Severe Acute Respiratory Syndrome Coronavirus-2 Lambda Variant Collected from a Child from Arkansas and Sequenced

Lori Wong¹, Christopher Randolph^{2

3}, Emily Kanwischer³, Ashton Ingold³, Bobby L Boyanton Jr^{4

5}, Jay Taylor⁵, Rachel A Frenner⁵, Susan E Harley⁴, Jordan T Bird², Timothy J Thurman², Sangam Kandel¹, David W Ussery¹, Stephanie D Byrum^{2

3}, Darrell Dinwiddie⁶, Daryl Domman⁷, Uday K Chalwadi⁸, Joshua Kennedy^{3

8

9}

Affiliations

¹ Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
² Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
³ Arkansas Children's Research Institute, Little Rock, Arkansas, USA.
⁴ Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
⁵ Department of Pathology, Arkansas Children's Hospital, Little Rock, Arkansas, USA.
⁶ Department of Pediatrics, University of New Mexico, Albuquerque, New Mexico, USA.
⁷ Center for Global Health, Dept of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA.
⁸ Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
⁹ Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.

PMID: 36779742
PMCID: PMC10019291
DOI: 10.1128/mra.00007-23

Severe Acute Respiratory Syndrome Coronavirus-2 Lambda Variant Collected from a Child from Arkansas and Sequenced

Lori Wong et al. Microbiol Resour Announc. 2023.

. 2023 Mar 16;12(3):e0000723.

doi: 10.1128/mra.00007-23. Epub 2023 Feb 13.

Authors

Affiliations

¹ Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
² Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
³ Arkansas Children's Research Institute, Little Rock, Arkansas, USA.
⁴ Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
⁵ Department of Pathology, Arkansas Children's Hospital, Little Rock, Arkansas, USA.
⁶ Department of Pediatrics, University of New Mexico, Albuquerque, New Mexico, USA.
⁷ Center for Global Health, Dept of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA.
⁸ Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
⁹ Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.

PMID: 36779742
PMCID: PMC10019291
DOI: 10.1128/mra.00007-23

Abstract

An eleven-year-old tested positive for SARS-CoV-2 Lambda variant. Sequencing was performed on the Oxford Nanopore and the Illumina NextSeq 500. Both platforms identified all 7 of the synonymous mutations in the sample, while all 28 nonsynonymous mutations were identified from Oxford Nanopore and 20 nonsynonymous mutations were identified from Illumina.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

**FIG 1**
Sequencing depth for the V00303 patient sample. Sequencing read depth is shown across the SARS-CoV-2 genome. The genes are identified by the colored bar. (A and B) Oxford Nanopore (A) and Illumina COVIDSeq test (B) sequencing platforms are shown.

See this image and copyright information in PMC

References

1. Quick J. 2020. nCoV-2019 sequencing protocol v3 (LoCost) V.3. https://www.protocols.io/view/ncov-2019-sequencing-protocol-v3-locost-bp.... Accessed August 2021.
1. Wick RR, Judd LM, Holt KE. 2019. Performance of neural network basecalling tools for Oxford Nanopore sequencing. Genome Biol 20:129. doi:10.1186/s13059-019-1727-y. - DOI - PMC - PubMed
1. Loman N, Rowe W, Rambaut A. 2020. nCoV-2019 novel coronavirus bioinformatics protocol. https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html. Accessed August 2021.
1. Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884–i890. doi:10.1093/bioinformatics/bty560. - DOI - PMC - PubMed
1. Li H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv 1303.3997v2 [q-bio.GN]. https://arxiv.org/abs/1303.3997.

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Severe Acute Respiratory Syndrome Coronavirus-2 Lambda Variant Collected from a Child from Arkansas and Sequenced

Affiliations

Severe Acute Respiratory Syndrome Coronavirus-2 Lambda Variant Collected from a Child from Arkansas and Sequenced

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

Grants and funding

LinkOut - more resources

Full Text Sources

Miscellaneous