Novel SARS-CoV-2 spike variant identified through viral genome sequencing of the pediatric Washington D.C. COVID-19 outbreak
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Abstract
The SARS-CoV-2 virus has emerged as a global pandemic, severely impacting everyday life. Significant resources have been dedicated towards profiling the viral genome in the adult population. We present an analysis of viral genomes acquired from pediatric patients presenting to Children’s National Hospital in Washington D.C, including 24 with primary SARS CoV2 infection and 3 with Multisystem Inflammatory Syndrome in Children (MIS-C) undergoing treatment at our facility. Viral genome analysis using next generation sequencing indicated that approximately 81% of the analyzed strains were of the GH clade, 7% of the cases belonged to the GR clade, and 12% of the cases belonged to S, V, or G clades. One sample, acquired from a neonatal patient, presented with the highest viral RNA load of all patients evaluated at our center. Viral sequencing of this sample identified a SARS-CoV-2 spike variant, S:N679S. Analysis of data deposited in the GISAID global database of viral sequences shows the S:N679S variant is present in eight other sequenced samples within the US mid-Atlantic region. The similarity of the regional sequences suggests transmission and persistence of the SARS-CoV-2 variant within the Capitol region, raising the importance of increasing the frequency of SARS-CoV-2 genomic surveillance.
IMPORTANCE
A variant in the SARS-CoV-2 spike protein was identified in a febrile neonate who was hospitalized with COVID-19. This patient exhibited the highest viral RNA load of any COVID-19 patient tested at our center. Viral sequencing identified a spike protein variant, S:N679S, which is proximal to the cleavage site at residue 681. The SARS-CoV-2 surface spike is a protein trimer (three subunits) which serves as the key target for antibody therapies and vaccine development. Study of viral sequences from the GISAID database revealed eight related sequences from the US mid-Atlantic region. The identification of this variant in a very young patient, its critical location in the spike polyprotein, and the evidence that it has been detected in other patients in our region underscores the need for increased viral sequencing to monitor variant prevalence and emergence, which may have a direct impact on recommended public health measures and vaccination strategies.
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SciScore for 10.1101/2021.02.08.21251344: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: To avoid potential primer bias, cDNA was synthesized using three different initiation sites in the viral genome Viral sequencing: Sequence data was generated on the Illumina MiSeq platform as a part of a collaborative effort between CNH and Children’s Hospital of Los Angeles with institutional review board approval. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Assembly was performed using the NovoAlign v4.02.00 algorithm with NC_045512 as the SARS-CoV-2 reference sequence. NovoAlignsuggested: (NovoAlign, RRID:SCR_014818)The PCR … SciScore for 10.1101/2021.02.08.21251344: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: To avoid potential primer bias, cDNA was synthesized using three different initiation sites in the viral genome Viral sequencing: Sequence data was generated on the Illumina MiSeq platform as a part of a collaborative effort between CNH and Children’s Hospital of Los Angeles with institutional review board approval. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Assembly was performed using the NovoAlign v4.02.00 algorithm with NC_045512 as the SARS-CoV-2 reference sequence. NovoAlignsuggested: (NovoAlign, RRID:SCR_014818)The PCR products were Sanger sequenced by GeneWiz (Frederick, MD). GeneWizsuggested: (GENEWIZ, RRID:SCR_003177)MSA were generated from consensus sequences from CNH samples and from GISAID through ClustalW alignment on default settings (32). ClustalWsuggested: (ClustalW, RRID:SCR_017277)An ML phylogenetic tree was generated on the MSA with MEGA 7.0 (33, 34). MEGAsuggested: (Mega BLAST, RRID:SCR_011920)NextClade assesses variation by aligning a query sequence to the SARS-CoV-2 reference sequence by scanning 21-mers across the genome followed by a banded Smith-Waterman alignment with affine gap penalty, while CoV-GLUE leverages MAFFT (38) and RAxML (39), with detailed methods described in their preprint. MAFFTsuggested: (MAFFT, RRID:SCR_011811)RAxMLsuggested: (RAxML, RRID:SCR_006086)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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