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Crone MA, Hakki S, Fenn J, Zhou J, de Oliveira CR, Madon KJ, Koycheva A, Badhan A, Jonnerby J, Nevin S, Conibear E, Derelle R, Varro R, Luca C, Ahmad S, Zambon M, Barclay WS, Dunning J, Freemont PS, Taylor GP, Lalvani A. Rapid emergence of transmissible SARS-CoV-2 variants in mild community cases. Microbiol Spectr 2024; 12:e0363423. [PMID: 38483161 PMCID: PMC10986593 DOI: 10.1128/spectrum.03634-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 02/06/2024] [Indexed: 04/06/2024] Open
Affiliation(s)
- Michael A. Crone
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
- UK Dementia Research Institute Centre for Care Research and Technology, Imperial College London, London, United Kingdom
- London Biofoundry, Imperial College Translation and Innovation Hub, London, United Kingdom
| | - Seran Hakki
- NIHR Health Protection Research Unit in Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Joe Fenn
- NIHR Health Protection Research Unit in Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Jie Zhou
- Section of Virology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | | | - Kieran J. Madon
- NIHR Health Protection Research Unit in Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Aleksandra Koycheva
- NIHR Health Protection Research Unit in Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Anjna Badhan
- Section of Virology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Jakob Jonnerby
- NIHR Health Protection Research Unit in Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Sean Nevin
- NIHR Health Protection Research Unit in Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Emily Conibear
- NIHR Health Protection Research Unit in Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Romain Derelle
- NIHR Health Protection Research Unit in Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Robert Varro
- NIHR Health Protection Research Unit in Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Constanta Luca
- NIHR Health Protection Research Unit in Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Shazaad Ahmad
- Department of Virology, Manchester Medical Microbiology Partnership, Manchester Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Maria Zambon
- UK Health Security Agency, London, United Kingdom
| | - Wendy S. Barclay
- Section of Virology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Jake Dunning
- UK Health Security Agency, London, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Oxford, Oxford, United Kingdom
| | - Paul S. Freemont
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
- UK Dementia Research Institute Centre for Care Research and Technology, Imperial College London, London, United Kingdom
- London Biofoundry, Imperial College Translation and Innovation Hub, London, United Kingdom
| | - Graham P. Taylor
- Section of Virology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Ajit Lalvani
- NIHR Health Protection Research Unit in Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
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2
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Ko SH, Radecki P, Belinky F, Bhiman JN, Meiring S, Kleynhans J, Amoako D, Guerra Canedo V, Lucas M, Kekana D, Martinson N, Lebina L, Everatt J, Tempia S, Bylund T, Rawi R, Kwong PD, Wolter N, von Gottberg A, Cohen C, Boritz EA. Rapid Emergence and Evolution of SARS-CoV-2 Variants in Advanced HIV Infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574420. [PMID: 38313289 PMCID: PMC10836083 DOI: 10.1101/2024.01.05.574420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Previous studies have linked the evolution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic variants to persistent infections in people with immunocompromising conditions1-4, but the evolutionary processes underlying these observations are incompletely understood. Here we used high-throughput, single-genome amplification and sequencing (HT-SGS) to obtain up to ~103 SARS-CoV-2 spike gene sequences in each of 184 respiratory samples from 22 people with HIV (PWH) and 25 people without HIV (PWOH). Twelve of 22 PWH had advanced HIV infection, defined by peripheral blood CD4 T cell counts (i.e., CD4 counts) <200 cells/μL. In PWOH and PWH with CD4 counts ≥200 cells/μL, most single-genome spike sequences in each person matched one haplotype that predominated throughout the infection. By contrast, people with advanced HIV showed elevated intra-host spike diversity with a median of 46 haplotypes per person (IQR 14-114). Higher intra-host spike diversity immediately after COVID-19 symptom onset predicted longer SARS-CoV-2 RNA shedding among PWH, and intra-host spike diversity at this timepoint was significantly higher in people with advanced HIV than in PWOH. Composition of spike sequence populations in people with advanced HIV fluctuated rapidly over time, with founder sequences often replaced by groups of new haplotypes. These population-level changes were associated with a high total burden of intra-host mutations and positive selection at functionally important residues. In several cases, delayed emergence of detectable serum binding to spike was associated with positive selection for presumptive antibody-escape mutations. Taken together, our findings show remarkable intra-host genetic diversity of SARS-CoV-2 in advanced HIV infection and suggest that adaptive intra-host SARS-CoV-2 evolution in this setting may contribute to the emergence of new variants of concern (VOCs).
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Affiliation(s)
- Sung Hee Ko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pierce Radecki
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Frida Belinky
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jinal N. Bhiman
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- SAMRC Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Susan Meiring
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Jackie Kleynhans
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Daniel Amoako
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Integrative Biology and Bioinformatics, College of Biological Sciences, University of Guelph, Ontario, Canada
| | - Vanessa Guerra Canedo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Margaret Lucas
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dikeledi Kekana
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Neil Martinson
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Johns Hopkins University, Center for TB Research, Baltimore, MD 21218, USA
| | - Limakatso Lebina
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Josie Everatt
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Stefano Tempia
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tatsiana Bylund
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole Wolter
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Eli A. Boritz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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3
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Oyola S. Characterization of SARS-CoV-2 genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population. RESEARCH SQUARE 2023:rs.3.rs-3457875. [PMID: 37961584 PMCID: PMC10635312 DOI: 10.21203/rs.3.rs-3457875/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Vaccination is a key control measure of COVID-19 by preventing severe effects of disease outcomes, reducing hospitalization rates and death, and increasing herd immunity. However, vaccination can affect the evolution and adaptation of SARS-CoV-2, largely through vaccine-induced immune pressure. Here we investigated the recombination events and single nucleotide polymorphisms (SNPs) on SARS-CoV-2 genome in non-vaccinated and vaccinated patients in the Kenyan population. We identified recombination hotspots in the S, N, and ORF1a/b genes and showed the genetic evolution landscape of SARS-CoV-2 by comparing within-wave and inter-wave recombination events from the beginning of the pandemic (June 2020) to (October 2022) in Kenya. An in-depth analysis of (SNPs) on the S, ORf1a/b, and N genes identified previously unreported mutations. We detected a minority variant in non-vaccinated patients in Kenya, that contained immune escape mutation S255F of the spike gene and showing a differential recombination pattern within the non-vaccinated patients. Detailed analysis of recombination between waves suggested an association between increased population immunity and declining risk of emergence of variants of concern. Overall, this work identified unique mutations in SARS-CoV-2 which could have significant implications for virus evolution, virulence, and immune escape.
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Misra G, Manzoor A, Chopra M, Upadhyay A, Katiyar A, Bhushan B, Anvikar A. Genomic epidemiology of SARS-CoV-2 from Uttar Pradesh, India. Sci Rep 2023; 13:14847. [PMID: 37684328 PMCID: PMC10491582 DOI: 10.1038/s41598-023-42065-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/05/2023] [Indexed: 09/10/2023] Open
Abstract
The various strains and mutations of SARS-CoV-2 have been tracked using several forms of genomic classification systems. The present study reports high-throughput sequencing and analysis of 99 SARS-CoV-2 specimens from Western Uttar Pradesh using sequences obtained from the GISAID database, followed by phylogeny and clade classification. Phylogenetic analysis revealed that Omicron lineages BA-2-like (55.55%) followed by Delta lineage-B.1.617.2 (45.5%) were predominantly circulating in this area Signature substitution at positions S: N501Y, S: D614G, S: T478K, S: K417N, S: E484A, S: P681H, and S: S477N were commonly detected in the Omicron variant-BA-2-like, however S: D614G, S: L452R, S: P681R and S: D950N were confined to Delta variant-B.1.617.2. We have also identified three escape variants in the S gene at codon position 19 (T19I/R), 484 (E484A/Q), and 681 (P681R/H) during the fourth and fifth waves in India. Based on the phylogenetic diversification studies and similar changes in other lineages, our analysis revealed indications of convergent evolution as the virus adjusts to the shifting immunological profile of its human host. To the best of our knowledge, this study is an approach to comprehensively map the circulating SARS-CoV-2 strains from Western Uttar Pradesh using an integrated approach of whole genome sequencing and phylogenetic analysis. These findings will be extremely valuable in developing a structured approach toward pandemic preparedness and evidence-based intervention plans in the future.
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Affiliation(s)
- Gauri Misra
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), A-32, Sector-62, Institutional Area, Noida, UP, 201309, India.
| | - Ashrat Manzoor
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), A-32, Sector-62, Institutional Area, Noida, UP, 201309, India
| | - Meenu Chopra
- National Dairy Research Institute, Karnal, Haryana, India
| | - Archana Upadhyay
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), A-32, Sector-62, Institutional Area, Noida, UP, 201309, India
| | - Amit Katiyar
- Bioinformatics Facility, Centralized Core Research Facility, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Brij Bhushan
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), A-32, Sector-62, Institutional Area, Noida, UP, 201309, India
| | - Anup Anvikar
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), A-32, Sector-62, Institutional Area, Noida, UP, 201309, India
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Mediavilla JR, Lozy T, Lee A, Kim J, Kan VW, Titova E, Amin A, Zody MC, Corvelo A, Oschwald DM, Baldwin A, Fennessey S, Zuckerman JM, Kirn T, Chen L, Zhao Y, Chow KF, Maniatis T, Perlin DS, Kreiswirth BN. Molecular and Clinical Epidemiology of SARS-CoV-2 Infection among Vaccinated and Unvaccinated Individuals in a Large Healthcare Organization from New Jersey. Viruses 2023; 15:1699. [PMID: 37632041 PMCID: PMC10457875 DOI: 10.3390/v15081699] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
New Jersey was among the first states impacted by the COVID-19 pandemic, with one of the highest overall death rates in the nation. Nevertheless, relatively few reports have been published focusing specifically on New Jersey. Here we report on molecular, clinical, and epidemiologic observations, from the largest healthcare network in the state, in a cohort of vaccinated and unvaccinated individuals with laboratory-confirmed SARS-CoV-2 infection. We conducted molecular surveillance of SARS-CoV-2-positive nasopharyngeal swabs collected in nine hospitals from December 2020 through June 2022, using both whole genome sequencing (WGS) and a real-time RT-PCR screening assay targeting spike protein mutations found in variants of concern (VOCs) within our region. De-identified clinical data were obtained retrospectively, including demographics, COVID-19 vaccination status, ICU admission, ventilator support, mortality, and medical history. Statistical analyses were performed to identify associations between SARS-CoV-2 variants, vaccination status, clinical outcomes, and medical risk factors. A total of 5007 SARS-CoV-2-positive nasopharyngeal swabs were successfully screened and/or sequenced. Variant screening identified three predominant VOCs, including Alpha (n = 714), Delta (n = 1877), and Omicron (n = 1802). Omicron isolates were further sub-typed as BA.1 (n = 899), BA.2 (n = 853), or BA.4/BA.5 (n = 50); the remaining 614 isolates were classified as "Other". Approximately 31.5% (1577/5007) of the samples were associated with vaccine breakthrough infections, which increased in frequency following the emergence of Delta and Omicron. Severe clinical outcomes included ICU admission (336/5007 = 6.7%), ventilator support (236/5007 = 4.7%), and mortality (430/5007 = 8.6%), with increasing age being the most significant contributor to each (p < 0.001). Unvaccinated individuals accounted for 79.7% (268/336) of ICU admissions, 78.3% (185/236) of ventilator cases, and 74.4% (320/430) of deaths. Highly significant (p < 0.001) increases in mortality were observed in individuals with cardiovascular disease, hypertension, cancer, diabetes, and hyperlipidemia, but not with obesity, thyroid disease, or respiratory disease. Significant differences (p < 0.001) in clinical outcomes were also noted between SARS-CoV-2 variants, including Delta, Omicron BA.1, and Omicron BA.2. Vaccination was associated with significantly improved clinical outcomes in our study, despite an increase in breakthrough infections associated with waning immunity, greater antigenic variability, or both. Underlying comorbidities contributed significantly to mortality in both vaccinated and unvaccinated individuals, with increasing risk based on the total number of comorbidities. Real-time RT-PCR-based screening facilitated timely identification of predominant variants using a minimal number of spike protein mutations, with faster turnaround time and reduced cost compared to WGS. Continued evolution of SARS-CoV-2 variants will likely require ongoing surveillance for new VOCs, with real-time assessment of clinical impact.
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Affiliation(s)
- José R. Mediavilla
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Tara Lozy
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
- Department of Pediatrics, Hackensack University Medical Center, Hackensack, NJ 07601, USA
| | - Annie Lee
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Justine Kim
- Hackensack Meridian Health Biorepository, Hackensack, NJ 07601, USA
| | - Veronica W. Kan
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Elizabeth Titova
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Ashish Amin
- Hackensack Meridian Health Biorepository, Hackensack, NJ 07601, USA
| | - Michael C. Zody
- New York Genome Center, New York, NY 10013, USA (S.F.); (T.M.)
| | - André Corvelo
- New York Genome Center, New York, NY 10013, USA (S.F.); (T.M.)
| | | | - Amy Baldwin
- New York Genome Center, New York, NY 10013, USA (S.F.); (T.M.)
| | | | - Jerry M. Zuckerman
- Department of Patient Safety and Quality, Hackensack Meridian Health, Edison, NJ 08837, USA
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
| | - Thomas Kirn
- Public Health and Environmental Laboratories, New Jersey Department of Health, Ewing, NJ 08628, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
| | - Yanan Zhao
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
| | - Kar Fai Chow
- Hackensack Meridian Health Biorepository, Hackensack, NJ 07601, USA
- Department of Pathology, Hackensack University Medical Center, Hackensack, NJ 07601, USA
| | - Tom Maniatis
- New York Genome Center, New York, NY 10013, USA (S.F.); (T.M.)
| | - David S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
| | - Barry N. Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
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6
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Jacob RA, Zhang A, Ajoge HO, D'Agostino MR, Nirmalarajah K, Shigayeva A, Demian WL, Baker SJC, Derakhshani H, Rossi L, Nasir JA, Panousis EM, Draia AN, Vermeiren C, Gilchrist J, Smieja N, Bulir D, Smieja M, Surette MG, McArthur AG, McGeer AJ, Mubareka S, Banerjee A, Miller MS, Mossman K. Sensitivity to Neutralizing Antibodies and Resistance to Type I Interferons in SARS-CoV-2 R.1 Lineage Variants, Canada. Emerg Infect Dis 2023; 29:1386-1396. [PMID: 37308158 PMCID: PMC10310370 DOI: 10.3201/eid2907.230198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023] Open
Abstract
Isolating and characterizing emerging SARS-CoV-2 variants is key to understanding virus pathogenesis. In this study, we isolated samples of the SARS-CoV-2 R.1 lineage, categorized as a variant under monitoring by the World Health Organization, and evaluated their sensitivity to neutralizing antibodies and type I interferons. We used convalescent serum samples from persons in Canada infected either with ancestral virus (wave 1) or the B.1.1.7 (Alpha) variant of concern (wave 3) for testing neutralization sensitivity. The R.1 isolates were potently neutralized by both the wave 1 and wave 3 convalescent serum samples, unlike the B.1.351 (Beta) variant of concern. Of note, the R.1 variant was significantly more resistant to type I interferons (IFN-α/β) than was the ancestral isolate. Our study demonstrates that the R.1 variant retained sensitivity to neutralizing antibodies but evolved resistance to type I interferons. This critical driving force will influence the trajectory of the pandemic.
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