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Bolze A, Basler T, White S, Dei Rossi A, Wyman D, Dai H, Roychoudhury P, Greninger AL, Hayashibara K, Beatty M, Shah S, Stous S, McCrone JT, Kil E, Cassens T, Tsan K, Nguyen J, Ramirez J, Carter S, Cirulli ET, Schiabor Barrett K, Washington NL, Belda-Ferre P, Jacobs S, Sandoval E, Becker D, Lu JT, Isaksson M, Lee W, Luo S. Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination. Med (N Y) 2022; 3:848-859.e4. [PMID: 36332633 PMCID: PMC9581791 DOI: 10.1016/j.medj.2022.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/14/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Between November 2021 and February 2022, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta and Omicron variants co-circulated in the United States, allowing for co-infections and possible recombination events. METHODS We sequenced 29,719 positive samples during this period and analyzed the presence and fraction of reads supporting mutations specific to either the Delta or Omicron variant. FINDINGS We identified 18 co-infections, one of which displayed evidence of a low Delta-Omicron recombinant viral population. We also identified two independent cases of infection by a Delta-Omicron recombinant virus, where 100% of the viral RNA came from one clonal recombinant. In the three cases, the 5' end of the viral genome was from the Delta genome and the 3' end from Omicron, including the majority of the spike protein gene, though the breakpoints were different. CONCLUSIONS Delta-Omicron recombinant viruses were rare, and there is currently no evidence that Delta-Omicron recombinant viruses are more transmissible between hosts compared with the circulating Omicron lineages. FUNDING This research was supported by the NIH RADx initiative and by the Centers for Disease Control Contract 75D30121C12730 (Helix).
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Affiliation(s)
| | | | | | | | | | | | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA 98195, USA
| | | | - Mark Beatty
- County of San Diego Health and Human Services, San Diego, CA 92110, USA
| | - Seema Shah
- County of San Diego Health and Human Services, San Diego, CA 92110, USA
| | - Sarah Stous
- County of San Diego Health and Human Services, San Diego, CA 92110, USA
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Roychoudhury P, Luo S, Hayashibara K, Hajian P, Mills MG, Lozach J, Cassens T, Wendm ST, Arnould I, Becker D, Wesselman T, Davis-Turak J, Creager R, Lai E, Jerome KR, Basler T, Dei Rossi A, Lee W, Greninger AL. Identification of Omicron-Delta Coinfections Using PCR-Based Genotyping. Microbiol Spectr 2022; 10:e0060522. [PMID: 35502920 PMCID: PMC9241779 DOI: 10.1128/spectrum.00605-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | - Pooneh Hajian
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Margaret G. Mills
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | | | | | - Seffir T. Wendm
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Isabel Arnould
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | | | | | | | | | - Eric Lai
- Personalized Science, LLC, South Burlington, Vermont, USA
| | - Keith R. Jerome
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | | | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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Bolze A, Luo S, White S, Cirulli ET, Wyman D, Dei Rossi A, Machado H, Cassens T, Jacobs S, Schiabor Barrett KM, Tanudjaja F, Tsan K, Nguyen J, Ramirez JM, Sandoval E, Wang X, Wong D, Becker D, Laurent M, Lu JT, Isaksson M, Washington NL, Lee W. SARS-CoV-2 variant Delta rapidly displaced variant Alpha in the United States and led to higher viral loads. Cell Rep Med 2022; 3:100564. [PMID: 35474739 PMCID: PMC8922438 DOI: 10.1016/j.xcrm.2022.100564] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/10/2022] [Accepted: 02/17/2022] [Indexed: 11/22/2022]
Abstract
We report on the sequencing of 74,348 SARS-CoV-2 positive samples collected across the United States and show that the Delta variant, first detected in the United States in March 2021, made up the majority of SARS-CoV-2 infections by July 1, 2021 and accounted for >99.9% of the infections by September 2021. Not only did Delta displace variant Alpha, which was the dominant variant at the time, it also displaced the Gamma, Iota, and Mu variants. Through an analysis of quantification cycle (Cq) values, we demonstrate that Delta infections tend to have a 1.7× higher viral load compared to Alpha infections (a decrease of 0.8 Cq) on average. Our results are consistent with the hypothesis that the increased transmissibility of the Delta variant could be due to the ability of the Delta variant to establish a higher viral load earlier in the infection as compared to the Alpha variant. Alpha was dominant in spring 2021 and went extinct in fall 2021 in the United States Delta also displaced Gamma, Iota, and Mu variants On average, viral load was ∼1.7× higher in Delta infections versus Alpha infections
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Washington NL, Gangavarapu K, Zeller M, Bolze A, Cirulli ET, Schiabor Barrett KM, Larsen BB, Anderson C, White S, Cassens T, Jacobs S, Levan G, Nguyen J, Ramirez JM, Rivera-Garcia C, Sandoval E, Wang X, Wong D, Spencer E, Robles-Sikisaka R, Kurzban E, Hughes LD, Deng X, Wang C, Servellita V, Valentine H, De Hoff P, Seaver P, Sathe S, Gietzen K, Sickler B, Antico J, Hoon K, Liu J, Harding A, Bakhtar O, Basler T, Austin B, MacCannell D, Isaksson M, Febbo PG, Becker D, Laurent M, McDonald E, Yeo GW, Knight R, Laurent LC, de Feo E, Worobey M, Chiu CY, Suchard MA, Lu JT, Lee W, Andersen KG. Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States. Cell 2021; 184:2587-2594.e7. [PMID: 33861950 PMCID: PMC8009040 DOI: 10.1016/j.cell.2021.03.052] [Citation(s) in RCA: 197] [Impact Index Per Article: 65.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/25/2021] [Accepted: 03/24/2021] [Indexed: 11/30/2022]
Abstract
The highly transmissible B.1.1.7 variant of SARS-CoV-2, first identified in the United Kingdom, has gained a foothold across the world. Using S gene target failure (SGTF) and SARS-CoV-2 genomic sequencing, we investigated the prevalence and dynamics of this variant in the United States (US), tracking it back to its early emergence. We found that, while the fraction of B.1.1.7 varied by state, the variant increased at a logistic rate with a roughly weekly doubling rate and an increased transmission of 40%–50%. We revealed several independent introductions of B.1.1.7 into the US as early as late November 2020, with community transmission spreading it to most states within months. We show that the US is on a similar trajectory as other countries where B.1.1.7 became dominant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality.
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Affiliation(s)
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | | | | | - Brendan B Larsen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Catelyn Anderson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | | | | | | | | | | | | | | | | | | | - Emily Spencer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Laura D Hughes
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92122, USA
| | - Xianding Deng
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Candace Wang
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Holly Valentine
- University of California, San Diego, San Diego, CA 92093, USA
| | - Peter De Hoff
- University of California, San Diego, San Diego, CA 92093, USA
| | - Phoebe Seaver
- University of California, San Diego, San Diego, CA 92093, USA
| | - Shashank Sathe
- University of California, San Diego, San Diego, CA 92093, USA
| | | | | | | | | | | | | | | | - Tracy Basler
- San Diego County Health and Human Services Agency, San Diego, CA 92101, USA
| | - Brett Austin
- San Diego County Health and Human Services Agency, San Diego, CA 92101, USA
| | - Duncan MacCannell
- Office of Advanced Molecular Detection, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | | | | | | | | | - Eric McDonald
- San Diego County Health and Human Services Agency, San Diego, CA 92101, USA
| | - Gene W Yeo
- University of California, San Diego, San Diego, CA 92093, USA
| | - Rob Knight
- University of California, San Diego, San Diego, CA 92093, USA
| | | | | | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; Innovative Genomics Institute, Berkeley, CA 94720, USA
| | - Marc A Suchard
- Department of Biostatistics, Fielding School of Public Health, and Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | | | | | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92122, USA.
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5
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Washington NL, Gangavarapu K, Zeller M, Bolze A, Cirulli ET, Barrett KMS, Larsen BB, Anderson C, White S, Cassens T, Jacobs S, Levan G, Nguyen J, Ramirez JM, Rivera-Garcia C, Sandoval E, Wang X, Wong D, Spencer E, Robles-Sikisaka R, Kurzban E, Hughes LD, Deng X, Wang C, Servellita V, Valentine H, De Hoff P, Seaver P, Sathe S, Gietzen K, Sickler B, Antico J, Hoon K, Liu J, Harding A, Bakhtar O, Basler T, Austin B, Isaksson M, Febbo PG, Becker D, Laurent M, McDonald E, Yeo GW, Knight R, Laurent LC, de Feo E, Worobey M, Chiu C, Suchard MA, Lu JT, Lee W, Andersen KG. Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States. medRxiv 2021:2021.02.06.21251159. [PMID: 33564780 PMCID: PMC7872373 DOI: 10.1101/2021.02.06.21251159] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
As of January of 2021, the highly transmissible B.1.1.7 variant of SARS-CoV-2, which was first identified in the United Kingdom (U.K.), has gained a strong foothold across the world. Because of the sudden and rapid rise of B.1.1.7, we investigated the prevalence and growth dynamics of this variant in the United States (U.S.), tracking it back to its early emergence and onward local transmission. We found that the RT-qPCR testing anomaly of S gene target failure (SGTF), first observed in the U.K., was a reliable proxy for B.1.1.7 detection. We sequenced 212 B.1.1.7 SARS-CoV-2 genomes collected from testing facilities in the U.S. from December 2020 to January 2021. We found that while the fraction of B.1.1.7 among SGTF samples varied by state, detection of the variant increased at a logistic rate similar to those observed elsewhere, with a doubling rate of a little over a week and an increased transmission rate of 35-45%. By performing time-aware Bayesian phylodynamic analyses, we revealed several independent introductions of B.1.1.7 into the U.S. as early as late November 2020, with onward community transmission enabling the variant to spread to at least 30 states as of January 2021. Our study shows that the U.S. is on a similar trajectory as other countries where B.1.1.7 rapidly became the dominant SARS-CoV-2 variant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality.
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Affiliation(s)
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
| | | | | | | | - Brendan B. Larsen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
| | - Catelyn Anderson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
| | | | | | | | | | | | | | | | | | | | | | - Emily Spencer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
| | | | - Ezra Kurzban
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
| | - Laura D. Hughes
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xianding Deng
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
| | - Candace Wang
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
| | | | | | | | | | | | | | | | | | | | | | | | - Tracy Basler
- San Diego County Health and Human Services Agency, San Diego, CA
| | - Brett Austin
- San Diego County Health and Human Services Agency, San Diego, CA
| | | | | | | | | | - Eric McDonald
- San Diego County Health and Human Services Agency, San Diego, CA
| | | | | | | | | | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
| | - Charles Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
- Innovative Genomics Institute, Berkeley, CA
| | - Marc A. Suchard
- Department of Biostatistics, Fielding School of Public Health, and Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | | | | | - Kristian G. Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
- Scripps Research Translational Institute, La Jolla, CA
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