1
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Wagner C, Kistler KE, Perchetti GA, Baker N, Frisbie LA, Torres LM, Aragona F, Yun C, Figgins M, Greninger AL, Cox A, Oltean HN, Roychoudhury P, Bedford T. Positive selection underlies repeated knockout of ORF8 in SARS-CoV-2 evolution. Nat Commun 2024; 15:3207. [PMID: 38615031 PMCID: PMC11016114 DOI: 10.1038/s41467-024-47599-5] [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] [Received: 09/27/2023] [Accepted: 04/04/2024] [Indexed: 04/15/2024] Open
Abstract
Knockout of the ORF8 protein has repeatedly spread through the global viral population during SARS-CoV-2 evolution. Here we use both regional and global pathogen sequencing to explore the selection pressures underlying its loss. In Washington State, we identified transmission clusters with ORF8 knockout throughout SARS-CoV-2 evolution, not just on novel, high fitness viral backbones. Indeed, ORF8 is truncated more frequently and knockouts circulate for longer than for any other gene. Using a global phylogeny, we find evidence of positive selection to explain this phenomenon: nonsense mutations resulting in shortened protein products occur more frequently and are associated with faster clade growth rates than synonymous mutations in ORF8. Loss of ORF8 is also associated with reduced clinical severity, highlighting the diverse clinical impacts of SARS-CoV-2 evolution.
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Affiliation(s)
- Cassia Wagner
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Kathryn E Kistler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Garrett A Perchetti
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Noah Baker
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | | | - Frank Aragona
- Washington State Department of Health, Shoreline, WA, USA
| | - Cory Yun
- Washington State Department of Health, Shoreline, WA, USA
| | - Marlin Figgins
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Alex Cox
- Washington State Department of Health, Shoreline, WA, USA
| | - Hanna N Oltean
- Washington State Department of Health, Shoreline, WA, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
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2
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Tran-Kiem C, Bedford T. Estimating the reproduction number and transmission heterogeneity from the size distribution of clusters of identical pathogen sequences. Proc Natl Acad Sci U S A 2024; 121:e2305299121. [PMID: 38568971 PMCID: PMC11009662 DOI: 10.1073/pnas.2305299121] [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] [Received: 04/06/2023] [Accepted: 02/26/2024] [Indexed: 04/05/2024] Open
Abstract
Quantifying transmission intensity and heterogeneity is crucial to ascertain the threat posed by infectious diseases and inform the design of interventions. Methods that jointly estimate the reproduction number R and the dispersion parameter k have however mainly remained limited to the analysis of epidemiological clusters or contact tracing data, whose collection often proves difficult. Here, we show that clusters of identical sequences are imprinted by the pathogen offspring distribution, and we derive an analytical formula for the distribution of the size of these clusters. We develop and evaluate an inference framework to jointly estimate the reproduction number and the dispersion parameter from the size distribution of clusters of identical sequences. We then illustrate its application across a range of epidemiological situations. Finally, we develop a hypothesis testing framework relying on clusters of identical sequences to determine whether a given pathogen genetic subpopulation is associated with increased or reduced transmissibility. Our work provides tools to estimate the reproduction number and transmission heterogeneity from pathogen sequences without building a phylogenetic tree, thus making it easily scalable to large pathogen genome datasets.
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Affiliation(s)
- Cécile Tran-Kiem
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- HHMI, Seattle, WA98109
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3
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Quek ZBR, Ng SH. Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology. Pathogens 2024; 13:275. [PMID: 38668230 PMCID: PMC11054155 DOI: 10.3390/pathogens13040275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 04/29/2024] Open
Abstract
High-throughput sequencing (HTS) has revolutionised the field of pathogen genomics, enabling the direct recovery of pathogen genomes from clinical and environmental samples. However, pathogen nucleic acids are often overwhelmed by those of the host, requiring deep metagenomic sequencing to recover sufficient sequences for downstream analyses (e.g., identification and genome characterisation). To circumvent this, hybrid-capture target enrichment (HC) is able to enrich pathogen nucleic acids across multiple scales of divergences and taxa, depending on the panel used. In this review, we outline the applications of HC in human pathogens-bacteria, fungi, parasites and viruses-including identification, genomic epidemiology, antimicrobial resistance genotyping, and evolution. Importantly, we explored the applicability of HC to clinical metagenomics, which ultimately requires more work before it is a reliable and accurate tool for clinical diagnosis. Relatedly, the utility of HC was exemplified by COVID-19, which was used as a case study to illustrate the maturity of HC for recovering pathogen sequences. As we unravel the origins of COVID-19, zoonoses remain more relevant than ever. Therefore, the role of HC in biosurveillance studies is also highlighted in this review, which is critical in preparing us for the next pandemic. We also found that while HC is a popular tool to study viruses, it remains underutilised in parasites and fungi and, to a lesser extent, bacteria. Finally, weevaluated the future of HC with respect to bait design in the eukaryotic groups and the prospect of combining HC with long-read HTS.
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Affiliation(s)
- Z. B. Randolph Quek
- Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore
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4
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Walas N, Müller NF, Parker E, Henderson A, Capone D, Brown J, Barker T, Graham JP. Application of phylodynamics to identify spread of antimicrobial-resistant Escherichia coli between humans and canines in an urban environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170139. [PMID: 38242459 DOI: 10.1016/j.scitotenv.2024.170139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/21/2024]
Abstract
The transmission of antimicrobial resistant bacteria in the urban environment is poorly understood. We utilized genomic sequencing and phylogenetics to characterize the transmission dynamics of antimicrobial resistant Escherichia coli (AMR-Ec) cultured from putative canine (caninep) and human feces present on urban sidewalks in San Francisco, California. We isolated a total of fifty-six AMR-Ec isolates from human (n = 20) and caninep (n = 36) fecal samples from the Tenderloin and South of Market (SoMa) neighborhoods of San Francisco. We then analyzed phenotypic and genotypic antimicrobial resistance (AMR) of the isolates, as well as clonal relationships based on cgMLST and single nucleotide polymorphisms (SNPs) of the core genomes. Using Bayesian inference, we reconstructed the transmission dynamics between humans and caninesp from multiple local outbreak clusters using the marginal structured coalescent approximation (MASCOT). Our results provide evidence for multiple sharing events of AMR-Ec between humans and caninesp. In particular, we found one instance of likely transmission from caninesp to humans as well as an additional local outbreak cluster consisting of one caninep and one human sample. Based on this analysis, it appears that non-human feces act as an important reservoir of clinically relevant AMR-Ec within the urban environment for this study population. This work showcases the utility of genomic epidemiology to reconstruct potential pathways by which antimicrobial resistance spreads.
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Affiliation(s)
| | | | | | | | - Drew Capone
- The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joe Brown
- The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Troy Barker
- The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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5
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Paredes MI, Ahmed N, Figgins M, Colizza V, Lemey P, McCrone JT, Müller N, Tran-Kiem C, Bedford T. Underdetected dispersal and extensive local transmission drove the 2022 mpox epidemic. Cell 2024; 187:1374-1386.e13. [PMID: 38428425 PMCID: PMC10962340 DOI: 10.1016/j.cell.2024.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/15/2023] [Accepted: 02/02/2024] [Indexed: 03/03/2024]
Abstract
The World Health Organization declared mpox a public health emergency of international concern in July 2022. To investigate global mpox transmission and population-level changes associated with controlling spread, we built phylogeographic and phylodynamic models to analyze MPXV genomes from five global regions together with air traffic and epidemiological data. Our models reveal community transmission prior to detection, changes in case reporting throughout the epidemic, and a large degree of transmission heterogeneity. We find that viral introductions played a limited role in prolonging spread after initial dissemination, suggesting that travel bans would have had only a minor impact. We find that mpox transmission in North America began declining before more than 10% of high-risk individuals in the USA had vaccine-induced immunity. Our findings highlight the importance of broader routine specimen screening surveillance for emerging infectious diseases and of joint integration of genomic and epidemiological information for early outbreak control.
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Affiliation(s)
- Miguel I Paredes
- Department of Epidemiology, University of Washington, Seattle, WA, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Nashwa Ahmed
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Marlin Figgins
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, Paris, France
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - John T McCrone
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Nicola Müller
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Cécile Tran-Kiem
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Trevor Bedford
- Department of Epidemiology, University of Washington, Seattle, WA, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA
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6
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Müller NF, Bouckaert RR, Wu CH, Bedford T. MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583734. [PMID: 38496513 PMCID: PMC10942421 DOI: 10.1101/2024.03.06.583734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The spread of infectious diseases is shaped by spatial and temporal aspects, such as host population structure or changes in the transmission rate or number of infected individuals over time. These spatiotemporal dynamics are imprinted in the genome of pathogens and can be recovered from those genomes using phylodynamics methods. However, phylodynamic methods typically quantify either the temporal or spatial transmission dynamics, which leads to unclear biases, as one can potentially not be inferred without the other. Here, we address this challenge by introducing a structured coalescent skyline approach, MASCOT-Skyline that allows us to jointly infer spatial and temporal transmission dynamics of infectious diseases using Markov chain Monte Carlo inference. To do so, we model the effective population size dynamics in different locations using a non-parametric function, allowing us to approximate a range of population size dynamics. We show, using a range of different viral outbreak datasets, potential issues with phylogeographic methods. We then use these viral datasets to motivate simulations of outbreaks that illuminate the nature of biases present in the different phylogeographic methods. We show that spatial and temporal dynamics should be modeled jointly even if one seeks to recover just one of the two. Further, we showcase conditions under which we can expect phylogeographic analyses to be biased, particularly different subsampling approaches, as well as provide recommendations of when we can expect them to perform well. We implemented MASCOT-Skyline as part of the open-source software package MASCOT for the Bayesian phylodynamics platform BEAST2.
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Affiliation(s)
- Nicola F. Müller
- Division of HIV, ID and Global Medicine, University of California San Francisco, San Francisco, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Remco R. Bouckaert
- Centre for Computational Evolution, The University of Auckland, New Zealand
| | - Chieh-Hsi Wu
- School of Mathematical Sciences, University of Southampton, UK
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
- Howard Hughes Medical Institute, Seattle, USA
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7
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Ceballos-Garzon A, Comtet-Marre S, Peyret P. Applying targeted gene hybridization capture to viruses with a focus to SARS-CoV-2. Virus Res 2024; 340:199293. [PMID: 38101578 PMCID: PMC10767490 DOI: 10.1016/j.virusres.2023.199293] [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: 04/03/2023] [Revised: 11/08/2023] [Accepted: 12/03/2023] [Indexed: 12/17/2023]
Abstract
Although next-generation sequencing technologies are advancing rapidly, many research topics often require selective sequencing of genomic regions of interest. In addition, sequencing low-titre viruses is challenging, especially for coronaviruses, which are the largest RNA viruses. Prior to sequencing, enrichment of viral particles can help to significantly increase target sequence information as well as avoid large sequencing efforts and, consequently, can increase sensitivity and reduce sequencing costs. Targeting nucleic acids using capture by hybridization is another efficient method that can be performed by applying complementary probes (DNA or RNA baits) to directly enrich genetic information of interest while removing background non-target material. In studies where sequence capture by hybridization has been applied to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, most authors agree that this technique is useful to easily access sequence targets in complex samples. Furthermore, this approach allows for complete or near-complete sequencing of the viral genome, even in samples with low viral load or poor nucleic acid integrity. In addition, this strategy is highly efficient at discovering new variants by facilitating downstream investigations, such as phylogenetics, epidemiology, and evolution. Commercial kits, as well as in-house protocols, have been developed for enrichment of viral sequences. However, these kits have multiple variations in procedure, with differences in performance. This review compiles and describes studies in which hybridization capture has been applied to SARS-CoV-2 variant genomes.
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Affiliation(s)
| | | | - Pierre Peyret
- Université Clermont Auvergne, INRAE, MEDiS, 63000, Clermont-Ferrand, France.
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8
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Ford ES, Mayer-Blackwell K, Jing L, Laing KJ, Sholukh AM, St Germain R, Bossard EL, Xie H, Pulliam TH, Jani S, Selke S, Burrow CJ, McClurkan CL, Wald A, Greninger AL, Holbrook MR, Eaton B, Eudy E, Murphy M, Postnikova E, Robins HS, Elyanow R, Gittelman RM, Ecsedi M, Wilcox E, Chapuis AG, Fiore-Gartland A, Koelle DM. Repeated mRNA vaccination sequentially boosts SARS-CoV-2-specific CD8 + T cells in persons with previous COVID-19. Nat Immunol 2024; 25:166-177. [PMID: 38057617 PMCID: PMC10981451 DOI: 10.1038/s41590-023-01692-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 10/27/2023] [Indexed: 12/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hybrid immunity is more protective than vaccination or previous infection alone. To investigate the kinetics of spike-reactive T (TS) cells from SARS-CoV-2 infection through messenger RNA vaccination in persons with hybrid immunity, we identified the T cell receptor (TCR) sequences of thousands of index TS cells and tracked their frequency in bulk TCRβ repertoires sampled longitudinally from the peripheral blood of persons who had recovered from coronavirus disease 2019 (COVID-19). Vaccinations led to large expansions in memory TS cell clonotypes, most of which were CD8+ T cells, while also eliciting diverse TS cell clonotypes not observed before vaccination. TCR sequence similarity clustering identified public CD8+ and CD4+ TCR motifs associated with spike (S) specificity. Synthesis of longitudinal bulk ex vivo single-chain TCRβ repertoires and paired-chain TCRɑβ sequences from droplet sequencing of TS cells provides a roadmap for the rapid assessment of T cell responses to vaccines and emerging pathogens.
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Affiliation(s)
- Emily S Ford
- Department of Medicine, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Kerry J Laing
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Anton M Sholukh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Russell St Germain
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Emily L Bossard
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Thomas H Pulliam
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Saumya Jani
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Stacy Selke
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | | | - Anna Wald
- Department of Medicine, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Michael R Holbrook
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Brett Eaton
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Elizabeth Eudy
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Michael Murphy
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Elena Postnikova
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | | | | | - Rachel M Gittelman
- Adaptive Biotechnologies, Seattle, WA, USA
- Guardant Health, Redwood City, CA, USA
| | - Matyas Ecsedi
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Takeda Oncology, Cambridge, MA, USA
| | - Elise Wilcox
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Aude G Chapuis
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David M Koelle
- Department of Medicine, University of Washington, Seattle, WA, USA.
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
- Department of Global Health, University of Washington, Seattle, WA, USA.
- Department of Translational Research, Benaroya Research Institute, Seattle, WA, USA.
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9
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Scotch M, Lauer K, Wieben ED, Cherukuri Y, Cunningham JM, Klee EW, Harrington JJ, Lau JS, McDonough SJ, Mutawe M, O'Horo JC, Rentmeester CE, Schlicher NR, White VT, Schneider SK, Vedell PT, Wang X, Yao JD, Pritt BS, Norgan AP. Genomic epidemiology reveals the dominance of Hennepin County in the transmission of SARS-CoV-2 in Minnesota from 2020 to 2022. mSphere 2023; 8:e0023223. [PMID: 37882516 PMCID: PMC10871168 DOI: 10.1128/msphere.00232-23] [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] [Received: 04/27/2023] [Accepted: 09/20/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE We analyzed over 22,000 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes of patient samples tested at Mayo Clinic Laboratories during a 2-year period in the COVID-19 pandemic, which included Alpha, Delta, and Omicron variants of concern to examine the roles and relationships of Minnesota virus transmission. We found that Hennepin County, the most populous county, drove the transmission of SARS-CoV-2 viruses in the state after including the formation of earlier clades including 20A, 20C, and 20G, as well as variants of concern Alpha and Delta. We also found that Hennepin County was the source for most of the county-to-county introductions after an initial predicted introduction with the virus in early 2020 from an international source, while other counties acted as transmission "sinks." In addition, major policies, such as the end of the lockdown period in 2020 or the end of all restrictions in 2021, did not appear to have an impact on virus diversity across individual counties.
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Affiliation(s)
- Matthew Scotch
- Research Affiliate, Mayo Clinic, Phoenix, Arizona, USA
- Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- College of Health Solutions, Arizona State University, Phoenix, Arizona, USA
| | - Kimberly Lauer
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric D. Wieben
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Julie M. Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric W. Klee
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
- Center for Individualized Medicine, Rochester, Minnesota, USA
| | | | - Julie S. Lau
- Center for Individualized Medicine, Rochester, Minnesota, USA
| | | | - Mark Mutawe
- Center for Individualized Medicine, Rochester, Minnesota, USA
| | - John C. O'Horo
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Chad E. Rentmeester
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Saint Mary’s University of Minnesota, Winona, Minnesota, USA
| | - Nicole R. Schlicher
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Valerie T. White
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Susan K. Schneider
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Peter T. Vedell
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Xiong Wang
- Minnesota Department of Health, St. Paul, Minnesota, USA
| | - Joseph D. Yao
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Bobbi S. Pritt
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Andrew P. Norgan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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10
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Paredes MI, Ahmed N, Figgins M, Colizza V, Lemey P, McCrone JT, Müller N, Tran-Kiem C, Bedford T. Early underdetected dissemination across countries followed by extensive local transmission propelled the 2022 mpox epidemic. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.07.27.23293266. [PMID: 37577709 PMCID: PMC10418578 DOI: 10.1101/2023.07.27.23293266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The World Health Organization declared mpox a public health emergency of international concern in July 2022. To investigate global mpox transmission and population-level changes associated with controlling spread, we built phylogeographic and phylodynamic models to analyze MPXV genomes from five global regions together with air traffic and epidemiological data. Our models reveal community transmission prior to detection, changes in case-reporting throughout the epidemic, and a large degree of transmission heterogeneity. We find that viral introductions played a limited role in prolonging spread after initial dissemination, suggesting that travel bans would have had only a minor impact. We find that mpox transmission in North America began declining before more than 10% of high-risk individuals in the USA had vaccine-induced immunity. Our findings highlight the importance of broader routine specimen screening surveillance for emerging infectious diseases and of joint integration of genomic and epidemiological information for early outbreak control.
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Affiliation(s)
- Miguel I. Paredes
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Nashwa Ahmed
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Marlin Figgins
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique IPLESP, Paris, France
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - John T. McCrone
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Nicola Müller
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Cécile Tran-Kiem
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Trevor Bedford
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
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11
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Ma W, Shi L, Li M. A fast and accurate method for SARS-CoV-2 genomic tracing. Brief Bioinform 2023; 24:bbad339. [PMID: 37779249 DOI: 10.1093/bib/bbad339] [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: 07/08/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 10/03/2023] Open
Abstract
To contain infectious diseases, it is crucial to determine the origin and transmission routes of the pathogen, as well as how the virus evolves. With the development of genome sequencing technology, genome epidemiology has emerged as a powerful approach for investigating the source and transmission of pathogens. In this study, we first presented the rationale for genomic tracing of SARS-CoV-2 and the challenges we currently face. Identifying the most genetically similar reference sequence to the query sequence is a critical step in genome tracing, typically achieved using either a phylogenetic tree or a sequence similarity search. However, these methods become inefficient or computationally prohibitive when dealing with tens of millions of sequences in the reference database, as we encountered during the COVID-19 pandemic. To address this challenge, we developed a novel genomic tracing algorithm capable of processing 6 million SARS-CoV-2 sequences in less than a minute. Instead of constructing a giant phylogenetic tree, we devised a weighted scoring system based on mutation characteristics to quantify sequences similarity. The developed method demonstrated superior performance compared to previous methods. Additionally, an online platform was developed to facilitate genomic tracing and visualization of the spatiotemporal distribution of sequences. The method will be a valuable addition to standard epidemiological investigations, enabling more efficient genomic tracing. Furthermore, the computational framework can be easily adapted to other pathogens, paving the way for routine genomic tracing of infectious diseases.
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Affiliation(s)
- Wentai Ma
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Leisheng Shi
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingkun Li
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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12
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May MR, Rothfels CJ. Diversification Models Conflate Likelihood and Prior, and Cannot be Compared Using Conventional Model-Comparison Tools. Syst Biol 2023; 72:713-722. [PMID: 36897743 DOI: 10.1093/sysbio/syad010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 02/14/2023] [Accepted: 02/28/2023] [Indexed: 03/11/2023] Open
Abstract
Time-calibrated phylogenetic trees are a tremendously powerful tool for studying evolutionary, ecological, and epidemiological phenomena. Such trees are predominantly inferred in a Bayesian framework, with the phylogeny itself treated as a parameter with a prior distribution (a "tree prior"). However, we show that the tree "parameter" consists, in part, of data, in the form of taxon samples. Treating the tree as a parameter fails to account for these data and compromises our ability to compare among models using standard techniques (e.g., marginal likelihoods estimated using path-sampling and stepping-stone sampling algorithms). Since accuracy of the inferred phylogeny strongly depends on how well the tree prior approximates the true diversification process that gave rise to the tree, the inability to accurately compare competing tree priors has broad implications for applications based on time-calibrated trees. We outline potential remedies to this problem, and provide guidance for researchers interested in assessing the fit of tree models. [Bayes factors; Bayesian model comparison; birth-death models; divergence-time estimation; lineage diversification].
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Affiliation(s)
- Michael R May
- Department of Integrative Biology, University of California, Berkeley, CA, USA
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, USA
- Intermountain Herbarium, Ecology Center, and Biology Department, Utah State University, Logan, UT, USA
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13
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Walas N, Müller NF, Parker E, Henderson A, Capone D, Brown J, Barker T, Graham JP. Phylodynamics Uncovers the Transmission of Antibiotic-Resistant Escherichia coli between Canines and Humans in an Urban Environment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543064. [PMID: 37398411 PMCID: PMC10312604 DOI: 10.1101/2023.06.01.543064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The role of canines in transmitting antibiotic resistant bacteria to humans in the urban environment is poorly understood. To elucidate this role, we utilized genomic sequencing and phylogenetics to characterize the burden and transmission dynamics of antibiotic resistant Escherichia coli (ABR-Ec) cultured from canine and human feces present on urban sidewalks in San Francisco, California. We collected a total of fifty-nine ABR-Ec from human (n=12) and canine (n=47) fecal samples from the Tenderloin and South of Market (SoMa) neighborhoods of San Francisco. We then analyzed phenotypic and genotypic antibiotic resistance (ABR) of the isolates, as well as clonal relationships based on cgMLST and single nucleotide polymorphisms (SNPs) of the core genomes. Using Bayesian inference, we reconstructed the transmission dynamics between humans and canines from multiple local outbreak clusters using the marginal structured coalescent approximation (MASCOT). Overall, we found human and canine samples to carry similar amounts and profiles of ABR genes. Our results provide evidence for multiple transmission events of ABR-Ec between humans and canines. In particular, we found one instance of likely transmission from canines to humans as well as an additional local outbreak cluster consisting of one canine and one human sample. Based on this analysis, it appears that canine feces act as an important reservoir of clinically relevant ABR-Ec within the urban environment. Our findings support that public health measures should continue to emphasize proper canine feces disposal practices, access to public toilets and sidewalk and street cleaning. Importance: Antibiotic resistance in E. coli is a growing public health concern with global attributable deaths projected to reach millions annually. Current research has focused heavily on clinical routes of antibiotic resistance transmission to design interventions while the role of alternative reservoirs such as domesticated animals remain less well understood. Our results suggest canines are part of the transmission network that disseminates high-risk multidrug resistance in E. coli within the urban San Francisco community. As such, this study highlights the need to consider canines, and potentially domesticated animals more broadly, when designing interventions to reduce the prevalence of antibiotic resistance in the community. Additionally, it showcases the utility of genomic epidemiology to reconstruct the pathways by which antimicrobial resistance spreads.
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Affiliation(s)
| | - Nicola F. Müller
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Emily Parker
- University of California, Berkeley, California, USA
| | | | - Drew Capone
- Indiana University, Bloomington, Indiana, USA
| | - Joe Brown
- The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Troy Barker
- The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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14
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Brett TS, Bansal S, Rohani P. Charting the spatial dynamics of early SARS-CoV-2 transmission in Washington state. PLoS Comput Biol 2023; 19:e1011263. [PMID: 37379328 PMCID: PMC10335681 DOI: 10.1371/journal.pcbi.1011263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 07/11/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023] Open
Abstract
The spread of SARS-CoV-2 has been geographically uneven. To understand the drivers of this spatial variation in SARS-CoV-2 transmission, in particular the role of stochasticity, we used the early stages of the SARS-CoV-2 invasion in Washington state as a case study. We analysed spatially-resolved COVID-19 epidemiological data using two distinct statistical analyses. The first analysis involved using hierarchical clustering on the matrix of correlations between county-level case report time series to identify geographical patterns in the spread of SARS-CoV-2 across the state. In the second analysis, we used a stochastic transmission model to perform likelihood-based inference on hospitalised cases from five counties in the Puget Sound region. Our clustering analysis identifies five distinct clusters and clear spatial patterning. Four of the clusters correspond to different geographical regions, with the final cluster spanning the state. Our inferential analysis suggests that a high degree of connectivity across the region is necessary for the model to explain the rapid inter-county spread observed early in the pandemic. In addition, our approach allows us to quantify the impact of stochastic events in determining the subsequent epidemic. We find that atypically rapid transmission during January and February 2020 is necessary to explain the observed epidemic trajectories in King and Snohomish counties, demonstrating a persisting impact of stochastic events. Our results highlight the limited utility of epidemiological measures calculated over broad spatial scales. Furthermore, our results make clear the challenges with predicting epidemic spread within spatially extensive metropolitan areas, and indicate the need for high-resolution mobility and epidemiological data.
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Affiliation(s)
- Tobias S. Brett
- Odum School of Ecology, University of Georgia, Athens, Georgia, United States of America
| | - Shweta Bansal
- Department of Biology, Georgetown University, Washington, D.C., United States of America
| | - Pejman Rohani
- Odum School of Ecology, University of Georgia, Athens, Georgia, United States of America
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
- Center for Influenza Disease & Emergence Research (CIDER), Athens, Georgia, United States of America
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15
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Scotch M, Lauer K, Wieben ED, Cherukuri Y, Cunningham JM, Klee EW, Harrington JJ, Lau JS, McDonough SJ, Mutawe M, O’Horo JC, Rentmeester CE, Schlicher NR, White VT, Schneider SK, Vedell PT, Wang X, Yao JD, Pritt BS, Norgan AP. Genomic epidemiology reveals the dominance of Hennepin County in transmission of SARS-CoV-2 in Minnesota from 2020-2022. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2022.07.24.22277978. [PMID: 35923324 PMCID: PMC9347287 DOI: 10.1101/2022.07.24.22277978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
SARS-CoV-2 has had an unprecedented impact on human health and highlights the need for genomic epidemiology studies to increase our understanding of virus evolution and spread, and to inform policy decisions. We sequenced viral genomes from over 22,000 patient samples tested at Mayo Clinic Laboratories between 2020-2022 and use Bayesian phylodynamics to describe county and regional spread in Minnesota. The earliest introduction into Minnesota was to Hennepin County from a domestic source around January 22, 2020; six weeks before the first confirmed case in the state. This led to the virus spreading to Northern Minnesota, and eventually, the rest of the state. International introductions were most abundant in Hennepin (home to the Minneapolis/St. Paul International (MSP) airport) totaling 45 (out of 107) over the two-year period. Southern Minnesota counties were most common for domestic introductions with 19 (out of 64), potentially driven by bordering states such as Iowa and Wisconsin as well as Illinois which is nearby. Hennepin also was, by far, the most dominant source of in-state transmissions to other Minnesota locations (n=772) over the two-year period. We also analyzed the diversity of the location source of SARS-CoV-2 viruses in each county and noted the timing of state-wide policies as well as trends in clinical cases. Neither the number of clinical cases or major policy decisions, such as the end of the lockdown period in 2020 or the end of all restrictions in 2021, appeared to have impact on virus diversity across each individual county.
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Affiliation(s)
- Matthew Scotch
- Research Affiliate, Mayo Clinic Arizona, Phoenix, AZ USA
- Biodesign Center for Environmental Health Engineering, Arizona State University, Tempe, AZ USA
- College of Health Solutions, Arizona State University, Phoenix, Arizona USA
| | - Kimberly Lauer
- Department of Quantitative Health Sciences, Mayo Clinic Rochester, Rochester, MN, USA
| | - Eric D. Wieben
- Department of Biochemistry and Molecular Biology, Mayo Clinic Rochester, Rochester, MN, USA
| | | | - Julie M Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric W Klee
- Department of Quantitative Health Sciences, Mayo Clinic Rochester, Rochester, MN, USA
- Center for Individualized Medicine, Rochester, MN, USA
| | | | - Julie S Lau
- Center for Individualized Medicine, Rochester, MN, USA
| | | | - Mark Mutawe
- Center for Individualized Medicine, Rochester, MN, USA
| | - John C. O’Horo
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Chad E. Rentmeester
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Saint Mary’s University of Minnesota, Winona, MN, USA
| | - Nicole R Schlicher
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Valerie T White
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Susan K Schneider
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Peter T Vedell
- Department of Quantitative Health Sciences, Mayo Clinic Rochester, Rochester, MN, USA
| | - Xiong Wang
- Minnesota Department of Health, St. Paul, MN, USA
| | - Joseph D Yao
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Bobbi S Pritt
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Andrew P Norgan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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16
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Layan M, Müller NF, Dellicour S, De Maio N, Bourhy H, Cauchemez S, Baele G. Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations. Virus Evol 2023; 9:vead010. [PMID: 36860641 PMCID: PMC9969415 DOI: 10.1093/ve/vead010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 01/06/2023] [Accepted: 02/02/2023] [Indexed: 02/08/2023] Open
Abstract
Bayesian phylogeographic inference is a powerful tool in molecular epidemiological studies, which enables reconstruction of the origin and subsequent geographic spread of pathogens. Such inference is, however, potentially affected by geographic sampling bias. Here, we investigated the impact of sampling bias on the spatiotemporal reconstruction of viral epidemics using Bayesian discrete phylogeographic models and explored different operational strategies to mitigate this impact. We considered the continuous-time Markov chain (CTMC) model and two structured coalescent approximations (Bayesian structured coalescent approximation [BASTA] and marginal approximation of the structured coalescent [MASCOT]). For each approach, we compared the estimated and simulated spatiotemporal histories in biased and unbiased conditions based on the simulated epidemics of rabies virus (RABV) in dogs in Morocco. While the reconstructed spatiotemporal histories were impacted by sampling bias for the three approaches, BASTA and MASCOT reconstructions were also biased when employing unbiased samples. Increasing the number of analyzed genomes led to more robust estimates at low sampling bias for the CTMC model. Alternative sampling strategies that maximize the spatiotemporal coverage greatly improved the inference at intermediate sampling bias for the CTMC model, and to a lesser extent, for BASTA and MASCOT. In contrast, allowing for time-varying population sizes in MASCOT resulted in robust inference. We further applied these approaches to two empirical datasets: a RABV dataset from the Philippines and a SARS-CoV-2 dataset describing its early spread across the world. In conclusion, sampling biases are ubiquitous in phylogeographic analyses but may be accommodated by increasing the sample size, balancing spatial and temporal composition in the samples, and informing structured coalescent models with reliable case count data.
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Affiliation(s)
| | | | | | | | - Hervé Bourhy
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, Université Paris Cité, 25-28 rue du Docteur Roux, Paris 75014, France,WHO Collaborating Centre for Reference and Research on Rabies, Institut Pasteur, Université Paris Cité, 28 rue du Docteur Roux, Paris 75724, France
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17
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Oltean HN, Allen KJ, Frisbie L, Lunn SM, Torres LM, Manahan L, Painter I, Russell D, Singh A, Peterson JM, Grant K, Peter C, Cao R, Garcia K, Mackellar D, Jones L, Halstead H, Gray H, Melly G, Nickerson D, Starita L, Frazar C, Greninger AL, Roychoudhury P, Mathias PC, Kalnoski MH, Ting CN, Lykken M, Rice T, Gonzalez-Robles D, Bina D, Johnson K, Wiley CL, Magnuson SC, Parsons CM, Chapman ED, Valencia CA, Fortna RR, Wolgamot G, Hughes JP, Baseman JG, Bedford T, Lindquist S. Sentinel Surveillance System Implementation and Evaluation for SARS-CoV-2 Genomic Data, Washington, USA, 2020-2021. Emerg Infect Dis 2023; 29:242-251. [PMID: 36596565 PMCID: PMC9881772 DOI: 10.3201/eid2902.221482] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Genomic data provides useful information for public health practice, particularly when combined with epidemiologic data. However, sampling bias is a concern because inferences from nonrandom data can be misleading. In March 2021, the Washington State Department of Health, USA, partnered with submitting and sequencing laboratories to establish sentinel surveillance for SARS-CoV-2 genomic data. We analyzed available genomic and epidemiologic data during presentinel and sentinel periods to assess representativeness and timeliness of availability. Genomic data during the presentinel period was largely unrepresentative of all COVID-19 cases. Data available during the sentinel period improved representativeness for age, death from COVID-19, outbreak association, long-term care facility-affiliated status, and geographic coverage; timeliness of data availability and captured viral diversity also improved. Hospitalized cases were underrepresented, indicating a need to increase inpatient sampling. Our analysis emphasizes the need to understand and quantify sampling bias in phylogenetic studies and continue evaluation and improvement of public health surveillance systems.
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18
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Nadeau SA, Vaughan TG, Beckmann C, Topolsky I, Chen C, Hodcroft E, Schär T, Nissen I, Santacroce N, Burcklen E, Ferreira P, Jablonski KP, Posada-Céspedes S, Capece V, Seidel S, Santamaria de Souza N, Martinez-Gomez JM, Cheng P, Bosshard PP, Levesque MP, Kufner V, Schmutz S, Zaheri M, Huber M, Trkola A, Cordey S, Laubscher F, Gonçalves AR, Aeby S, Pillonel T, Jacot D, Bertelli C, Greub G, Leuzinger K, Stange M, Mari A, Roloff T, Seth-Smith H, Hirsch HH, Egli A, Redondo M, Kobel O, Noppen C, du Plessis L, Beerenwinkel N, Neher RA, Beisel C, Stadler T. Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data. Sci Transl Med 2023; 15:eabn7979. [PMID: 36346321 PMCID: PMC9765449 DOI: 10.1126/scitranslmed.abn7979] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genome sequences from evolving infectious pathogens allow quantification of case introductions and local transmission dynamics. We sequenced 11,357 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Switzerland in 2020-the sixth largest effort globally. Using a representative subset of these data, we estimated viral introductions to Switzerland and their persistence over the course of 2020. We contrasted these estimates with simple null models representing the absence of certain public health measures. We show that Switzerland's border closures decoupled case introductions from incidence in neighboring countries. Under a simple model, we estimate an 86 to 98% reduction in introductions during Switzerland's strictest border closures. Furthermore, the Swiss 2020 partial lockdown roughly halved the time for sampled introductions to die out. Last, we quantified local transmission dynamics once introductions into Switzerland occurred using a phylodynamic model. We found that transmission slowed 35 to 63% upon outbreak detection in summer 2020 but not in fall. This finding may indicate successful contact tracing over summer before overburdening in fall. The study highlights the added value of genome sequencing data for understanding transmission dynamics.
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Affiliation(s)
- Sarah A. Nadeau
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.,Corresponding author. (T.S.); (S.A.N.)
| | - Timothy G. Vaughan
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland
| | | | - Ivan Topolsky
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland
| | - Chaoran Chen
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland
| | - Emma Hodcroft
- SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.,Institute for Social and Preventive Medicine, University of Bern; 3012, Bern, Switzerland
| | - Tobias Schär
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland
| | - Ina Nissen
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland
| | - Natascha Santacroce
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland
| | - Elodie Burcklen
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland
| | - Pedro Ferreira
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland
| | - Kim Philipp Jablonski
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland
| | - Susana Posada-Céspedes
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland
| | - Vincenzo Capece
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland
| | - Sophie Seidel
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland
| | | | - Julia M. Martinez-Gomez
- Department of Dermatology, University Hospital Zurich, University of Zurich; 8091, Zurich, Switzerland
| | - Phil Cheng
- Department of Dermatology, University Hospital Zurich, University of Zurich; 8091, Zurich, Switzerland
| | - Philipp P. Bosshard
- Department of Dermatology, University Hospital Zurich, University of Zurich; 8091, Zurich, Switzerland
| | - Mitchell P. Levesque
- Department of Dermatology, University Hospital Zurich, University of Zurich; 8091, Zurich, Switzerland
| | - Verena Kufner
- Institute of Medical Virology, University of Zurich; 8057, Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich; 8057, Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich; 8057, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich; 8057, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich; 8057, Zurich, Switzerland
| | - Samuel Cordey
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine; 1205, Geneva, Switzerland
| | - Florian Laubscher
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine; 1205, Geneva, Switzerland
| | - Ana Rita Gonçalves
- Swiss National Reference Centre for Influenza, University Hospitals of Geneva; 1205, Geneva, Switzerland
| | - Sébastien Aeby
- Institute of Microbiology, University Hospital Centre and University of Lausanne; 1011, Lausanne, Switzerland
| | - Trestan Pillonel
- Institute of Microbiology, University Hospital Centre and University of Lausanne; 1011, Lausanne, Switzerland
| | - Damien Jacot
- Institute of Microbiology, University Hospital Centre and University of Lausanne; 1011, Lausanne, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, University Hospital Centre and University of Lausanne; 1011, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University Hospital Centre and University of Lausanne; 1011, Lausanne, Switzerland
| | - Karoline Leuzinger
- Division of Clinical Virology, University Hospital Basel; 4051, Basel, Switzerland.,Department of Biomedicine, University of Basel; 4031, Basel, Switzerland
| | - Madlen Stange
- SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.,Department of Biomedicine, University of Basel; 4031, Basel, Switzerland.,Division of Clinical Bacteriology and Mycology, University Hospital Basel; 4031, Basel, Switzerland
| | - Alfredo Mari
- SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.,Department of Biomedicine, University of Basel; 4031, Basel, Switzerland.,Division of Clinical Bacteriology and Mycology, University Hospital Basel; 4031, Basel, Switzerland
| | - Tim Roloff
- SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.,Department of Biomedicine, University of Basel; 4031, Basel, Switzerland.,Division of Clinical Bacteriology and Mycology, University Hospital Basel; 4031, Basel, Switzerland
| | - Helena Seth-Smith
- SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.,Department of Biomedicine, University of Basel; 4031, Basel, Switzerland.,Division of Clinical Bacteriology and Mycology, University Hospital Basel; 4031, Basel, Switzerland
| | - Hans H. Hirsch
- Division of Clinical Virology, University Hospital Basel; 4051, Basel, Switzerland.,Department of Biomedicine, University of Basel; 4031, Basel, Switzerland
| | - Adrian Egli
- Department of Biomedicine, University of Basel; 4031, Basel, Switzerland.,Division of Clinical Bacteriology and Mycology, University Hospital Basel; 4031, Basel, Switzerland
| | | | | | | | - Louis du Plessis
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland
| | - Richard A. Neher
- SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.,Biozentrum, University of Basel; 4056, Basel, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.,Corresponding author. (T.S.); (S.A.N.)
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19
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Paredes MI, Perofsky AC, Frisbie L, Moncla LH, Roychoudhury P, Xie H, Mohamed Bakhash SA, Kong K, Arnould I, Nguyen TV, Wendm ST, Hajian P, Ellis S, Mathias PC, Greninger AL, Starita LM, Frazar CD, Ryke E, Zhong W, Gamboa L, Threlkeld M, Lee J, Stone J, McDermot E, Truong M, Shendure J, Oltean HN, Viboud C, Chu H, Müller NF, Bedford T. Local-Scale phylodynamics reveal differential community impact of SARS-CoV-2 in metropolitan US county. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.12.15.22283536. [PMID: 36561171 PMCID: PMC9774227 DOI: 10.1101/2022.12.15.22283536] [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: 12/23/2022]
Abstract
SARS-CoV-2 transmission is largely driven by heterogeneous dynamics at a local scale, leaving local health departments to design interventions with limited information. We analyzed SARS-CoV-2 genomes sampled between February 2020 and March 2022 jointly with epidemiological and cell phone mobility data to investigate fine scale spatiotemporal SARS-CoV-2 transmission dynamics in King County, Washington, a diverse, metropolitan US county. We applied an approximate structured coalescent approach to model transmission within and between North King County and South King County alongside the rate of outside introductions into the county. Our phylodynamic analyses reveal that following stay-at-home orders, the epidemic trajectories of North and South King County began to diverge. We find that South King County consistently had more reported and estimated cases, COVID-19 hospitalizations, and longer persistence of local viral transmission when compared to North King County, where viral importations from outside drove a larger proportion of new cases. Using mobility and demographic data, we also find that South King County experienced a more modest and less sustained reduction in mobility following stay-at-home orders than North King County, while also bearing more socioeconomic inequities that might contribute to a disproportionate burden of SARS-CoV-2 transmission. Overall, our findings suggest a role for local-scale phylodynamics in understanding the heterogeneous transmission landscape.
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Affiliation(s)
- Miguel I. Paredes
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Amanda C. Perofsky
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Lauren Frisbie
- Washington State Department of Health, Shoreline, WA USA
| | - Louise H. Moncla
- The University of Pennsylvania, Department of Pathobiology, Philadelphia, PA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | - Kevin Kong
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Isabel Arnould
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Tien V. Nguyen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Seffir T. Wendm
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Pooneh Hajian
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Sean Ellis
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Patrick C. Mathias
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Alexander L. Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Lea M. Starita
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Chris D. Frazar
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Erica Ryke
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Weizhi Zhong
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA USA
| | - Luis Gamboa
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA USA
| | - Machiko Threlkeld
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jover Lee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Jeremy Stone
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA USA
| | - Evan McDermot
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA USA
| | - Melissa Truong
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | | | - Cécile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Helen Chu
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA
| | - Nicola F. Müller
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Trevor Bedford
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
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20
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Jiang B, Yang Y, Chen L, Liu X, Wu X, Chen B, Webster C, Sullivan WC, Larsen L, Wang J, Lu Y. Green spaces, especially nearby forest, may reduce the SARS-CoV-2 infection rate: A nationwide study in the United States. LANDSCAPE AND URBAN PLANNING 2022; 228:104583. [PMID: 36158763 PMCID: PMC9485427 DOI: 10.1016/j.landurbplan.2022.104583] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 05/10/2023]
Abstract
The coronavirus pandemic is an ongoing global crisis that has profoundly harmed public health. Although studies found exposure to green spaces can provide multiple health benefits, the relationship between exposure to green spaces and the SARS-CoV-2 infection rate is unclear. This is a critical knowledge gap for research and practice. In this study, we examined the relationship between total green space, seven types of green space, and a year of SARS-CoV-2 infection data across 3,108 counties in the contiguous United States, after controlling for spatial autocorrelation and multiple types of covariates. First, we examined the association between total green space and SARS-CoV-2 infection rate. Next, we examined the association between different types of green space and SARS-CoV-2 infection rate. Then, we examined forest-infection rate association across five time periods and five urbanicity levels. Lastly, we examined the association between infection rate and population-weighted exposure to forest at varying buffer distances (100 m to 4 km). We found that total green space was negative associated with the SARS-CoV-2 infection rate. Furthermore, two forest variables (forest outside park and forest inside park) had the strongest negative association with the infection rate, while open space variables had mixed associations with the infection rate. Forest outside park was more effective than forest inside park. The optimal buffer distances associated with lowest infection rate are within 1,200 m for forest outside park and within 600 m for forest inside park. Altogether, the findings suggest that green spaces, especially nearby forest, may significantly mitigate risk of SARS-CoV-2 infection.
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Affiliation(s)
- Bin Jiang
- Urban Environments and Human Health Lab, HKUrbanLabs, Faculty of Architecture, The University of Hong Kong, Hong Kong Special Administrative Region
- Division of Landscape Architecture, Department of Architecture, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Yuwen Yang
- Urban Environments and Human Health Lab, HKUrbanLabs, Faculty of Architecture, The University of Hong Kong, Hong Kong Special Administrative Region
- Division of Landscape Architecture, Department of Architecture, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Long Chen
- Department of Architecture and Civil Engineering, College of Engineering, City University of Hong Kong, Hong Kong Special Administrative Region
| | - Xueming Liu
- Urban Environments and Human Health Lab, HKUrbanLabs, Faculty of Architecture, The University of Hong Kong, Hong Kong Special Administrative Region
- Division of Landscape Architecture, Department of Architecture, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Xueying Wu
- Department of Architecture and Civil Engineering, College of Engineering, City University of Hong Kong, Hong Kong Special Administrative Region
| | - Bin Chen
- Future Urbanity & Sustainable Environment (FUSE) Lab, Division of Landscape Architecture, Department of Architecture, Faculty of Architecture, The University of Hong Kong, Hong Kong Special Administrative Region
- Urban Systems Institute, The University of Hong Kong, Hong Kong Special Administrative Region
- HKU Musketeers Foundation Institute of Data Science, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Chris Webster
- HKUrbanLabs, Faculty of Architecture, The University of Hong Kong, Hong Kong Special Administrative Region
| | - William C Sullivan
- Smart, Healthy Communities Initiative, University of Illinois at Urbana-Champaign, USA
- Department of Landscape Architecture, University of Illinois at Urbana-Champaign, USA
| | - Linda Larsen
- Smart Energy Design Assistance Center, University of Illinois at Urbana-Champaign, USA
| | - Jingjing Wang
- Department of Architecture and Civil Engineering, City University of Hong Kong, Hong Kong Special Administrative Region
| | - Yi Lu
- Department of Architecture and Civil Engineering, City University of Hong Kong, Hong Kong Special Administrative Region
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21
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Valenzuela-Fernández A, Cabrera-Rodriguez R, Ciuffreda L, Perez-Yanes S, Estevez-Herrera J, González-Montelongo R, Alcoba-Florez J, Trujillo-González R, García-Martínez de Artola D, Gil-Campesino H, Díez-Gil O, Lorenzo-Salazar JM, Flores C, Garcia-Luis J. Nanomaterials to combat SARS-CoV-2: Strategies to prevent, diagnose and treat COVID-19. Front Bioeng Biotechnol 2022; 10:1052436. [PMID: 36507266 PMCID: PMC9732709 DOI: 10.3389/fbioe.2022.1052436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/09/2022] [Indexed: 11/26/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the associated coronavirus disease 2019 (COVID-19), which severely affect the respiratory system and several organs and tissues, and may lead to death, have shown how science can respond when challenged by a global emergency, offering as a response a myriad of rapid technological developments. Development of vaccines at lightning speed is one of them. SARS-CoV-2 outbreaks have stressed healthcare systems, questioning patients care by using standard non-adapted therapies and diagnostic tools. In this scenario, nanotechnology has offered new tools, techniques and opportunities for prevention, for rapid, accurate and sensitive diagnosis and treatment of COVID-19. In this review, we focus on the nanotechnological applications and nano-based materials (i.e., personal protective equipment) to combat SARS-CoV-2 transmission, infection, organ damage and for the development of new tools for virosurveillance, diagnose and immune protection by mRNA and other nano-based vaccines. All the nano-based developed tools have allowed a historical, unprecedented, real time epidemiological surveillance and diagnosis of SARS-CoV-2 infection, at community and international levels. The nano-based technology has help to predict and detect how this Sarbecovirus is mutating and the severity of the associated COVID-19 disease, thereby assisting the administration and public health services to make decisions and measures for preparedness against the emerging variants of SARS-CoV-2 and severe or lethal COVID-19.
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Affiliation(s)
- Agustín Valenzuela-Fernández
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Romina Cabrera-Rodriguez
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Laura Ciuffreda
- Research Unit, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Silvia Perez-Yanes
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Judith Estevez-Herrera
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | | | - Julia Alcoba-Florez
- Servicio de Microbiología, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Rodrigo Trujillo-González
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
- Departamento de Análisis Matemático, Facultad de Ciencias, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | | | - Helena Gil-Campesino
- Servicio de Microbiología, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Oscar Díez-Gil
- Servicio de Microbiología, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - José M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Carlos Flores
- Research Unit, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Jonay Garcia-Luis
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
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22
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Ford ES, Mayer-Blackwell K, Jing L, Sholukh AM, St Germain R, Bossard EL, Xie H, Pulliam TH, Jani S, Selke S, Burrow CJ, McClurkan CL, Wald A, Holbrook MR, Eaton B, Eudy E, Murphy M, Postnikova E, Robins HS, Elyanow R, Gittelman RM, Ecsedi M, Wilcox E, Chapuis AG, Fiore-Gartland A, Koelle DM. CD8 + T cell clonotypes from prior SARS-CoV-2 infection predominate during the cellular immune response to mRNA vaccination. RESEARCH SQUARE 2022:rs.3.rs-2146712. [PMID: 36263073 PMCID: PMC9580387 DOI: 10.21203/rs.3.rs-2146712/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Almost three years into the SARS-CoV-2 pandemic, hybrid immunity is highly prevalent worldwide and more protective than vaccination or prior infection alone. Given emerging resistance of variant strains to neutralizing antibodies (nAb), it is likely that T cells contribute to this protection. To understand how sequential SARS-CoV-2 infection and mRNA-vectored SARS-CoV-2 spike (S) vaccines affect T cell clonotype-level expansion kinetics, we identified and cross-referenced TCR sequences from thousands of S-reactive single cells against deeply sequenced peripheral blood TCR repertoires longitudinally collected from persons during COVID-19 convalescence through booster vaccination. Successive vaccinations recalled memory T cells and elicited antigen-specific T cell clonotypes not detected after infection. Vaccine-related recruitment of novel clonotypes and the expansion of S-specific clones were most strongly observed for CD8+ T cells. Severe COVID-19 illness was associated with a more diverse CD4+ T cell response to SARS-CoV-2 both prior to and after mRNA vaccination, suggesting imprinting of CD4+ T cells by severe infection. TCR sequence similarity search algorithms revealed myriad public TCR clusters correlating with human leukocyte antigen (HLA) alleles. Selected TCRs from distinct clusters functionally recognized S in the predicted HLA context, with fine viral peptide requirements differing between TCRs. Most subjects tested had S-specific T cells in the nasal mucosa after a 3rd mRNA vaccine dose. The blood and nasal T cell responses to vaccination revealed by clonal tracking were more heterogeneous than nAb boosts. Analysis of bulk and single cell TCR sequences reveals T cell kinetics and diversity at the clonotype level, without requiring prior knowledge of T cell epitopes or HLA restriction, providing a roadmap for rapid assessment of T cell responses to emerging pathogens.
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23
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Lubinski B, Frazier LE, Phan MVT, Bugembe DL, Cunningham JL, Tang T, Daniel S, Cotten M, Jaimes JA, Whittaker GR. Spike Protein Cleavage-Activation in the Context of the SARS-CoV-2 P681R Mutation: an Analysis from Its First Appearance in Lineage A.23.1 Identified in Uganda. Microbiol Spectr 2022; 10:e0151422. [PMID: 35766497 PMCID: PMC9430374 DOI: 10.1128/spectrum.01514-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/06/2022] [Indexed: 11/20/2022] Open
Abstract
Based on its predicted ability to affect transmissibility and pathogenesis, surveillance studies have highlighted the role of a specific mutation (P681R) in the S1/S2 furin cleavage site of the SARS-CoV-2 spike protein. Here we analyzed A.23.1, first identified in Uganda, as a P681R-containing virus several months prior to the emergence of B.1.617.2 (Delta variant). We performed assays using peptides mimicking the S1/S2 from A.23.1 and B.1.617 and observed significantly increased cleavability with furin compared to both an original B lineage (Wuhan-Hu1) and B.1.1.7 (Alpha variant). We also performed cell-cell fusion and functional infectivity assays using pseudotyped particles and observed an increase in activity for A.23.1 compared to an original B lineage spike. However, these changes in activity were not reproduced in the B lineage spike bearing only the P681R substitution. Our findings suggest that while A.23.1 has increased furin-mediated cleavage linked to the P681R substitution, this substitution needs to occur on the background of other spike protein changes to enable its functional consequences. IMPORTANCE During the course of the SARS-CoV-2 pandemic, viral variants have emerged that often contain notable mutations in the spike gene. Mutations that encode changes in the spike S1/S2 (furin) activation site have been considered especially impactful. The S1/S2 change from proline to arginine at position 681 (P681R) first emerged in the A.23.1 variant in Uganda, and subsequently occurred in the more widely transmitted Delta variant. We show that the A.23.1 spike is more readily activated by the host cell protease furin, but that this is not reproduced in an original SARS-CoV-2 spike containing the P681R mutation. Changes to the S1/S2 (furin) activation site play a role in SARS-CoV-2 infection and spread, but successful viruses combine these mutations with other less well identified changes, occurring as part of natural selection.
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Affiliation(s)
- Bailey Lubinski
- Graduate Program in Biological & Biomedical Sciences, Cornell University, Ithaca, New York, USA
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Laura E. Frazier
- Graduate Program in Biological & Biomedical Sciences, Cornell University, Ithaca, New York, USA
| | - My V. T. Phan
- MRC/UVRI and London School of Hygiene and Tropical Medicine – Uganda Research Unit, Entebbe, Uganda
| | - Daniel L. Bugembe
- MRC/UVRI and London School of Hygiene and Tropical Medicine – Uganda Research Unit, Entebbe, Uganda
| | - Jessie L. Cunningham
- Graduate Program in Biological & Biomedical Sciences, Cornell University, Ithaca, New York, USA
| | - Tiffany Tang
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA
| | - Susan Daniel
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA
| | - Matthew Cotten
- MRC/UVRI and London School of Hygiene and Tropical Medicine – Uganda Research Unit, Entebbe, Uganda
- MRC Centre of Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Javier A. Jaimes
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Gary R. Whittaker
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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24
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Hale M, Netland J, Chen Y, Thouvenel CD, Smith KN, Rich LM, Vanderwall ER, Miranda MC, Eggenberger J, Hao L, Watson MJ, Mundorff CC, Rodda LB, King NP, Guttman M, Gale M, Abraham J, Debley JS, Pepper M, Rawlings DJ. IgM antibodies derived from memory B cells are potent cross-variant neutralizers of SARS-CoV-2. J Exp Med 2022; 219:213384. [PMID: 35938988 PMCID: PMC9365875 DOI: 10.1084/jem.20220849] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/22/2022] [Accepted: 07/12/2022] [Indexed: 01/14/2023] Open
Abstract
Humoral immunity to SARS-CoV-2 can be supplemented with polyclonal sera from convalescent donors or an engineered monoclonal antibody (mAb) product. While pentameric IgM antibodies are responsible for much of convalescent sera's neutralizing capacity, all available mAbs are based on the monomeric IgG antibody subtype. We now show that IgM mAbs derived from immune memory B cell receptors are potent neutralizers of SARS-CoV-2. IgM mAbs outperformed clonally identical IgG antibodies across a range of affinities and SARS-CoV-2 receptor-binding domain epitopes. Strikingly, efficacy against SARS-CoV-2 viral variants was retained for IgM but not for clonally identical IgG. To investigate the biological role for IgM memory in SARS-CoV-2, we also generated IgM mAbs from antigen-experienced IgM+ memory B cells in convalescent donors, identifying a potent neutralizing antibody. Our results highlight the therapeutic potential of IgM mAbs and inform our understanding of the role for IgM memory against a rapidly mutating pathogen.
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Affiliation(s)
- Malika Hale
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA
| | - Jason Netland
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Yu Chen
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA
| | | | | | - Lucille M. Rich
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA
| | | | - Marcos C. Miranda
- Institute for Protein Design, University of Washington, Seattle, WA,Department of Biochemistry, University of Washington School of Medicine, Seattle, WA
| | - Julie Eggenberger
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Linhui Hao
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Michael J. Watson
- Department of Medicinal Chemistry, University of Washington, Seattle, WA
| | | | - Lauren B. Rodda
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Neil P. King
- Institute for Protein Design, University of Washington, Seattle, WA,Department of Biochemistry, University of Washington School of Medicine, Seattle, WA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA
| | - Michael Gale
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Jonathan Abraham
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA
| | - Jason S. Debley
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA
| | - Marion Pepper
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - David J. Rawlings
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA,Department of Immunology, University of Washington School of Medicine, Seattle, WA,Department of Pediatrics, University of Washington School of Medicine, Seattle, WA,Correspondence to David J. Rawlings:
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25
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Gao J, May MR, Rannala B, Moore BR. New Phylogenetic Models Incorporating Interval-Specific Dispersal Dynamics Improve Inference of Disease Spread. Mol Biol Evol 2022; 39:6647827. [PMID: 35861314 PMCID: PMC9384482 DOI: 10.1093/molbev/msac159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Phylodynamic methods reveal the spatial and temporal dynamics of viral geographic spread, and have featured prominently in studies of the COVID-19 pandemic. Virtually all such studies are based on phylodynamic models that assume—despite direct and compelling evidence to the contrary—that rates of viral geographic dispersal are constant through time. Here, we: (1) extend phylodynamic models to allow both the average and relative rates of viral dispersal to vary independently between pre-specified time intervals; (2) implement methods to infer the number and timing of viral dispersal events between areas; and (3) develop statistics to assess the absolute fit of discrete-geographic phylodynamic models to empirical datasets. We first validate our new methods using simulations, and then apply them to a SARS-CoV-2 dataset from the early phase of the COVID-19 pandemic. We show that: (1) under simulation, failure to accommodate interval-specific variation in the study data will severely bias parameter estimates; (2) in practice, our interval-specific discrete-geographic phylodynamic models can significantly improve the relative and absolute fit to empirical data; and (3) the increased realism of our interval-specific models provides qualitatively different inferences regarding key aspects of the COVID-19 pandemic—revealing significant temporal variation in global viral dispersal rates, viral dispersal routes, and the number of viral dispersal events between areas—and alters interpretations regarding the efficacy of intervention measures to mitigate the pandemic.
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Affiliation(s)
- Jiansi Gao
- Department of Evolution and Ecology, University of California, Davis, Storer Hall, Davis, CA 95616, U.S.A
| | - Michael R May
- Department of Evolution and Ecology, University of California, Davis, Storer Hall, Davis, CA 95616, U.S.A.,Department of Integrative Biology, University of California, Berkeley, 3060 VLSB, Berkeley, CA 94720-3140, U.S.A
| | - Bruce Rannala
- Department of Evolution and Ecology, University of California, Davis, Storer Hall, Davis, CA 95616, U.S.A
| | - Brian R Moore
- Department of Evolution and Ecology, University of California, Davis, Storer Hall, Davis, CA 95616, U.S.A
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26
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Cárdenas P, Corredor V, Santos-Vega M. Genomic epidemiological models describe pathogen evolution across fitness valleys. SCIENCE ADVANCES 2022; 8:eabo0173. [PMID: 35857510 PMCID: PMC9278859 DOI: 10.1126/sciadv.abo0173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Genomics is fundamentally changing epidemiological research. However, systematically exploring hypotheses in pathogen evolution requires new modeling tools. Models intertwining pathogen epidemiology and genomic evolution can help understand processes such as the emergence of novel pathogen genotypes with higher transmissibility or resistance to treatment. In this work, we present Opqua, a flexible simulation framework that explicitly links epidemiology to sequence evolution and selection. We use Opqua to study determinants of evolution across fitness valleys. We confirm that competition can limit evolution in high-transmission environments and find that low transmission, host mobility, and complex pathogen life cycles facilitate reaching new adaptive peaks through population bottlenecks and decoupling of selective pressures. The results show the potential of genomic epidemiological modeling as a tool in infectious disease research.
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Affiliation(s)
- Pablo Cárdenas
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Vladimir Corredor
- Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, D.C., Colombia
| | - Mauricio Santos-Vega
- Grupo Biología Matemática y Computacional, Departamento Ingeniería Biomédica, Universidad de los Andes, Bogotá, D.C., Colombia
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27
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Safina KR, Sidorina Y, Efendieva N, Belonosova E, Saleeva D, Kirichenko A, Kireev D, Pokrovsky V, Bazykin GA. Molecular Epidemiology of HIV-1 in Oryol Oblast, Russia. Virus Evol 2022; 8:veac044. [PMID: 35775027 PMCID: PMC9239399 DOI: 10.1093/ve/veac044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 05/15/2022] [Accepted: 05/31/2022] [Indexed: 11/29/2022] Open
Abstract
The HIV/AIDS epidemic in Russia is growing, with approximately 100,000 people infected annually. Molecular epidemiology can provide insight into the structure and dynamics of the epidemic. However, its applicability in Russia is limited by the weakness of genetic surveillance, as viral genetic data are only available for <1 per cent of cases. Here, we provide a detailed description of the HIV-1 epidemic for one geographic region of Russia, Oryol Oblast, by collecting and sequencing viral samples from about a third of its known HIV-positive population (768 out of 2,157 patients). We identify multiple introductions of HIV-1 into Oryol Oblast, resulting in eighty-two transmission lineages that together comprise 66 per cent of the samples. Most introductions are of subtype A (315/332), the predominant HIV-1 subtype in Russia, followed by CRF63 and subtype B. Bayesian analysis estimates the effective reproduction number Re for subtype A at 2.8 [1.7–4.4], in line with a growing epidemic. The frequency of CRF63 has been growing more rapidly, with the median Re of 11.8 [4.6–28.7], in agreement with recent reports of this variant rising in frequency in some regions of Russia. In contrast to the patterns described previously in European and North American countries, we see no overrepresentation of males in transmission lineages; meanwhile, injecting drug users are overrepresented in transmission lineages. This likely reflects the structure of the HIV-1 epidemic in Russia dominated by heterosexual and, to a smaller extent, people who inject drugs transmission. Samples attributed to men who have sex with men (MSM) transmission are associated with subtype B and are less prevalent than expected from the male-to-female ratio for this subtype, suggesting underreporting of the MSM transmission route. Together, our results provide a high-resolution description of the HIV-1 epidemic in Oryol Oblast, Russia, characterized by frequent interregional transmission, rapid growth of the epidemic, and rapid displacement of subtype A with the recombinant CRF63 variant.
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Affiliation(s)
- Ksenia R Safina
- The Institute for Information Transmission Problems of Russian Academy of Sciences , Moscow, Russian Federation
- Skolkovo Institute of Science and Technology , Moscow, Russian Federation
| | - Yulia Sidorina
- Oryol Regional Center for AIDS and Infectious Diseases Control and Prevention , Oryol, Russian Federation
| | - Natalya Efendieva
- Oryol Regional Center for AIDS and Infectious Diseases Control and Prevention , Oryol, Russian Federation
| | - Elena Belonosova
- Oryol Regional Center for AIDS and Infectious Diseases Control and Prevention , Oryol, Russian Federation
| | - Darya Saleeva
- Central Research Institute of Epidemiology , Moscow, Russian Federation
| | - Alina Kirichenko
- Central Research Institute of Epidemiology , Moscow, Russian Federation
| | - Dmitry Kireev
- Central Research Institute of Epidemiology , Moscow, Russian Federation
| | - Vadim Pokrovsky
- Central Research Institute of Epidemiology , Moscow, Russian Federation
| | - Georgii A Bazykin
- The Institute for Information Transmission Problems of Russian Academy of Sciences , Moscow, Russian Federation
- Skolkovo Institute of Science and Technology , Moscow, Russian Federation
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28
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Michaelsen TY, Bennedbæk M, Christiansen LE, Jørgensen MSF, Møller CH, Sørensen EA, Knutsson S, Brandt J, Jensen TBN, Chiche-Lapierre C, Collados EF, Sørensen T, Petersen C, Le-Quy V, Sereika M, Hansen FT, Rasmussen M, Fonager J, Karst SM, Marvig RL, Stegger M, Sieber RN, Skov R, Legarth R, Krause TG, Fomsgaard A, Albertsen M. Introduction and transmission of SARS-CoV-2 lineage B.1.1.7, Alpha variant, in Denmark. Genome Med 2022; 14:47. [PMID: 35505393 PMCID: PMC9064402 DOI: 10.1186/s13073-022-01045-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 04/12/2022] [Indexed: 11/18/2022] Open
Abstract
Background In early 2021, the SARS-CoV-2 lineage B.1.1.7 (Alpha variant) became dominant across large parts of the world. In Denmark, comprehensive and real-time test, contact-tracing, and sequencing efforts were applied to sustain epidemic control. Here, we use these data to investigate the transmissibility, introduction, and onward transmission of B.1.1.7 in Denmark. Methods We analyzed a comprehensive set of 60,178 SARS-CoV-2 genomes generated from high-throughput sequencing by the Danish COVID-19 Genome Consortium, representing 34% of all positive cases in the period 14 November 2020 to 7 February 2021. We calculated the transmissibility of B.1.1.7 relative to other lineages using Poisson regression. Including all 1976 high-quality B.1.1.7 genomes collected in the study period, we constructed a time-scaled phylogeny, which was coupled with detailed travel history and register data to outline the introduction and onward transmission of B.1.1.7 in Denmark. Results In a period with unchanged restrictions, we estimated an increased B.1.1.7 transmissibility of 58% (95% CI: [56%, 60%]) relative to other lineages. Epidemiological and phylogenetic analyses revealed that 37% of B.1.1.7 cases were related to the initial introduction in November 2020. The relative number of cases directly linked to introductions varied between 10 and 50% throughout the study period. Conclusions Our findings corroborate early estimates of increased transmissibility of B.1.1.7. Both substantial early expansion when B.1.1.7 was still unmonitored and continuous foreign introductions contributed considerably to case numbers. Finally, our study highlights the benefit of balanced travel restrictions and self-isolation procedures coupled with comprehensive surveillance efforts, to sustain epidemic control in the face of emerging variants. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01045-7.
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Affiliation(s)
- Thomas Y Michaelsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Marc Bennedbæk
- Centre of Excellence for Health, Immunity and Infection (CHIP), Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Lasse E Christiansen
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Lyngby, Denmark
| | - Mia S F Jørgensen
- Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Camilla H Møller
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Emil A Sørensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Simon Knutsson
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Jakob Brandt
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Thomas B N Jensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Emilio F Collados
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Trine Sørensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Celine Petersen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Vang Le-Quy
- Unit for Research Data Services (CLAAUDIA), Aalborg University, Aalborg, Denmark
| | - Mantas Sereika
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Frederik T Hansen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten Rasmussen
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Søren M Karst
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Rasmus L Marvig
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Raphael N Sieber
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Robert Skov
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Rebecca Legarth
- Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Tyra G Krause
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Fomsgaard
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | | | - Mads Albertsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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29
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Yermanos A, Hong KL, Agrafiotis A, Han J, Nadeau S, Valenzuela C, Azizoglu A, Ehling R, Gao B, Spahr M, Neumeier D, Chang CH, Dounas A, Petrillo E, Nissen I, Burcklen E, Feldkamp M, Beisel C, Oxenius A, Savic M, Stadler T, Rudolf F, Reddy ST. DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2. BMC Genomics 2022; 23:289. [PMID: 35410128 PMCID: PMC8995413 DOI: 10.1186/s12864-022-08403-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The continued spread of SARS-CoV-2 and emergence of new variants with higher transmission rates and/or partial resistance to vaccines has further highlighted the need for large-scale testing and genomic surveillance. However, current diagnostic testing (e.g., PCR) and genomic surveillance methods (e.g., whole genome sequencing) are performed separately, thus limiting the detection and tracing of SARS-CoV-2 and emerging variants. RESULTS Here, we developed DeepSARS, a high-throughput platform for simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2 by the integration of molecular barcoding, targeted deep sequencing, and computational phylogenetics. DeepSARS enables highly sensitive viral detection, while also capturing genomic diversity and viral evolution. We show that DeepSARS can be rapidly adapted for identification of emerging variants, such as alpha, beta, gamma, and delta strains, and profile mutational changes at the population level. CONCLUSIONS DeepSARS sets the foundation for quantitative diagnostics that capture viral evolution and diversity. DeepSARS uses molecular barcodes (BCs) and multiplexed targeted deep sequencing (NGS) to enable simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2. Image was created using Biorender.com .
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Affiliation(s)
- Alexander Yermanos
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland. .,Botnar Research Centre for Child Health, Basel, Switzerland. .,Institute of Microbiology, ETH Zurich, Zurich, Switzerland. .,Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland.
| | - Kai-Lin Hong
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Botnar Research Centre for Child Health, Basel, Switzerland
| | - Andreas Agrafiotis
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Botnar Research Centre for Child Health, Basel, Switzerland.,Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Jiami Han
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Botnar Research Centre for Child Health, Basel, Switzerland
| | - Sarah Nadeau
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Cecilia Valenzuela
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Asli Azizoglu
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Roy Ehling
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Beichen Gao
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Michael Spahr
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Daniel Neumeier
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Ching-Hsiang Chang
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Andreas Dounas
- Institute for Biomedical Engineering, University and ETH Zurich, Zurich, Switzerland
| | - Ezequiel Petrillo
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Ciudad Universitaria, Buenos Aires, Argentina.,Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Ina Nissen
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Elodie Burcklen
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Mirjam Feldkamp
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Miodrag Savic
- Department of Health, Economics and Health Directorate Canton Basel-Landschaft, Liestal, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Fabian Rudolf
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland. .,Botnar Research Centre for Child Health, Basel, Switzerland.
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30
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Lin MJ, Rachleff VM, Xie H, Shrestha L, Lieberman NAP, Peddu V, Addetia A, Casto AM, Breit N, Mathias PC, Huang ML, Jerome KR, Greninger AL, Roychoudhury P. Host-pathogen dynamics in longitudinal clinical specimens from patients with COVID-19. Sci Rep 2022; 12:5856. [PMID: 35393464 PMCID: PMC8987511 DOI: 10.1038/s41598-022-09752-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/16/2022] [Indexed: 12/30/2022] Open
Abstract
Rapid dissemination of SARS-CoV-2 sequencing data to public repositories has enabled widespread study of viral genomes, but studies of longitudinal specimens from infected persons are relatively limited. Analysis of longitudinal specimens enables understanding of how host immune pressures drive viral evolution in vivo. Here we performed sequencing of 49 longitudinal SARS-CoV-2-positive samples from 20 patients in Washington State collected between March and September of 2020. Viral loads declined over time with an average increase in RT-QPCR cycle threshold of 0.87 per day. We found that there was negligible change in SARS-CoV-2 consensus sequences over time, but identified a number of nonsynonymous variants at low frequencies across the genome. We observed enrichment for a relatively small number of these variants, all of which are now seen in consensus genomes across the globe at low prevalence. In one patient, we saw rapid emergence of various low-level deletion variants at the N-terminal domain of the spike glycoprotein, some of which have previously been shown to be associated with reduced neutralization potency from sera. In a subset of samples that were sequenced using metagenomic methods, differential gene expression analysis showed a downregulation of cytoskeletal genes that was consistent with a loss of ciliated epithelium during infection and recovery. We also identified co-occurrence of bacterial species in samples from multiple hospitalized individuals. These results demonstrate that the intrahost genetic composition of SARS-CoV-2 is dynamic during the course of COVID-19, and highlight the need for continued surveillance and deep sequencing of minor variants.
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Affiliation(s)
- Michelle J Lin
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA
| | - Victoria M Rachleff
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Program in Molecular and Cellular Biology, University of Washington School of Medicine, Seattle, WA, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA
| | - Lasata Shrestha
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA
| | - Nicole A P Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA
| | - Vikas Peddu
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA
| | - Amin Addetia
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA
| | - Amanda M Casto
- Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, WA, USA
| | - Nathan Breit
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA
| | - Patrick C Mathias
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Keith R Jerome
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA. .,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA. .,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA. .,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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31
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Wang Y, Tang CY, Wan XF. Antigenic characterization of influenza and SARS-CoV-2 viruses. Anal Bioanal Chem 2022; 414:2841-2881. [PMID: 34905077 PMCID: PMC8669429 DOI: 10.1007/s00216-021-03806-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/21/2021] [Accepted: 11/24/2021] [Indexed: 12/24/2022]
Abstract
Antigenic characterization of emerging and re-emerging viruses is necessary for the prevention of and response to outbreaks, evaluation of infection mechanisms, understanding of virus evolution, and selection of strains for vaccine development. Primary analytic methods, including enzyme-linked immunosorbent/lectin assays, hemagglutination inhibition, neuraminidase inhibition, micro-neutralization assays, and antigenic cartography, have been widely used in the field of influenza research. These techniques have been improved upon over time for increased analytical capacity, and some have been mobilized for the rapid characterization of the SARS-CoV-2 virus as well as its variants, facilitating the development of highly effective vaccines within 1 year of the initially reported outbreak. While great strides have been made for evaluating the antigenic properties of these viruses, multiple challenges prevent efficient vaccine strain selection and accurate assessment. For influenza, these barriers include the requirement for a large virus quantity to perform the assays, more than what can typically be provided by the clinical samples alone, cell- or egg-adapted mutations that can cause antigenic mismatch between the vaccine strain and circulating viruses, and up to a 6-month duration of vaccine development after vaccine strain selection, which allows viruses to continue evolving with potential for antigenic drift and, thus, antigenic mismatch between the vaccine strain and the emerging epidemic strain. SARS-CoV-2 characterization has faced similar challenges with the additional barrier of the need for facilities with high biosafety levels due to its infectious nature. In this study, we review the primary analytic methods used for antigenic characterization of influenza and SARS-CoV-2 and discuss the barriers of these methods and current developments for addressing these challenges.
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Affiliation(s)
- Yang Wang
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Cynthia Y Tang
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Xiu-Feng Wan
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA.
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA.
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA.
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA.
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32
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Lubinski B, Frazier LE, Phan MV, Bugembe DL, Cunningham JL, Tang T, Daniel S, Cotten M, Jaimes JA, Whittaker GR. Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2021.06.30.450632. [PMID: 34230931 PMCID: PMC8259907 DOI: 10.1101/2021.06.30.450632] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The African continent like all other parts of the world with high infection/low vaccination rates can, and will, be a source of novel SARS-CoV-2 variants. The A.23 viral lineage, characterized by three spike mutations F157L, V367F and Q613H, was first identified in COVID-19 cases from a Ugandan prison in July 2020, and then was identified in the general population with additional spike mutations (R102I, L141F, E484K and P681R) to comprise lineage A.23.1 by September 2020, with this virus being designated a variant of interest (VOI) in Africa and with subsequent spread to 26 other countries. The P681R spike substitution of the A.23.1 VOI is of note as it increases the number of basic residues in the sub-optimal SARS-CoV-2 spike protein furin cleavage site; as such, this substitution may affect viral replication, transmissibility or pathogenic properties. The same P681R substitution has also appeared in B.1.617 variants, including B.1.617.2 (Delta). Here, we performed assays using fluorogenic peptides mimicking the S1/S2 sequence from A.23.1 and B.1.617.2 and observed significantly increased cleavability with furin, compared to sequences derived from the original Wuhan-Hu1 S1/S2. We performed functional infectivity assays using pseudotyped MLV particles harboring SARS-CoV-2 spike proteins and observed an increase in transduction for A.23.1-pseudotyped particles compared to Wuhan-Hu-1 in Vero-TMPRSS2 and Calu-3 cells (with a presumed early entry pathway), although lowered infection in Vero E6 cells (with a presumed late entry pathway). However, these changes in infectivity were not reproduced in the original Wuhan-Hu-1 spike bearing only the P681R substitution. Our findings suggest that while A.23.1 has increased furin-mediated cleavage linked to the P681R substitution, which may affect viral infection and transmissibility, this substitution alone is not sufficient and needs to occur on the background of other spike protein changes to enable its full functional consequences.
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Affiliation(s)
- Bailey Lubinski
- Graduate Program in Biological & Biomedical Sciences, Cornell University, Ithaca, NY, 14853, USA
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Laura E. Frazier
- Graduate Program in Biological & Biomedical Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - My V.T. Phan
- MRC/UVRI & London School of Hygiene and Tropical Medicine – Uganda Research Unit, Entebbe, Uganda
| | - Daniel L. Bugembe
- MRC/UVRI & London School of Hygiene and Tropical Medicine – Uganda Research Unit, Entebbe, Uganda
| | - Jessie L. Cunningham
- Graduate Program in Biological & Biomedical Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Tiffany Tang
- Robert Frederick Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Susan Daniel
- Robert Frederick Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Matthew Cotten
- MRC/UVRI & London School of Hygiene and Tropical Medicine – Uganda Research Unit, Entebbe, Uganda
- MRC Centre of Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Javier A. Jaimes
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Gary R. Whittaker
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Master of Public Health Program, Cornell University, Ithaca, NY, 14853, USA
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33
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Greaney AJ, Starr TN, Eguia RT, Loes AN, Khan K, Karim F, Cele S, Bowen JE, Logue JK, Corti D, Veesler D, Chu HY, Sigal A, Bloom JD. A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy. PLoS Pathog 2022; 18:e1010248. [PMID: 35134084 PMCID: PMC8856557 DOI: 10.1371/journal.ppat.1010248] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/18/2022] [Accepted: 01/06/2022] [Indexed: 12/22/2022] Open
Abstract
Many SARS-CoV-2 variants have mutations at key sites targeted by antibodies. However, it is unknown if antibodies elicited by infection with these variants target the same or different regions of the viral spike as antibodies elicited by earlier viral isolates. Here we compare the specificities of polyclonal antibodies produced by humans infected with early 2020 isolates versus the B.1.351 variant of concern (also known as Beta or 20H/501Y.V2), which contains mutations in multiple key spike epitopes. The serum neutralizing activity of antibodies elicited by infection with both early 2020 viruses and B.1.351 is heavily focused on the spike receptor-binding domain (RBD). However, within the RBD, B.1.351-elicited antibodies are more focused on the "class 3" epitope spanning sites 443 to 452, and neutralization by these antibodies is notably less affected by mutations at residue 484. Our results show that SARS-CoV-2 variants can elicit polyclonal antibodies with different immunodominance hierarchies.
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Affiliation(s)
- Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, Washington, United States of America
| | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Rachel T. Eguia
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Andrea N. Loes
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Khadija Khan
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
| | - Farina Karim
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
| | - Sandile Cele
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Jennifer K. Logue
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Davide Corti
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - David Veesler
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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34
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Mendiola-Pastrana IR, López-Ortiz E, Río de la Loza-Zamora JG, González J, Gómez-García A, López-Ortiz G. SARS-CoV-2 Variants and Clinical Outcomes: A Systematic Review. Life (Basel) 2022; 12:life12020170. [PMID: 35207458 PMCID: PMC8879159 DOI: 10.3390/life12020170] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/19/2022] Open
Abstract
Background: From the start of the COVID-19 pandemic, new SARS-CoV-2 variants have emerged that potentially affect transmissibility, severity, and immune evasion in infected individuals. In the present systematic review, the impact of different SARS-CoV-2 variants on clinical outcomes is analyzed. Methods: A systematic review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020. Two databases (PubMed and ScienceDirect) were searched for original articles published from 1 January 2020 to 23 November 2021. The articles that met the selection criteria were appraised according to the Newcastle–Ottawa Quality Assessment Scale. Results: Thirty-three articles were included, involving a total of 253,209 patients and 188,944 partial or complete SARS-CoV-2 sequences. The most reported SARS-CoV-2 variants showed changes in the spike protein, N protein, RdRp and NSP3. In 28 scenarios, SARS-CoV-2 variants were found to be associated with a mild to severe or even fatal clinical outcome, 15 articles reported such association to be statistically significant. Adjustments in eight of them were made for age, sex and other covariates. Conclusions: SARS-CoV-2 variants can potentially have an impact on clinical outcomes; future studies focused on this topic should consider several covariates that influence the clinical course of the disease.
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Affiliation(s)
- Indira R. Mendiola-Pastrana
- Subdivisión de Medicina Familiar, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico; (I.R.M.-P.); (E.L.-O.); (J.G.R.d.l.L.-Z.)
| | - Eduardo López-Ortiz
- Subdivisión de Medicina Familiar, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico; (I.R.M.-P.); (E.L.-O.); (J.G.R.d.l.L.-Z.)
| | - José G. Río de la Loza-Zamora
- Subdivisión de Medicina Familiar, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico; (I.R.M.-P.); (E.L.-O.); (J.G.R.d.l.L.-Z.)
| | - James González
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico;
| | - Anel Gómez-García
- Centro de Investigación Biomédica de Michoacán, Instituto Mexicano del Seguro Social, Morelia 58351, Mexico;
| | - Geovani López-Ortiz
- Subdivisión de Medicina Familiar, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico; (I.R.M.-P.); (E.L.-O.); (J.G.R.d.l.L.-Z.)
- Correspondence:
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Fass E, Zizelski Valenci G, Rubinstein M, Freidlin PJ, Rosencwaig S, Kutikov I, Werner R, Ben-Tovim N, Bucris E, Erster O, Zuckerman NS, Mor O, Mendelson E, Dveyrin Z, Rorman E, Nissan I. HiSpike Method for High-Throughput Cost Effective Sequencing of the SARS-CoV-2 Spike Gene. Front Med (Lausanne) 2022; 8:798130. [PMID: 35087848 PMCID: PMC8787038 DOI: 10.3389/fmed.2021.798130] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/13/2021] [Indexed: 11/15/2022] Open
Abstract
The changing nature of the SARS-CoV-2 pandemic poses unprecedented challenges to the world's health systems. Emerging spike gene variants jeopardize global efforts to produce immunity and reduce morbidity and mortality. These challenges require effective real-time genomic surveillance solutions that the medical community can quickly adopt. The SARS-CoV-2 spike protein mediates host receptor recognition and entry into the cell and is susceptible to generation of variants with increased transmissibility and pathogenicity. The spike protein is the primary target of neutralizing antibodies in COVID-19 patients and the most common antigen for induction of effective vaccine immunity. Tight monitoring of spike protein gene variants is key to mitigating COVID-19 spread and generation of vaccine escape mutants. Currently, SARS-CoV-2 sequencing methods are labor intensive and expensive. When sequence demands are high sequencing resources are quickly exhausted. Consequently, most SARS-CoV-2 strains are sequenced in only a few developed countries and rarely in developing regions. This poses the risk that undetected, dangerous variants will emerge. In this work, we present HiSpike, a method for high-throughput cost effective targeted next generation sequencing of the spike gene. This simple three-step method can be completed in < 30 h, can sequence 10-fold more samples compared to conventional methods and at a fraction of their cost. HiSpike has been validated in Israel, and has identified multiple spike variants from real-time field samples including Alpha, Beta, Delta and the emerging Omicron variants. HiSpike provides affordable sequencing options to help laboratories conserve resources for widespread high-throughput, near real-time monitoring of spike gene variants.
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Affiliation(s)
- Ephraim Fass
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Gal Zizelski Valenci
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Mor Rubinstein
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Paul J. Freidlin
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Shira Rosencwaig
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Inna Kutikov
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Robert Werner
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Nofar Ben-Tovim
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Efrat Bucris
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Oran Erster
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Neta S. Zuckerman
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ella Mendelson
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zeev Dveyrin
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Efrat Rorman
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Israel Nissan
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
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Valesano AL, Fitzsimmons WJ, Blair CN, Woods RJ, Gilbert J, Rudnik D, Mortenson L, Friedrich TC, O’Connor DH, MacCannell DR, Petrie JG, Martin ET, Lauring AS. SARS-CoV-2 Genomic Surveillance Reveals Little Spread From a Large University Campus to the Surrounding Community. Open Forum Infect Dis 2021; 8:ofab518. [PMID: 34805437 PMCID: PMC8600169 DOI: 10.1093/ofid/ofab518] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 10/07/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) has had high incidence rates at institutions of higher education (IHE) in the United States, but the transmission dynamics in these settings are poorly understood. It remains unclear to what extent IHE-associated outbreaks have contributed to transmission in nearby communities. METHODS We implemented high-density prospective genomic surveillance to investigate these dynamics at the University of Michigan and the surrounding community during the Fall 2020 semester (August 16-November 24). We sequenced complete severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from 1659 individuals, including 468 students, representing 20% of cases in students and 25% of total cases in Washtenaw County over the study interval. RESULTS Phylogenetic analysis identified >200 introductions into the student population, most of which were not related to other student cases. There were 2 prolonged student transmission clusters, of 115 and 73 individuals, that spanned multiple on-campus residences. Remarkably, <5% of nonstudent genomes were descended from student clusters, and viral descendants of student cases were rare during a subsequent wave of infections in the community. CONCLUSIONS The largest outbreaks among students at the University of Michigan did not significantly contribute to the rise in community cases in Fall 2020. These results provide valuable insights into SARS-CoV-2 transmission dynamics at the regional level.
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Affiliation(s)
- Andrew L Valesano
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - William J Fitzsimmons
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Christopher N Blair
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Robert J Woods
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Julie Gilbert
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Dawn Rudnik
- University Health Service, University of Michigan, Ann Arbor, Michigan, USA
| | - Lindsey Mortenson
- University Health Service, University of Michigan, Ann Arbor, Michigan, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David H O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Joshua G Petrie
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Emily T Martin
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Adam S Lauring
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
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Greaney AJ, Starr TN, Eguia RT, Loes AN, Khan K, Karim F, Cele S, Bowen JE, Logue JK, Corti D, Veesler D, Chu HY, Sigal A, Bloom JD. A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.10.12.464114. [PMID: 34671768 PMCID: PMC8528074 DOI: 10.1101/2021.10.12.464114] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Many SARS-CoV-2 variants have mutations at key sites targeted by antibodies. However, it is unknown if antibodies elicited by infection with these variants target the same or different regions of the viral spike as antibodies elicited by earlier viral isolates. Here we compare the specificities of polyclonal antibodies produced by humans infected with early 2020 isolates versus the B.1.351 variant of concern (also known as Beta or 20H/501Y.V2), which contains mutations in multiple key spike epitopes. The serum neutralizing activity of antibodies elicited by infection with both early 2020 viruses and B.1.351 is heavily focused on the spike receptor-binding domain (RBD). However, within the RBD, B.1.351-elicited antibodies are more focused on the "class 3" epitope spanning sites 443 to 452, and neutralization by these antibodies is notably less affected by mutations at residue 484. Our results show that SARS-CoV-2 variants can elicit polyclonal antibodies with different immunodominance hierarchies.
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Affiliation(s)
- Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington; Seattle, WA 98195, USA
| | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
| | - Rachel T. Eguia
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
| | - Andrea N. Loes
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
| | - Khadija Khan
- Africa Health Research Institute, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban 4001, South Africa
| | - Farina Karim
- Africa Health Research Institute, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban 4001, South Africa
| | - Sandile Cele
- Africa Health Research Institute, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban 4001, South Africa
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jennifer K. Logue
- Division of Allergy and Infectious Diseases, University of Washington; Seattle, WA 98195, USA
| | - Davide Corti
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - David Veesler
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, University of Washington; Seattle, WA 98195, USA
| | - Alex Sigal
- Africa Health Research Institute, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban 4001, South Africa
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center; Seattle, WA 98109, USA
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
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Justo Arevalo S, Zapata Sifuentes D, J Huallpa C, Landa Bianchi G, Castillo Chávez A, Garavito-Salini Casas R, Uribe Calampa CS, Uceda-Campos G, Pineda Chavarría R. Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures. Sci Rep 2021; 11:17755. [PMID: 34493762 PMCID: PMC8423746 DOI: 10.1038/s41598-021-97267-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 08/24/2021] [Indexed: 12/19/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This disease has spread globally, causing more than 161.5 million cases and 3.3 million deaths to date. Surveillance and monitoring of new mutations in the virus' genome are crucial to our understanding of the adaptation of SARS-CoV-2. Moreover, how the temporal dynamics of these mutations is influenced by control measures and non-pharmaceutical interventions (NPIs) is poorly understood. Using 1,058,020 SARS-CoV-2 from sequenced COVID-19 cases from 98 countries (totaling 714 country-month combinations), we perform a normalization by COVID-19 cases to calculate the relative frequency of SARS-CoV-2 mutations and explore their dynamics over time. We found 115 mutations estimated to be present in more than 3% of global COVID-19 cases and determined three types of mutation dynamics: high-frequency, medium-frequency, and low-frequency. Classification of mutations based on temporal dynamics enable us to examine viral adaptation and evaluate the effects of implemented control measures in virus evolution during the pandemic. We showed that medium-frequency mutations are characterized by high prevalence in specific regions and/or in constant competition with other mutations in several regions. Finally, taking N501Y mutation as representative of high-frequency mutations, we showed that level of control measure stringency negatively correlates with the effective reproduction number of SARS-CoV-2 with high-frequency or not-high-frequency and both follows similar trends in different levels of stringency.
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Affiliation(s)
- Santiago Justo Arevalo
- Facultad de Ciencias Biológicas, Universidad Ricardo Palma, Lima, Peru.
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil.
| | | | - César J Huallpa
- Facultad de Ciencias, Universidad Nacional Agraria la Molina, Lima, Peru
| | | | | | | | | | - Guillermo Uceda-Campos
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
- Facultad de Ciencias Biológicas, Universidad Nacional Pedro Ruiz Gallo, Lambayeque, Peru
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Affiliation(s)
- Dana C. Crawford
- Departments of Population and Quantitative Health Sciences and Genetics and Genome Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Scott M. Williams
- Departments of Population and Quantitative Health Sciences and Genetics and Genome Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
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40
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Tordoff DM, Greninger AL, Roychoudhury P, Shrestha L, Xie H, Jerome KR, Breit N, Huang ML, Famulare M, Herbeck JT. Phylogenetic estimates of SARS-CoV-2 introductions into Washington State. LANCET REGIONAL HEALTH. AMERICAS 2021; 1:100018. [PMID: 35013735 PMCID: PMC8733893 DOI: 10.1016/j.lana.2021.100018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/24/2021] [Accepted: 06/24/2021] [Indexed: 02/03/2023]
Abstract
BACKGROUND The first confirmed case of SARS-CoV-2 in North America was identified in Washington state on January 21, 2020. We aimed to quantify the number and temporal trends of out-of-state introductions of SARS-CoV-2 into Washington. METHODS We conducted a molecular epidemiologic analysis of 11,422 publicly available whole genome SARS-CoV-2 sequences from GISAID sampled between December 2019 and September 2020. We used maximum parsimony ancestral state reconstruction methods on time-calibrated phylogenies to enumerate introductions/exports, their likely geographic source (US, non-US, and between eastern and western Washington), and estimated date of introduction. To incorporate phylogenetic uncertainty into our estimates, we conducted 5,000 replicate analyses by generating 25 random time-stratified samples of non-Washington reference sequences, 20 random polytomy resolutions, and 10 random resolutions of the reconstructed ancestral state. FINDINGS We estimated a minimum 287 introductions (range 244-320) into Washington and 204 exported lineages (range 188-227) of SARS-CoV-2 out of Washington. Introductions began in mid-January and peaked on March 29, 2020. Lineages with the Spike D614G variant accounted for the majority (88%) of introductions. Overall, 61% (range 55-65%) of introductions into Washington likely originated from a source elsewhere within the US, while the remaining 39% (range 35-45%) likely originated from outside of the US. Intra-state transmission accounted for 65% and 28% of introductions into eastern and western Washington, respectively. INTERPRETATION The SARS-CoV-2 epidemic in Washington was continually seeded by a large number of introductions. Our findings highlight the importance of genomic surveillance to monitor for emerging variants due to high levels of inter- and intra-state transmission of SARS-CoV-2. FUNDING SOURCE None.
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Affiliation(s)
- Diana M. Tordoff
- University of Washington, Department of Epidemiology, Seattle, WA, USA,Institute for Disease Modeling, Seattle, WA, USA,Corresponding Author. Diana M. Tordoff, MPH. University of Washington, Department of Epidemiology, UW Box # 351619, Seattle, WA 98195
| | - Alexander L. Greninger
- University of Washington, Department of Laboratory Medicine & Pathology, Seattle, WA, USA
| | - Pavitra Roychoudhury
- University of Washington, Department of Laboratory Medicine & Pathology, Seattle, WA, USA
| | - Lasata Shrestha
- University of Washington, Department of Laboratory Medicine & Pathology, Seattle, WA, USA
| | - Hong Xie
- University of Washington, Department of Laboratory Medicine & Pathology, Seattle, WA, USA
| | - Keith R. Jerome
- University of Washington, Department of Laboratory Medicine & Pathology, Seattle, WA, USA,Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Nathan Breit
- University of Washington, Department of Laboratory Medicine & Pathology, Seattle, WA, USA
| | - Meei-Li Huang
- University of Washington, Department of Laboratory Medicine & Pathology, Seattle, WA, USA
| | | | - Joshua T. Herbeck
- Institute for Disease Modeling, Seattle, WA, USA,International Clinical Research Center, University of Washington, Department of Global Health, Seattle, WA, USA
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The Transmission of SARS-CoV-2 Infection on the Ocular Surface and Prevention Strategies. Cells 2021; 10:cells10040796. [PMID: 33918318 PMCID: PMC8065845 DOI: 10.3390/cells10040796] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/27/2021] [Accepted: 03/31/2021] [Indexed: 01/08/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global health problem. Although the respiratory system is the main impaired organ, conjunctivitis is one of its common findings. However, it is not yet understood if SARS-CoV-2 can infect the eye and if the ocular surface can be a potential route of SARS-CoV-2 transmissions. Our review focuses on the viral entry mechanisms to give a better understanding of the interaction between SARS-CoV-2 and the eye. We highlighted findings that give evidence for multiple potential receptors of SARS-CoV-2 on the ocular surface. Additionally, we focused on data concerning the detection of viral RNA and its spike protein in the various ocular tissues from patients. However, the expression level seemed to be relatively low compared to the respiratory tissues as a result of a unique environment surrounding the ocular surface and the innate immune response of SARS-CoV-2. Nevertheless, our review suggests the ocular surface as a potential route for SARS-CoV-2 transmission, and as a result of this study we strongly recommend the protection of the eyes for ophthalmologists and patients at risk.
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