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Judson SD, Dowdy DW. Modeling zoonotic and vector-borne viruses. Curr Opin Virol 2024; 67:101428. [PMID: 39047313 PMCID: PMC11292992 DOI: 10.1016/j.coviro.2024.101428] [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: 02/02/2024] [Accepted: 07/06/2024] [Indexed: 07/27/2024]
Abstract
The 2013-2016 Ebola virus disease epidemic and the coronavirus disease 2019 pandemic galvanized tremendous growth in models for emerging zoonotic and vector-borne viruses. Therefore, we have reviewed the main goals and methods of models to guide scientists and decision-makers. The elements of models for emerging viruses vary across spectrums: from understanding the past to forecasting the future, using data across space and time, and using statistical versus mechanistic methods. Hybrid/ensemble models and artificial intelligence offer new opportunities for modeling. Despite this progress, challenges remain in translating models into actionable decisions, particularly in areas at highest risk for viral disease outbreaks. To address this issue, we must identify gaps in models for specific viruses, strengthen validation, and involve policymakers in model development.
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Affiliation(s)
- Seth D Judson
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
| | - David W Dowdy
- Division of Infectious Disease Epidemiology, Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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2
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Bonetti Franceschi V, Volz E. Phylogenetic signatures reveal multilevel selection and fitness costs in SARS-CoV-2. Wellcome Open Res 2024; 9:85. [PMID: 39132669 PMCID: PMC11316176 DOI: 10.12688/wellcomeopenres.20704.2] [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] [Accepted: 07/16/2024] [Indexed: 08/13/2024] Open
Abstract
Background Large-scale sequencing of SARS-CoV-2 has enabled the study of viral evolution during the COVID-19 pandemic. Some viral mutations may be advantageous to viral replication within hosts but detrimental to transmission, thus carrying a transient fitness advantage. By affecting the number of descendants, persistence times and growth rates of associated clades, these mutations generate localised imbalance in phylogenies. Quantifying these features in closely-related clades with and without recurring mutations can elucidate the tradeoffs between within-host replication and between-host transmission. Methods We implemented a novel phylogenetic clustering algorithm ( mlscluster, https://github.com/mrc-ide/mlscluster) to systematically explore time-scaled phylogenies for mutations under transient/multilevel selection. We applied this method to a SARS-CoV-2 time-calibrated phylogeny with >1.2 million sequences from England, and characterised these recurrent mutations that may influence transmission fitness across PANGO-lineages and genomic regions using Poisson regressions and summary statistics. Results We found no major differences across two epidemic stages (before and after Omicron), PANGO-lineages, and genomic regions. However, spike, nucleocapsid, and ORF3a were proportionally more enriched for transmission fitness polymorphisms (TFP)-homoplasies than other proteins. We provide a catalog of SARS-CoV-2 sites under multilevel selection, which can guide experimental investigations within and beyond the spike protein. Conclusions This study provides empirical evidence for the existence of important tradeoffs between within-host replication and between-host transmission shaping the fitness landscape of SARS-CoV-2. This method may be used as a fast and scalable means to shortlist large sequence databases for sites under putative multilevel selection which may warrant subsequent confirmatory analyses and experimental confirmation.
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Affiliation(s)
- Vinicius Bonetti Franceschi
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, England, W2 1PG, UK
| | - Erik Volz
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, England, W2 1PG, UK
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3
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Lopes R, Pham K, Klaassen F, Chitwood MH, Hahn AM, Redmond S, Swartwood NA, Salomon JA, Menzies NA, Cohen T, Grubaugh ND. Combining genomic data and infection estimates to characterize the complex dynamics of SARS-CoV-2 Omicron variants in the US. Cell Rep 2024; 43:114451. [PMID: 38970788 DOI: 10.1016/j.celrep.2024.114451] [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: 01/18/2024] [Revised: 05/03/2024] [Accepted: 06/20/2024] [Indexed: 07/08/2024] Open
Abstract
Omicron surged as a variant of concern in late 2021. Several distinct Omicron variants appeared and overtook each other. We combined variant frequencies and infection estimates from a nowcasting model for each US state to estimate variant-specific infections, attack rates, and effective reproduction numbers (Rt). BA.1 rapidly emerged, and we estimate that it infected 47.7% of the US population before it was replaced by BA.2. We estimate that BA.5 infected 35.7% of the US population, persisting in circulation for nearly 6 months. Other variants-BA.2, BA.4, and XBB-together infected 30.7% of the US population. We found a positive correlation between the state-level BA.1 attack rate and social vulnerability and a negative correlation between the BA.1 and BA.2 attack rates. Our findings illustrate the complex interplay between viral evolution, population susceptibility, and social factors during the Omicron emergence in the US.
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Affiliation(s)
- Rafael Lopes
- Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA.
| | - Kien Pham
- Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA
| | - Fayette Klaassen
- Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Melanie H Chitwood
- Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA
| | - Seth Redmond
- Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA
| | - Nicole A Swartwood
- Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Joshua A Salomon
- Department of Health Policy, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicolas A Menzies
- Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA.
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
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4
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Wu Y, Lai SK, En-Zuo Chan C, Tan BH, Sugrue RJ. Evidence that the SARS-CoV-2 S protein undergoes a conformational change at the Golgi complex that leads to the formation of virus neutralising antibody binding epitopes in the S1 protein subunit. Virology 2024; 598:110187. [PMID: 39094503 DOI: 10.1016/j.virol.2024.110187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 07/11/2024] [Accepted: 07/20/2024] [Indexed: 08/04/2024]
Abstract
Recombinant SARS-CoV-2 S protein expression was examined in Vero cells by imaging using the human monoclonal antibody panel (PD4, PD5, sc23, and sc29). The PD4 and sc29 antibodies recognised conformational specific epitopes in the S2 protein subunit at the Endoplasmic reticulum and Golgi complex. While PD5 and sc23 detected conformationally specific epitopes in the S1 protein subunit at the Golgi complex, only PD5 recognised the receptor binding domain (RBD). A comparison of the staining patterns of PD5 with non-conformationally specific antibodies that recognises the S1 subunit and RBD suggested the PD5 recognised a conformational structure within the S1 protein subunit. Our data suggests the antibody binding epitopes recognised by the human monoclonal antibodies formed at different locations in the secretory pathway during S protein transport, but a conformational change in the S1 protein subunit at the Golgi complex formed antibody binding epitopes that are recognised by virus neutralising antibodies.
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Affiliation(s)
- Yanjun Wu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Soak Kuan Lai
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Conrad En-Zuo Chan
- Infectious Disease Research Laboratory, National Centre for Infectious Diseases, 16 Jalan Tan Tock Seng, Singapore, 308442
| | - Boon Huan Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Richard J Sugrue
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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Kendall M, Ferretti L, Wymant C, Tsallis D, Petrie J, Di Francia A, Di Lauro F, Abeler-Dörner L, Manley H, Panovska-Griffiths J, Ledda A, Didelot X, Fraser C. Drivers of epidemic dynamics in real time from daily digital COVID-19 measurements. Science 2024:eadm8103. [PMID: 38991048 DOI: 10.1126/science.adm8103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 06/19/2024] [Indexed: 07/13/2024]
Abstract
Understanding the drivers of respiratory pathogen spread is challenging, particularly in a timely manner during an ongoing epidemic. Here we present insights obtained using daily data from the NHS COVID-19 app for England and Wales and shared with health authorities in almost real time. Our indicator of the reproduction number R(t) was available days earlier than other estimates, with a novel capability to decompose R(t) into contact rates and probabilities of infection. When Omicron arrived, the main epidemic driver switched from contacts to transmissibility. We separate contacts and transmissions by day of exposure and setting, finding pronounced variability over days of the week and during Christmas holidays and events. As an example, during the Euro football tournament in 2021, days with England matches showed sharp spikes in exposures and transmissibility. Digital contact tracing technologies can help control epidemics not only by directly preventing transmissions but also by enabling rapid analysis at scale and with unprecedented resolution.
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Affiliation(s)
- Michelle Kendall
- Department of Statistics, University of Warwick, Coventry CV4 7AL, UK
| | - Luca Ferretti
- Pandemic Sciences Institute, Nuffield Department for Medicine, University of Oxford, Old Road Campus, Oxford OX3 7DQ, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford OX3 7LF, UK
| | - Chris Wymant
- Pandemic Sciences Institute, Nuffield Department for Medicine, University of Oxford, Old Road Campus, Oxford OX3 7DQ, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford OX3 7LF, UK
| | - Daphne Tsallis
- Zühlke Engineering Ltd., 80 Great Eastern Street, London EC2A 3JL, UK
| | - James Petrie
- Pandemic Sciences Institute, Nuffield Department for Medicine, University of Oxford, Old Road Campus, Oxford OX3 7DQ, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford OX3 7LF, UK
| | - Andrea Di Francia
- UK Health Security Agency, Nobel House, 17 Smith Square, London SW1P 3JR, UK
| | - Francesco Di Lauro
- Pandemic Sciences Institute, Nuffield Department for Medicine, University of Oxford, Old Road Campus, Oxford OX3 7DQ, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford OX3 7LF, UK
| | - Lucie Abeler-Dörner
- Pandemic Sciences Institute, Nuffield Department for Medicine, University of Oxford, Old Road Campus, Oxford OX3 7DQ, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford OX3 7LF, UK
| | - Harrison Manley
- UK Health Security Agency, Nobel House, 17 Smith Square, London SW1P 3JR, UK
| | - Jasmina Panovska-Griffiths
- Pandemic Sciences Institute, Nuffield Department for Medicine, University of Oxford, Old Road Campus, Oxford OX3 7DQ, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford OX3 7LF, UK
- UK Health Security Agency, Nobel House, 17 Smith Square, London SW1P 3JR, UK
| | - Alice Ledda
- UK Health Security Agency, Nobel House, 17 Smith Square, London SW1P 3JR, UK
| | - Xavier Didelot
- Department of Statistics, University of Warwick, Coventry CV4 7AL, UK
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Christophe Fraser
- Pandemic Sciences Institute, Nuffield Department for Medicine, University of Oxford, Old Road Campus, Oxford OX3 7DQ, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford OX3 7LF, UK
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6
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Donker T, Papathanassopoulos A, Ghosh H, Kociurzynski R, Felder M, Grundmann H, Reuter S. Estimation of SARS-CoV-2 fitness gains from genomic surveillance data without prior lineage classification. Proc Natl Acad Sci U S A 2024; 121:e2314262121. [PMID: 38861609 PMCID: PMC11194495 DOI: 10.1073/pnas.2314262121] [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: 08/18/2023] [Accepted: 05/01/2024] [Indexed: 06/13/2024] Open
Abstract
The emergence of SARS-CoV-2 variants with increased fitness has had a strong impact on the epidemiology of COVID-19, with the higher effective reproduction number of the viral variants leading to new epidemic waves. Tracking such variants and their genetic signatures, using data collected through genomic surveillance, is therefore crucial for forecasting likely surges in incidence. Current methods of estimating fitness advantages of variants rely on tracking the changing proportion of a particular lineage over time, but describing successful lineages in a rapidly evolving viral population is a difficult task. We propose a method of estimating fitness gains directly from nucleotide information generated by genomic surveillance, without a priori assigning isolates to lineages from phylogenies, based solely on the abundance of single nucleotide polymorphisms (SNPs). The method is based on mapping changes in the genetic population structure over time. Changes in the abundance of SNPs associated with periods of increasing fitness allow for the unbiased discovery of new variants, thereby obviating a deliberate lineage assignment and phylogenetic inference. We conclude that the method provides a fast and reliable way to estimate fitness advantages of variants without the need for a priori assigning isolates to lineages.
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Affiliation(s)
- Tjibbe Donker
- Institute for Infection Prevention and Control, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau79106, Germany
| | - Alexis Papathanassopoulos
- Institute for Infection Prevention and Control, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau79106, Germany
| | - Hiren Ghosh
- Institute for Infection Prevention and Control, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau79106, Germany
| | - Raisa Kociurzynski
- Institute for Infection Prevention and Control, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau79106, Germany
| | - Marius Felder
- Institute for Infection Prevention and Control, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau79106, Germany
| | - Hajo Grundmann
- Institute for Infection Prevention and Control, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau79106, Germany
| | - Sandra Reuter
- Institute for Infection Prevention and Control, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau79106, Germany
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Gupta S, Sharma R, Williams AE, Sanchez-Vargas I, Rose NH, Zhang C, Crosbie-Villaseca A, Zhu Z, Dayama G, Gloria-Soria A, Brackney DE, Manning J, Wheeler SS, Caranci A, Reyes T, Sylla M, Badolo A, Akorli J, Aribodor OB, Ayala D, Liu WL, Chen CH, Vasquez C, Acosta CG, Ponlawat A, Magalhaes T, Carter B, Wesson D, Surin D, Younger MA, Costa-da-Silva AL, DeGennaro M, Bergman A, Lambrechts L, McBride CS, Olson KE, Calvo E, Lau NC. Global genomics of Aedes aegypti unveils widespread and novel infectious viruses capable of triggering a small RNA response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597482. [PMID: 38895463 PMCID: PMC11185646 DOI: 10.1101/2024.06.06.597482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The mosquito Aedes aegypti is a prominent vector for arboviruses, but the breadth of mosquito viruses that infects this specie is not fully understood. In the broadest global survey to date of over 200 Ae. aegypti small RNA samples, we detected viral small interfering RNAs (siRNAs) and Piwi interacting RNAs (piRNAs) arising from mosquito viruses. We confirmed that most academic laboratory colonies of Ae. aegypti lack persisting viruses, yet two commercial strains were infected by a novel tombus-like virus. Ae. aegypti from North to South American locations were also teeming with multiple insect viruses, with Anphevirus and a bunyavirus displaying geographical boundaries from the viral small RNA patterns. Asian Ae. aegypti small RNA patterns indicate infections by similar mosquito viruses from the Americas and reveal the first wild example of dengue virus infection generating viral small RNAs. African Ae. aegypti also contained various viral small RNAs including novel viruses only found in these African substrains. Intriguingly, viral long RNA patterns can differ from small RNA patterns, indicative of viral transcripts evading the mosquitoes' RNA interference (RNAi) machinery. To determine whether the viruses we discovered via small RNA sequencing were replicating and transmissible, we infected C6/36 and Aag2 cells with Ae. aegypti homogenates. Through blind passaging, we generated cell lines stably infected by these mosquito viruses which then generated abundant viral siRNAs and piRNAs that resemble the native mosquito viral small RNA patterns. This mosquito small RNA genomics approach augments surveillance approaches for emerging infectious diseases.
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Chinazzi M, Davis JT, Y Piontti AP, Mu K, Gozzi N, Ajelli M, Perra N, Vespignani A. A multiscale modeling framework for Scenario Modeling: Characterizing the heterogeneity of the COVID-19 epidemic in the US. Epidemics 2024; 47:100757. [PMID: 38493708 DOI: 10.1016/j.epidem.2024.100757] [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: 08/15/2023] [Revised: 01/22/2024] [Accepted: 02/26/2024] [Indexed: 03/19/2024] Open
Abstract
The Scenario Modeling Hub (SMH) initiative provides projections of potential epidemic scenarios in the United States (US) by using a multi-model approach. Our contribution to the SMH is generated by a multiscale model that combines the global epidemic metapopulation modeling approach (GLEAM) with a local epidemic and mobility model of the US (LEAM-US), first introduced here. The LEAM-US model consists of 3142 subpopulations each representing a single county across the 50 US states and the District of Columbia, enabling us to project state and national trajectories of COVID-19 cases, hospitalizations, and deaths under different epidemic scenarios. The model is age-structured, and multi-strain. It integrates data on vaccine administration, human mobility, and non-pharmaceutical interventions. The model contributed to all 17 rounds of the SMH, and allows for the mechanistic characterization of the spatio-temporal heterogeneities observed during the COVID-19 pandemic. Here we describe the mathematical and computational structure of our model, and present the results concerning the emergence of the SARS-CoV-2 Alpha variant (lineage designation B.1.1.7) as a case study. Our findings show considerable spatial and temporal heterogeneity in the introduction and diffusion of the Alpha variant, both at the level of individual states and combined statistical areas, as it competes against the ancestral lineage. We discuss the key factors driving the time required for the Alpha variant to rise to dominance within a population, and quantify the impact that the emergence of the Alpha variant had on the effective reproduction number at the state level. Overall, we show that our multiscale modeling approach is able to capture the complexity and heterogeneity of the COVID-19 pandemic response in the US.
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Affiliation(s)
- Matteo Chinazzi
- The Roux Institute, Northeastern University, Portland, ME, USA; Laboratory for the Modeling of Biological and Socio-technical Systems, Network Science Institute, Northeastern University, Boston, MA, USA
| | - Jessica T Davis
- Laboratory for the Modeling of Biological and Socio-technical Systems, Network Science Institute, Northeastern University, Boston, MA, USA
| | - Ana Pastore Y Piontti
- Laboratory for the Modeling of Biological and Socio-technical Systems, Network Science Institute, Northeastern University, Boston, MA, USA
| | - Kunpeng Mu
- Laboratory for the Modeling of Biological and Socio-technical Systems, Network Science Institute, Northeastern University, Boston, MA, USA
| | - Nicolò Gozzi
- Institute for Scientific Interchange Foundation, Turin, Italy
| | - Marco Ajelli
- Laboratory for Computational Epidemiology and Public Health, Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | - Nicola Perra
- Laboratory for the Modeling of Biological and Socio-technical Systems, Network Science Institute, Northeastern University, Boston, MA, USA; School of Mathematical Sciences, Queen Mary University, London, UK
| | - Alessandro Vespignani
- Laboratory for the Modeling of Biological and Socio-technical Systems, Network Science Institute, Northeastern University, Boston, MA, USA; Institute for Scientific Interchange Foundation, Turin, Italy.
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9
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Drake KO, Boyd O, Franceschi VB, Colquhoun RM, Ellaby NAF, Volz EM. Phylogenomic early warning signals for SARS-CoV-2 epidemic waves. EBioMedicine 2024; 100:104939. [PMID: 38194742 PMCID: PMC10792554 DOI: 10.1016/j.ebiom.2023.104939] [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: 08/14/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND Epidemic waves of coronavirus disease 2019 (COVID-19) infections have often been associated with the emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. Rapid detection of growing genomic variants can therefore serve as a predictor of future waves, enabling timely implementation of countermeasures such as non-pharmaceutical interventions (social distancing), additional vaccination (booster campaigns), or healthcare capacity adjustments. The large amount of SARS-CoV-2 genomic sequence data produced during the pandemic has provided a unique opportunity to explore the utility of these data for generating early warning signals (EWS). METHODS We developed an analytical pipeline (Transmission Fitness Polymorphism Scanner - designated in an R package mrc-ide/tfpscanner) for systematically exploring all clades within a SARS-CoV-2 virus phylogeny to detect variants showing unusually high growth rates. We investigated the use of these cluster growth rates as the basis for a variety of statistical time series to use as leading indicators for the epidemic waves in the UK during the pandemic between August 2020 and March 2022. We also compared the performance of these phylogeny-derived leading indicators with a range of non-phylogeny-derived leading indicators. Our experiments simulated data generation and real-time analysis. FINDINGS Using phylogenomic analysis, we identified leading indicators that would have generated EWS ahead of significant increases in COVID-19 hospitalisations in the UK between August 2020 and March 2022. Our results also show that EWS lead time is sensitive to the threshold set for the number of false positive (FP) EWS. It is often possible to generate longer EWS lead times if more FP EWS are tolerated. On the basis of maximising lead time and minimising the number of FP EWS, the best performing leading indicators that we identified, amongst a set of 1.4 million, were the maximum logistic growth rate (LGR) amongst clusters of the dominant Pango lineage and the mean simple LGR across a broader set of clusters. In the case of the former, the time between the EWS and wave inflection points (a conservative measure of wave start dates) for the seven waves ranged between a 20-day lead time and a 7-day lag, with a mean lead time of 5.4 days. The maximum number of FP EWS generated prior to a true positive (TP) EWS was two and this only occurred for two of the seven waves in the period. The mean simple LGR amongst a broader set of clusters also performed well in terms of lead time but with slightly more FP EWS. INTERPRETATION As a result of the significant surveillance effort during the pandemic, early detection of SARS-CoV-2 variants of concern Alpha, Delta, and Omicron provided some of the first examples where timely detection and characterisation of pathogen variants has been used to tailor public health response. The success of our method in generating early warning signals based on phylogenomic analysis for SARS-CoV-2 in the UK may make it a worthwhile addition to existing surveillance strategies. In addition, the method may be translatable to other countries and/or regions, and to other pathogens with large-scale and rapid genomic surveillance. FUNDING This research was funded in whole, or in part, by the Wellcome Trust (220885_Z_20_Z). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. KOD, OB, VBF and EMV acknowledge funding from the MRC Centre for Global Infectious Disease Analysis (reference MR/X020258/1), jointly funded by the UK Medical Research Council (MRC) and the UK Foreign, Commonwealth & Development Office (FCDO), under the MRC/FCDO Concordat agreement and is also part of the EDCTP2 programme supported by the European Union. RMC acknowledges funding from the Wellcome Trust Collaborators Award (206298/Z/17/Z).
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Affiliation(s)
- Kieran O Drake
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom.
| | - Olivia Boyd
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Vinicius B Franceschi
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Rachel M Colquhoun
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Erik M Volz
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
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10
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Silva Souza M, Pires Farias J, Barros Luiz W, Birbrair A, Durães-Carvalho R, de Souza Ferreira LC, Amorim JH. Immune targets to stop future SARS-CoV-2 variants. Microbiol Spectr 2023; 11:e0289223. [PMID: 37966210 PMCID: PMC10714790 DOI: 10.1128/spectrum.02892-23] [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: 07/20/2023] [Accepted: 10/08/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE The emergence of SARS-CoV-2 had a major impact across the world. It is true that the collaboration of scientists from all over the world resulted in a rapid response against COVID-19, mainly with the development of vaccines against the disease. However, many viral genetic variants that threaten vaccines have emerged. Our study reveals highly conserved antigenic regions in the vaccines have emerged. Our study reveals highly conserved antigenic regions in the spike protein in all variants of concern (Alpha, Beta, Gamma, Delta, and Omicron) as well as in the wild-type virus. Such immune targets can be used to fight future SARS-CoV-2 variants.
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Affiliation(s)
- Milena Silva Souza
- Western Bahia Virology Institute, Center of Biological Sciences and Health, Federal University of Western Bahia, Barreiras, Bahia, Brazil
- Department of Biological Sciences, Laboratory of Applied Pathology and Genetics, State University of Santa Cruz, Ilhéus, Bahia, Brazil
| | - Jéssica Pires Farias
- Western Bahia Virology Institute, Center of Biological Sciences and Health, Federal University of Western Bahia, Barreiras, Bahia, Brazil
| | - Wilson Barros Luiz
- Department of Biological Sciences, Laboratory of Applied Pathology and Genetics, State University of Santa Cruz, Ilhéus, Bahia, Brazil
| | - Alexander Birbrair
- Department of Dermatology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Radiology, Columbia University Medical Center, New York, New York, USA
| | - Ricardo Durães-Carvalho
- Department of Microbiology, Immunology and Parasitology, São Paulo School of Medicine, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - Luís Carlos de Souza Ferreira
- Department of Microbiology, Vaccine Development Laboratory, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Jaime Henrique Amorim
- Western Bahia Virology Institute, Center of Biological Sciences and Health, Federal University of Western Bahia, Barreiras, Bahia, Brazil
- Department of Biological Sciences, Laboratory of Applied Pathology and Genetics, State University of Santa Cruz, Ilhéus, Bahia, Brazil
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Panteleev MA, Sveshnikova AN, Shakhidzhanov SS, Zamaraev AV, Ataullakhanov FI, Rumyantsev AG. The Ways of the Virus: Interactions of Platelets and Red Blood Cells with SARS-CoV-2, and Their Potential Pathophysiological Significance in COVID-19. Int J Mol Sci 2023; 24:17291. [PMID: 38139118 PMCID: PMC10743882 DOI: 10.3390/ijms242417291] [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: 11/15/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
The hematological effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are important in COVID-19 pathophysiology. However, the interactions of SARS-CoV-2 with platelets and red blood cells are still poorly understood. There are conflicting data regarding the mechanisms and significance of these interactions. The aim of this review is to put together available data and discuss hypotheses, the known and suspected effects of the virus on these blood cells, their pathophysiological and diagnostic significance, and the potential role of platelets and red blood cells in the virus's transport, propagation, and clearance by the immune system. We pay particular attention to the mutual activation of platelets, the immune system, the endothelium, and blood coagulation and how this changes with the evolution of SARS-CoV-2. There is now convincing evidence that platelets, along with platelet and erythroid precursors (but not mature erythrocytes), are frequently infected by SARS-CoV-2 and functionally changed. The mechanisms of infection of these cells and their role are not yet entirely clear. Still, the changes in platelets and red blood cells in COVID-19 are significantly associated with disease severity and are likely to have prognostic and pathophysiological significance in the development of thrombotic and pulmonary complications.
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Affiliation(s)
- Mikhail A. Panteleev
- Department of Medical Physics, Physics Faculty, Lomonosov Moscow State University, 1 Leninskie Gory, 119991 Moscow, Russia
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Ministry of Healthcare of Russian Federation, 1 Samory Mashela, 117198 Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, 30 Srednyaya Kalitnikovskaya Str., 109029 Moscow, Russia
| | - Anastasia N. Sveshnikova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Ministry of Healthcare of Russian Federation, 1 Samory Mashela, 117198 Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, 30 Srednyaya Kalitnikovskaya Str., 109029 Moscow, Russia
- Faculty of Fundamental Physics and Chemical Engineering, Lomonosov Moscow State University, 1 Leninskie Gory, 119991 Moscow, Russia
| | - Soslan S. Shakhidzhanov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Ministry of Healthcare of Russian Federation, 1 Samory Mashela, 117198 Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, 30 Srednyaya Kalitnikovskaya Str., 109029 Moscow, Russia
| | - Alexey V. Zamaraev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Ulitsa Vavilova, 119991 Moscow, Russia
- Faculty of Medicine, Lomonosov Moscow State University, 1 Leninskie Gory, 119991 Moscow, Russia
| | - Fazoil I. Ataullakhanov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Ministry of Healthcare of Russian Federation, 1 Samory Mashela, 117198 Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, 30 Srednyaya Kalitnikovskaya Str., 109029 Moscow, Russia
- Moscow Institute of Physics and Technology, National Research University, 9 Institutskiy Per., 141701 Dolgoprudny, Russia
- Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Aleksandr G. Rumyantsev
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Ministry of Healthcare of Russian Federation, 1 Samory Mashela, 117198 Moscow, Russia
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12
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Weber A, Översti S, Kühnert D. Reconstructing relative transmission rates in Bayesian phylodynamics: Two-fold transmission advantage of Omicron in Berlin, Germany during December 2021. Virus Evol 2023; 9:vead070. [PMID: 38107332 PMCID: PMC10725310 DOI: 10.1093/ve/vead070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/08/2023] [Accepted: 11/27/2023] [Indexed: 12/19/2023] Open
Abstract
Phylodynamic methods have lately played a key role in understanding the spread of infectious diseases. During the coronavirus disease (COVID-19) pandemic, large scale genomic surveillance has further increased the potential of dynamic inference from viral genomes. With the continual emergence of novel severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) variants, explicitly allowing transmission rate differences between simultaneously circulating variants in phylodynamic inference is crucial. In this study, we present and empirically validate an extension to the BEAST2 package birth-death skyline model (BDSKY), BDSKY[Formula: see text], which introduces a scaling factor for the transmission rate between independent, jointly inferred trees. In an extensive simulation study, we show that BDSKY[Formula: see text] robustly infers the relative transmission rates under different epidemic scenarios. Using publicly available genome data of SARS-CoV-2, we apply BDSKY[Formula: see text] to quantify the transmission advantage of the Omicron over the Delta variant in Berlin, Germany. We find the overall transmission rate of Omicron to be scaled by a factor of two with pronounced variation between the individual clusters of each variant. These results quantify the transmission advantage of Omicron over the previously circulating Delta variant, in a crucial period of pre-established non-pharmaceutical interventions. By inferring variant- as well as cluster-specific transmission rate scaling factors, we show the differences in transmission dynamics for each variant. This highlights the importance of incorporating lineage-specific transmission differences in phylodynamic inference.
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Affiliation(s)
- Ariane Weber
- Transmission, Infection, Diversification & Evolution Group (tide), Max Planck Institute of Geoanthropology, Kahlaische Strasse 10, Jena, Thuringia 07745, Germany
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Saxony 04103, Germany
| | | | - Denise Kühnert
- Transmission, Infection, Diversification & Evolution Group (tide), Max Planck Institute of Geoanthropology, Kahlaische Strasse 10, Jena, Thuringia 07745, Germany
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Saxony 04103, Germany
- Centre for Artificial Intelligence in Public Health Research, Robert Koch Institute, Ludwig-Witthöft-Straße 14, Wildau, Brandenburg 15745, Germany
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13
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Hu M, Wang X, Li B, Wang B, Zhao Y, Chai Z, Jin Y, Yue J, Ren H. Fitness evaluation of SARS-CoV-2 variants: A retrospective study. J Med Virol 2023; 95:e29123. [PMID: 37772646 DOI: 10.1002/jmv.29123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/30/2023] [Accepted: 09/14/2023] [Indexed: 09/30/2023]
Affiliation(s)
- Mingda Hu
- Laboratory of Advanced Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Xin Wang
- Laboratory of Advanced Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Beiping Li
- Laboratory of Advanced Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Boqian Wang
- Laboratory of Advanced Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Yunxiang Zhao
- Laboratory of Advanced Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Zili Chai
- Laboratory of Advanced Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Yuan Jin
- Laboratory of Advanced Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Junjie Yue
- Laboratory of Advanced Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Hongguang Ren
- Laboratory of Advanced Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
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14
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Quirk GE, Schoenle MV, Peyton KL, Uhrlaub JL, Lau B, Burgess JL, Ellingson K, Beitel S, Romine J, Lutrick K, Fowlkes A, Britton A, Tyner HL, Caban-Martinez AJ, Naleway A, Gaglani M, Yoon S, Edwards L, Olsho L, Dake M, LaFleur BJ, Nikolich JŽ, Sprissler R, Worobey M, Bhattacharya D. Determinants of de novo B cell responses to drifted epitopes in post-vaccination SARS-CoV-2 infections. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.12.23295384. [PMID: 37745498 PMCID: PMC10516057 DOI: 10.1101/2023.09.12.23295384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Vaccine-induced immunity may impact subsequent de novo responses to drifted epitopes in SARS-CoV-2 variants, but this has been difficult to quantify due to the challenges in recruiting unvaccinated control groups whose first exposure to SARS-CoV-2 is a primary infection. Through local, statewide, and national SARS-CoV-2 testing programs, we were able to recruit cohorts of individuals who had recovered from either primary or post-vaccination infections by either the Delta or Omicron BA.1 variants. Regardless of variant, we observed greater Spike-specific and neutralizing antibody responses in post-vaccination infections than in those who were infected without prior vaccination. Through analysis of variant-specific memory B cells as markers of de novo responses, we observed that Delta and Omicron BA.1 infections led to a marked shift in immunodominance in which some drifted epitopes elicited minimal responses, even in primary infections. Prior immunity through vaccination had a small negative impact on these de novo responses, but this did not correlate with cross-reactive memory B cells, arguing against competitive inhibition of naïve B cells. We conclude that dampened de novo B cell responses against drifted epitopes are mostly a function of altered immunodominance hierarchies that are apparent even in primary infections, with a more modest contribution from pre-existing immunity, perhaps due to accelerated antigen clearance.
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Affiliation(s)
- Grace E Quirk
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Marta V Schoenle
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Kameron L Peyton
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Jennifer L Uhrlaub
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Branden Lau
- University of Arizona Genomics Core and the Arizona Research Labs, University of Arizona Genetics Core, University of Arizona, Tucson, AZ, USA
| | - Jefferey L Burgess
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, Arizona, USA
| | - Katherine Ellingson
- Department of Epidemiology and Biostatistics, Zuckerman College of Public Health, University of Arizona, Tucson
| | - Shawn Beitel
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, Arizona, USA
| | - James Romine
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, Arizona, USA
| | - Karen Lutrick
- College of Medicine-Tucson, University of Arizona, Tucson, Arizona, USA
| | - Ashley Fowlkes
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA
| | - Amadea Britton
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA
| | - Harmony L Tyner
- St. Luke's Regional Health Care System, Duluth, Minnesota, USA
| | | | - Allison Naleway
- Kaiser Permanente Northwest Center for Health Research, Portland, Oregon, USA
| | - Manjusha Gaglani
- Baylor Scott & White Health and Texas A&M University College of Medicine, Temple, Texas, USA
| | - Sarang Yoon
- Rocky Mountain Center for Occupational and Environmental Health, Department of Family and Preventive Medicine, University of Utah Health, Salt Lake City, Utah, USA
| | | | | | - Michael Dake
- Office of the Senior Vice-President for Health Sciences, University of Arizona, Tucson, AZ, USA
| | | | - Janko Ž Nikolich
- BIO5 Institute, University of Arizona, Tucson, AZ, USA
- University of Arizona Center on Aging, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Ryan Sprissler
- University of Arizona Genomics Core and the Arizona Research Labs, University of Arizona Genetics Core, University of Arizona, Tucson, AZ, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
- BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - Deepta Bhattacharya
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, USA
- BIO5 Institute, University of Arizona, Tucson, AZ, USA
- Department of Surgery, University of Arizona College of Medicine, Tucson, AZ, USA
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