1
|
Rios-Guzman E, Simons LM, Dean TJ, Agnes F, Pawlowski A, Alisoltanidehkordi A, Nam HH, Ison MG, Ozer EA, Lorenzo-Redondo R, Hultquist JF. Deviations in RSV epidemiological patterns and population structures in the United States following the COVID-19 pandemic. Nat Commun 2024; 15:3374. [PMID: 38643200 PMCID: PMC11032338 DOI: 10.1038/s41467-024-47757-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/11/2024] [Indexed: 04/22/2024] Open
Abstract
Respiratory Syncytial Virus (RSV) is a leading cause of acute respiratory tract infection, with the greatest impact on infants, immunocompromised individuals, and older adults. RSV prevalence decreased substantially in the United States (US) following the implementation of COVID-19-related non-pharmaceutical interventions but later rebounded with abnormal seasonality. The biological and epidemiological factors underlying this altered behavior remain poorly defined. In this retrospective cohort study from 2009 to 2023 in Chicago, Illinois, US, we examined RSV epidemiology, clinical severity, and genetic diversity. We found that changes in RSV diagnostic platforms drove increased detections in outpatient settings post-2020 and that hospitalized adults infected with RSV-A were at higher risk of intensive care admission than those with RSV-B. While population structures of RSV-A remained unchanged, RSV-B exhibited a genetic shift into geographically distinct clusters. Mutations in the antigenic regions of the fusion protein suggest convergent evolution with potential implications for vaccine and therapeutic development.
Collapse
Affiliation(s)
- Estefany Rios-Guzman
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | - Lacy M Simons
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | - Taylor J Dean
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | - Francesca Agnes
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | - Anna Pawlowski
- Northwestern Medicine Enterprise Data Warehouse, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Arghavan Alisoltanidehkordi
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | - Hannah H Nam
- Department of Infectious Diseases, University of California - Irvine, Orange, CA, 92868, USA
| | - Michael G Ison
- Division of Microbiology and Infectious Diseases (DMID), National Institute of Health, Rockville, MD, 20852, USA
| | - Egon A Ozer
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | - Ramon Lorenzo-Redondo
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | - Judd F Hultquist
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA.
| |
Collapse
|
2
|
Ling-Hu T, Simons LM, Dean TJ, Rios-Guzman E, Caputo MT, Alisoltani A, Qi C, Malczynski M, Blanke T, Jennings LJ, Ison MG, Achenbach CJ, Larkin PM, Kaul KL, Lorenzo-Redondo R, Ozer EA, Hultquist JF. Integration of individualized and population-level molecular epidemiology data to model COVID-19 outcomes. Cell Rep Med 2024; 5:101361. [PMID: 38232695 PMCID: PMC10829796 DOI: 10.1016/j.xcrm.2023.101361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 08/07/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with enhanced transmissibility and immune escape have emerged periodically throughout the coronavirus disease 2019 (COVID-19) pandemic, but the impact of these variants on disease severity has remained unclear. In this single-center, retrospective cohort study, we examined the association between SARS-CoV-2 clade and patient outcome over a two-year period in Chicago, Illinois. Between March 2020 and March 2022, 14,252 residual diagnostic specimens were collected from SARS-CoV-2-positive inpatients and outpatients alongside linked clinical and demographic metadata, of which 2,114 were processed for viral whole-genome sequencing. When controlling for patient demographics and vaccination status, several viral clades were associated with risk for hospitalization, but this association was negated by the inclusion of population-level confounders, including case count, sampling bias, and shifting standards of care. These data highlight the importance of integrating non-virological factors into disease severity and outcome models for the accurate assessment of patient risk.
Collapse
Affiliation(s)
- Ted Ling-Hu
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Lacy M Simons
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Taylor J Dean
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Estefany Rios-Guzman
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Matthew T Caputo
- Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Arghavan Alisoltani
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Chao Qi
- Clinical Microbiology Laboratory, Department of Pathology, Northwestern Memorial Hospital, Chicago, IL 60611, USA
| | - Michael Malczynski
- Clinical Microbiology Laboratory, Department of Pathology, Northwestern Memorial Hospital, Chicago, IL 60611, USA
| | - Timothy Blanke
- Diagnostic Molecular Biology Laboratory, Northwestern Memorial Hospital, Chicago, IL 60611, USA
| | - Lawrence J Jennings
- Clinical Microbiology Laboratory, Department of Pathology, Northwestern Memorial Hospital, Chicago, IL 60611, USA
| | - Michael G Ison
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Chad J Achenbach
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Paige M Larkin
- Department of Molecular Microbiology, Northshore University HealthSystem, Evanston, IL 60201, USA
| | - Karen L Kaul
- Department of Pathology, Northshore University HealthSystem, Evanston, IL 60201, USA
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Egon A Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Judd F Hultquist
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA.
| |
Collapse
|
3
|
Alisoltani A, Jaroszewski L, Godzik A, Iranzadeh A, Simons LM, Dean TJ, Lorenzo-Redondo R, Hultquist JF, Ozer EA. ViralVar: A Web Tool for Multilevel Visualization of SARS-CoV-2 Genomes. Viruses 2022; 14:v14122714. [PMID: 36560718 PMCID: PMC9781208 DOI: 10.3390/v14122714] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/14/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
The unprecedented growth of publicly available SARS-CoV-2 genome sequence data has increased the demand for effective and accessible SARS-CoV-2 data analysis and visualization tools. The majority of the currently available tools either require computational expertise to deploy them or limit user input to preselected subsets of SARS-CoV-2 genomes. To address these limitations, we developed ViralVar, a publicly available, point-and-click webtool that gives users the freedom to investigate and visualize user-selected subsets of SARS-CoV-2 genomes obtained from the GISAID public database. ViralVar has two primary features that enable: (1) the visualization of the spatiotemporal dynamics of SARS-CoV-2 lineages and (2) a structural/functional analysis of genomic mutations. As proof-of-principle, ViralVar was used to explore the evolution of the SARS-CoV-2 pandemic in the USA in pediatric, adult, and elderly populations (n > 1.7 million genomes). Whereas the spatiotemporal dynamics of the variants did not differ between these age groups, several USA-specific sublineages arose relative to the rest of the world. Our development and utilization of ViralVar to provide insights on the evolution of SARS-CoV-2 in the USA demonstrates the importance of developing accessible tools to facilitate and accelerate the large-scale surveillance of circulating pathogens.
Collapse
Affiliation(s)
- Arghavan Alisoltani
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Correspondence: (A.A.); (E.A.O.)
| | - Lukasz Jaroszewski
- Biosciences Division, School of Medicine, University of California Riverside, Riverside, CA 92507, USA
| | - Adam Godzik
- Biosciences Division, School of Medicine, University of California Riverside, Riverside, CA 92507, USA
| | - Arash Iranzadeh
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Lacy M. Simons
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Taylor J. Dean
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Judd F. Hultquist
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Egon A. Ozer
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Correspondence: (A.A.); (E.A.O.)
| |
Collapse
|
4
|
Simons LM, Ozer EA, Gambut S, Dean TJ, Zhang L, Bhimalli P, Schneider JR, Mamede JI, Ison MG, Karmali R, Gordon LI, Lorenzo-Redondo R, Hultquist JF. De novo emergence of SARS-CoV-2 spike mutations in immunosuppressed patients. Transpl Infect Dis 2022; 24:e13914. [PMID: 35899968 PMCID: PMC9353292 DOI: 10.1111/tid.13914] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/21/2022] [Accepted: 06/30/2022] [Indexed: 12/26/2022]
Abstract
BACKGROUND The continuing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with decreased susceptibility to neutralizing antibodies is of clinical importance. Several spike mutations associated with immune escape have evolved independently in association with different variants of concern (VOCs). How and when these mutations arise is still unclear. We hypothesized that such mutations might arise in the context of persistent viral replication in immunosuppressed hosts. METHODS Nasopharyngeal specimens were collected longitudinally from two immunosuppressed patients with persistent SARS-CoV-2 infection. Plasma was collected from these same patients late in disease course. SARS-CoV-2 whole genome sequencing was performed to assess the emergence and frequency of mutations over time. Select Spike mutations were assessed for their impact on viral entry and antibody neutralization in vitro. RESULTS Our sequencing results revealed the intrahost emergence of spike mutations that are associated with circulating VOCs in both immunosuppressed patients (del241-243 and E484Q in one patient, and E484K in the other). These mutations decreased antibody-mediated neutralization of pseudotyped virus particles in cell culture, but also decreased efficiency of spike-mediated cell entry. CONCLUSIONS These observations demonstrate the de novo emergence of SARS-CoV-2 spike mutations with enhanced immune evasion in immunosuppressed patients with persistent infection. These data suggest one potential mechanism for the evolution of VOCs and emphasize the importance of continued efforts to develop antiviral drugs for suppression of viral replication in hospitalized settings.
Collapse
Affiliation(s)
- Lacy M. Simons
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, USA
| | - Egon A. Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, USA
| | - Stephanie Gambut
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Taylor J. Dean
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, USA
| | - Li Zhang
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Pavan Bhimalli
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Jeffrey R. Schneider
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - João I. Mamede
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Michael G. Ison
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Surgery, Division of Organ Transplantation, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Reem Karmali
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Chicago, IL, USA
| | - Leo I. Gordon
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, USA
| | - Judd F. Hultquist
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, USA
| |
Collapse
|
5
|
Edward PR, Lorenzo-Redondo R, Reyna ME, Simons LM, Hultquist JF, Patel AB, Ozer EA, Muller WJ, Heald-Sargent T, McHugh M, Dean TJ, Dalal RM, John J, Manz SC, Kociolek LK. Severity of Illness Caused by Severe Acute Respiratory Syndrome Coronavirus 2 Variants of Concern in Children: A Single-Center Retrospective Cohort Study. medRxiv 2021:2021.10.23.21265402. [PMID: 34729568 PMCID: PMC8562552 DOI: 10.1101/2021.10.23.21265402] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 11/24/2022]
Abstract
BACKGROUND Recent surges in coronavirus 2019 disease (COVID-19) is attributed to the emergence of more transmissible severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs). However, the relative severity of SARS-CoV-2 VOCs in children is unknown. METHODS This retrospective single-center cohort study was performed at the Ann & Robert H. Lurie Children's Hospital of Chicago, academic free-standing children's hospital. We included all children ≤ 18 years-old diagnosed with COVID-19 between October 15 th , 2020 and August 31 st , 2021 and whose SARS-CoV-2 isolate was sequenced using the Illumina platform. For each patient sample, we identified the SARS-CoV-2 lineage, which was assigned to one of the following groups: Non-VOC, alpha VOC, beta VOC, gamma VOC, or delta VOC. We measured frequency of 5 markers of COVID-19 severity: hospitalization; COVID-19 pharmacologic treatment; respiratory support; intensive care unit admission; and severe disease as classified by the COVID-19 World Health Organization (WHO) Clinical Progression Scale (severe disease; score ≥ 6). A series of logistic regression models were fitted to estimate odds of each severity marker with each VOC (in comparison to non-VOCs), adjusting for COVID-19 community incidence and demographic and clinical co-variates. RESULTS During the study period, 2,025 patients tested positive for SARS-CoV-2; 1,422 (70.2%) had sufficient viral load to permit sequencing. Among the 499 (35.1%) patients whose isolate was sequenced, median (inter-quartile range) age was 7 (1,12) years; 256 (51.3%) isolates were a VOC: 96 (37.5%) alpha, 38 (14.8%) gamma, and 119 (46.5%) delta. After adjusting for age, Black race, Hispanic ethnicity, high-risk medical conditions, and COVID-19 community incidence, neither alpha nor delta was associated with severe COVID-19. Gamma was independently associated with hospitalization (OR 5.9, 95% CI 1.6-21.5, p =0.007), respiratory support (OR 8.3, 95% CI 1.5-56.3, p =0.02), and severe disease as classified by the WHO Clinical Progression Scale (OR 7.7, 95% CI 1.0-78.1, p =0.05). CONCLUSIONS Compared to non-VOC COVID-19 infections, the gamma VOC, but not the alpha or delta VOCs, was associated with increased severity. These data suggest that recent increased in pediatric COVID-19 hospitalizations are related to increased delta COVID-19 incidence rather than increased delta virulence in children.
Collapse
Affiliation(s)
- Priya R Edward
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Ramon Lorenzo-Redondo
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Institute for Global Health, Chicago, IL 60611, USA
| | - Megan E Reyna
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Lacy M Simons
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Institute for Global Health, Chicago, IL 60611, USA
| | - Judd F Hultquist
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Institute for Global Health, Chicago, IL 60611, USA
| | - Ami B Patel
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Egon A Ozer
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Institute for Global Health, Chicago, IL 60611, USA
| | - William J Muller
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Taylor Heald-Sargent
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Matthew McHugh
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Taylor J Dean
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Institute for Global Health, Chicago, IL 60611, USA
| | - Raj M Dalal
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jordan John
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Shannon C Manz
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Larry K Kociolek
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| |
Collapse
|
6
|
Ozer EA, Simons LM, Adewumi OM, Fowotade AA, Omoruyi EC, Adeniji JA, Dean TJ, Zayas J, Bhimalli PP, Ash MK, Godzik A, Schneider JR, Mamede JI, Taiwo BO, Hultquist JF, Lorenzo-Redondo R. Coincident rapid expansion of two SARS-CoV-2 lineages with enhanced infectivity in Nigeria. medRxiv 2021:2021.04.09.21255206. [PMID: 33880483 PMCID: PMC8057251 DOI: 10.1101/2021.04.09.21255206] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The emergence of new SARS-CoV-2 variants with enhanced transmissibility or decreased susceptibility to immune responses is a major threat to global efforts to end the coronavirus disease 2019 (COVID-19) pandemic. Disparities in viral genomic surveillance capabilities and efforts have resulted in gaps in our understanding of the viral population dynamics across the globe. Nigeria, despite having the largest population of any nation in Africa, has had relatively little SARS-CoV-2 sequence data made publicly available. Here we report the whole-genome sequences of 74 SARS-CoV-2 isolates collected from individuals in Oyo State, Nigeria in January 2021. Most isolates belonged to either the B.1.1.7 Alpha "variant of concern" or the B.1.525 Eta lineage, which is currently considered a "variant of interest" containing multiple spike protein mutations previously associated with enhanced transmissibility and possible immune escape. Nigeria has the highest reported frequency of the B.1.525 lineage globally with phylogenetic characteristics consistent with a recent monophyletic origin and rapid expansion. Spike protein from the B.1.525 lineage displayed both increased infectivity and decreased neutralization by convalescent sera compared to Spike proteins from other clades. These results, along with indications that the virus is outpacing the B.1.1.7 lineage in Nigeria, suggest that the B.1.525 lineage represents another "variant of concern" and further underline the importance of genomic surveillance in undersampled regions across the globe.
Collapse
Affiliation(s)
- Egon A. Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Institute for Global Health, Chicago, IL, USA
| | - Lacy M. Simons
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Institute for Global Health, Chicago, IL, USA
| | - Olubusuyi M. Adewumi
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Adeola A. Fowotade
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Biorepository and Clinical Virology Laboratory, College of Medicine, University College Hospital, University of Ibadan, Ibadan, Nigeria
| | - Ewean C. Omoruyi
- Biorepository and Clinical Virology Laboratory, College of Medicine, University College Hospital, University of Ibadan, Ibadan, Nigeria
| | - Johnson A. Adeniji
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Taylor J. Dean
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Institute for Global Health, Chicago, IL, USA
| | - Janet Zayas
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Pavan P. Bhimalli
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Michelle K. Ash
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Adam Godzik
- University of California Riverside School of Medicine, Biosciences Division, Riverside, CA, USA
| | - Jeffrey R. Schneider
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - João I. Mamede
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Babafemi O. Taiwo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Judd F. Hultquist
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Institute for Global Health, Chicago, IL, USA
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Institute for Global Health, Chicago, IL, USA
| |
Collapse
|
7
|
|