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Zhao LP, Cohen S, Zhao M, Madeleine M, Payne TH, Lybrand TP, Geraghty DE, Jerome KR, Corey L. Using Haplotype-Based Artificial Intelligence to Evaluate SARS-CoV-2 Novel Variants and Mutations. JAMA Netw Open 2023; 6:e230191. [PMID: 36809468 PMCID: PMC9945077 DOI: 10.1001/jamanetworkopen.2023.0191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/05/2023] [Indexed: 02/23/2023] Open
Abstract
Importance Earlier detection of emerging novel SARS-COV-2 variants is important for public health surveillance of potential viral threats and for earlier prevention research. Artificial intelligence may facilitate early detection of SARS-CoV2 emerging novel variants based on variant-specific mutation haplotypes and, in turn, be associated with enhanced implementation of risk-stratified public health prevention strategies. Objective To develop a haplotype-based artificial intelligence (HAI) model for identifying novel variants, including mixture variants (MVs) of known variants and new variants with novel mutations. Design, Setting, and Participants This cross-sectional study used serially observed viral genomic sequences globally (prior to March 14, 2022) to train and validate the HAI model and used it to identify variants arising from a prospective set of viruses from March 15 to May 18, 2022. Main Outcomes and Measures Viral sequences, collection dates, and locations were subjected to statistical learning analysis to estimate variant-specific core mutations and haplotype frequencies, which were then used to construct an HAI model to identify novel variants. Results Through training on more than 5 million viral sequences, an HAI model was built, and its identification performance was validated on an independent validation set of more than 5 million viruses. Its identification performance was assessed on a prospective set of 344 901 viruses. In addition to achieving an accuracy of 92.8% (95% CI within 0.1%), the HAI model identified 4 Omicron MVs (Omicron-Alpha, Omicron-Delta, Omicron-Epsilon, and Omicron-Zeta), 2 Delta MVs (Delta-Kappa and Delta-Zeta), and 1 Alpha-Epsilon MV, among which Omicron-Epsilon MVs were most frequent (609/657 MVs [92.7%]). Furthermore, the HAI model found that 1699 Omicron viruses had unidentifiable variants given that these variants acquired novel mutations. Lastly, 524 variant-unassigned and variant-unidentifiable viruses carried 16 novel mutations, 8 of which were increasing in prevalence percentages as of May 2022. Conclusions and Relevance In this cross-sectional study, an HAI model found SARS-COV-2 viruses with MV or novel mutations in the global population, which may require closer examination and monitoring. These results suggest that HAI may complement phylogenic variant assignment, providing additional insights into emerging novel variants in the population.
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Affiliation(s)
- Lue Ping Zhao
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Seth Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Medicine, University of Washington School of Medicine, Seattle
| | | | - Margaret Madeleine
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Thomas H. Payne
- Department of Medicine, University of Washington School of Medicine, Seattle
| | - Terry P. Lybrand
- Quintepa Computing LLC, Nashville, Tennessee
- Department of Chemistry, Vanderbilt University; Nashville, Tennessee
| | - Daniel E. Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Keith R. Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Medicine, University of Washington School of Medicine, Seattle
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Medicine, University of Washington School of Medicine, Seattle
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Giannakopoulos S, Strange DP, Jiyarom B, Abdelaal O, Bradshaw AW, Nerurkar VR, Ward MA, Bakse J, Yap J, Vanapruks S, Boisvert W, Tallquist MD, Shikuma C, Sadri-Ardekani H, Clapp P, Murphy S, Verma S. In vitro evidence against productive SARS-CoV-2 infection of human testicular cells: Bystander effects of infection mediate testicular injury. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.09.21.508904. [PMID: 36172118 PMCID: PMC9516847 DOI: 10.1101/2022.09.21.508904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The hallmark of severe COVID-19 involves systemic cytokine storm and multi-organ failure including testicular injury and germ cell depletion. The ACE2 receptor is also expressed in the resident testicular cells however, SARS-CoV-2 infection and mechanisms of testicular injury are not fully understood. The testicular injury can likely result either from direct virus infection of resident cells or by exposure to systemic inflammatory mediators or virus antigens. We here characterized SARS-CoV-2 infection in different human testicular 2D and 3D models including primary Sertoli cells, Leydig cells, mixed seminiferous tubule cells (STC), and 3D human testicular organoids (HTO). Data shows that SARS-CoV-2 does not establish a productive infection in any testicular cell types. However, exposure of STC and HTO to inflammatory supernatant from infected airway epithelial cells and COVID-19 plasma depicted a significant decrease in cell viability and death of undifferentiated spermatogonia. Further, exposure to only SARS-CoV-2 envelope protein, but not Spike or nucleocapsid proteins led to cytopathic effects on testicular cells that was dependent on the TLR2 receptor. A similar trend was observed in the K18h-ACE2 mouse model which revealed gross pathology in the absence of virus replication in the testis. Collectively, data strongly indicates that the testicular injury is not due to direct infection of SARS-CoV-2 but more likely an indirect effect of exposure to systemic inflammation or SARS-CoV-2 antigens. Data also provide novel insights into the mechanism of testicular injury and could explain the clinical manifestation of testicular symptoms associated with severe COVID-19.
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Affiliation(s)
- Stefanos Giannakopoulos
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Daniel P Strange
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Boonyanudh Jiyarom
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Omar Abdelaal
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Aaron W Bradshaw
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
- Department of Urology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Vivek R Nerurkar
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Monika A Ward
- Institute for Biogenesis Research, John A Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Jackson Bakse
- Institute for Biogenesis Research, John A Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Jonathan Yap
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Selena Vanapruks
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - William Boisvert
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Michelle D Tallquist
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Cecilia Shikuma
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Hooman Sadri-Ardekani
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
- Department of Urology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Philip Clapp
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Sean Murphy
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Saguna Verma
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
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