Novel SARS-CoV-2 spike variant identified through viral genome sequencing of the pediatric Washington D.C. COVID-19 outbreak Article Swipe
Jonathan LoTempio
,
Erik Billings
,
Kyah Draper
,
Christal Ralph
,
Mahdi Moshgriz
,
Nhat Duong
,
Jennifer Dien Bard
,
Xiaowu Gai
,
David Wessel
,
Roberta L. DeBiasi
,
Joseph M. Campos
,
Éric Vilain
,
Meghan Delaney
,
Drew G. Michael
·
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.1101/2021.02.08.21251344
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.1101/2021.02.08.21251344
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.
Related Topics
Concepts
Clade
Genome
Virology
Outbreak
Pandemic
Biology
DNA sequencing
Viral load
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
Virus
Whole genome sequencing
Coronavirus disease 2019 (COVID-19)
Deep sequencing
Population
Genetics
Phylogenetics
Medicine
Gene
Infectious disease (medical specialty)
Disease
Environmental health
Pathology
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2021.02.08.21251344
- https://www.medrxiv.org/content/medrxiv/early/2021/02/10/2021.02.08.21251344.full.pdf
- OA Status
- green
- Cited By
- 5
- References
- 33
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W3127376305
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W3127376305Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1101/2021.02.08.21251344Digital Object Identifier
- Title
-
Novel SARS-CoV-2 spike variant identified through viral genome sequencing of the pediatric Washington D.C. COVID-19 outbreakWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
-
2021Year of publication
- Publication date
-
2021-02-10Full publication date if available
- Authors
-
Jonathan LoTempio, Erik Billings, Kyah Draper, Christal Ralph, Mahdi Moshgriz, Nhat Duong, Jennifer Dien Bard, Xiaowu Gai, David Wessel, Roberta L. DeBiasi, Joseph M. Campos, Éric Vilain, Meghan Delaney, Drew G. MichaelList of authors in order
- Landing page
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https://doi.org/10.1101/2021.02.08.21251344Publisher landing page
- PDF URL
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https://www.medrxiv.org/content/medrxiv/early/2021/02/10/2021.02.08.21251344.full.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
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greenOpen access status per OpenAlex
- OA URL
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https://www.medrxiv.org/content/medrxiv/early/2021/02/10/2021.02.08.21251344.full.pdfDirect OA link when available
- Concepts
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Clade, Genome, Virology, Outbreak, Pandemic, Biology, DNA sequencing, Viral load, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Virus, Whole genome sequencing, Coronavirus disease 2019 (COVID-19), Deep sequencing, Population, Genetics, Phylogenetics, Medicine, Gene, Infectious disease (medical specialty), Disease, Environmental health, PathologyTop concepts (fields/topics) attached by OpenAlex
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5Total citation count in OpenAlex
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2022: 3, 2021: 2Per-year citation counts (last 5 years)
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| abstract_inverted_index.this | 133, 293 |
| abstract_inverted_index.very | 297 |
| abstract_inverted_index.were | 83 |
| abstract_inverted_index.with | 49, 56, 117, 215 |
| abstract_inverted_index.Study | 273 |
| abstract_inverted_index.Viral | 68, 130, 233 |
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| abstract_inverted_index.cases | 91, 101 |
| abstract_inverted_index.eight | 160, 282 |
| abstract_inverted_index.life. | 13 |
| abstract_inverted_index.other | 161, 316 |
| abstract_inverted_index.shows | 153 |
| abstract_inverted_index.spike | 138, 204, 237, 254, 305 |
| abstract_inverted_index.using | 71 |
| abstract_inverted_index.viral | 22, 33, 120, 151, 222, 275, 326 |
| abstract_inverted_index.virus | 3 |
| abstract_inverted_index.which | 241, 261, 334 |
| abstract_inverted_index.young | 298 |
| abstract_inverted_index.(three | 259 |
| abstract_inverted_index.GISAID | 147, 279 |
| abstract_inverted_index.clade, | 87, 96 |
| abstract_inverted_index.direct | 338 |
| abstract_inverted_index.genome | 23, 69 |
| abstract_inverted_index.global | 8, 148 |
| abstract_inverted_index.health | 343 |
| abstract_inverted_index.impact | 339 |
| abstract_inverted_index.public | 342 |
| abstract_inverted_index.region | 320 |
| abstract_inverted_index.sample | 134 |
| abstract_inverted_index.serves | 262 |
| abstract_inverted_index.target | 266 |
| abstract_inverted_index.tested | 229 |
| abstract_inverted_index.trimer | 258 |
| abstract_inverted_index.within | 164, 183 |
| abstract_inverted_index.(MIS-C) | 62 |
| abstract_inverted_index.Capitol | 185 |
| abstract_inverted_index.S:N679S | 155 |
| abstract_inverted_index.center. | 129, 232 |
| abstract_inverted_index.clades. | 108 |
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| abstract_inverted_index.genomic | 196 |
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| abstract_inverted_index.patient | 218, 228 |
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| abstract_inverted_index.primary | 50 |
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| abstract_inverted_index.region, | 186 |
| abstract_inverted_index.region. | 168, 289 |
| abstract_inverted_index.related | 283 |
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| abstract_inverted_index.sample, | 110 |
| abstract_inverted_index.samples | 163 |
| abstract_inverted_index.strains | 82 |
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| abstract_inverted_index.towards | 19 |
| abstract_inverted_index.vaccine | 271 |
| abstract_inverted_index.variant | 156, 182, 200, 294, 330 |
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| abstract_inverted_index.Hospital | 43 |
| abstract_inverted_index.National | 42 |
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| abstract_inverted_index.S:N679S. | 140 |
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| abstract_inverted_index.analysis | 31, 70 |
| abstract_inverted_index.analyzed | 81 |
| abstract_inverted_index.antibody | 268 |
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| abstract_inverted_index.measures | 344 |
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| abstract_inverted_index.suggests | 175 |
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| abstract_inverted_index.COVID-19. | 216 |
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| abstract_inverted_index.evaluated | 126 |
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| abstract_inverted_index.frequency | 193 |
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| abstract_inverted_index.including | 47 |
| abstract_inverted_index.increased | 325 |
| abstract_inverted_index.indicated | 75 |
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| abstract_inverted_index.pandemic, | 9 |
| abstract_inverted_index.pediatric | 37 |
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| abstract_inverted_index.resources | 15 |
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| abstract_inverted_index.sequences | 152, 174, 276, 284 |
| abstract_inverted_index.subunits) | 260 |
| abstract_inverted_index.therapies | 269 |
| abstract_inverted_index.treatment | 64 |
| abstract_inverted_index.IMPORTANCE | 198 |
| abstract_inverted_index.SARS-CoV-2 | 2, 137, 181, 195, 203, 252 |
| abstract_inverted_index.Washington | 45 |
| abstract_inverted_index.emergence, | 333 |
| abstract_inverted_index.generation | 73 |
| abstract_inverted_index.identified | 135, 207, 235 |
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| abstract_inverted_index.increasing | 191 |
| abstract_inverted_index.presenting | 39 |
| abstract_inverted_index.prevalence | 331 |
| abstract_inverted_index.sequencing | 74, 131, 234, 327 |
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| abstract_inverted_index.undergoing | 63 |
| abstract_inverted_index.Multisystem | 57 |
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| abstract_inverted_index.strategies. | 347 |
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| abstract_inverted_index.Children’s | 41 |
| abstract_inverted_index.Inflammatory | 58 |
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| abstract_inverted_index.hospitalized | 214 |
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| abstract_inverted_index.transmission | 176 |
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| cited_by_percentile_year.min | 93 |
| corresponding_author_ids | https://openalex.org/A5065633370 |
| countries_distinct_count | 2 |
| institutions_distinct_count | 14 |
| corresponding_institution_ids | https://openalex.org/I193531525, https://openalex.org/I4210087204 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/3 |
| sustainable_development_goals[0].score | 0.8600000143051147 |
| sustainable_development_goals[0].display_name | Good health and well-being |
| citation_normalized_percentile.value | 0.59707974 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |