutational pattern related to polymerase inhibitor resistance. This study highlights the importance of continuous genomic surveillance to monitor SARS-CoV-2 evolution in the general population, as well as in restricted communities.

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Navigating the new norm: The FDA's final rule on laboratory developed tests (LDTs) and its impact on clinical laboratory operations

Carpenter

2024

Clinical Microbiology Newsletter

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SARS-CoV-2 Next Generation Sequencing (NGS) data from clinical isolates from the East Texas Region of the United States

Cited by 5 publications

References 7 publications

Genomic Characterization of SARS-CoV-2 Variants from Clinical Isolates during the COVID-19 Epidemic in Mauritania

Genomic Characterization of SARS-CoV-2 Variants from Clinical Isolates during the COVID-19 Epidemic in Mauritania

Characterization of SARS-CoV-2 Variants in Military and Civilian Personnel of an Air Force Airport during Three Pandemic Waves in Italy

Navigating the new norm: The FDA's final rule on laboratory developed tests (LDTs) and its impact on clinical laboratory operations

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