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Vogels CBF, Hill V, Breban MI, Chaguza C, Paul LM, Sodeinde A, Taylor-Salmon E, Ott IM, Petrone ME, Dijk D, Jonges M, Welkers MRA, Locksmith T, Dong Y, Tarigopula N, Tekin O, Schmedes S, Bunch S, Cano N, Jaber R, Panzera C, Stryker I, Vergara J, Zimler R, Kopp E, Heberlein L, Herzog KS, Fauver JR, Morrison AM, Michael SF, Grubaugh ND. DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus. BMC Genomics 2024; 25:433. [PMID: 38693476 PMCID: PMC11062901 DOI: 10.1186/s12864-024-10350-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 04/25/2024] [Indexed: 05/03/2024] Open
Abstract
BACKGROUND The increasing burden of dengue virus on public health due to more explosive and frequent outbreaks highlights the need for improved surveillance and control. Genomic surveillance of dengue virus not only provides important insights into the emergence and spread of genetically diverse serotypes and genotypes, but it is also critical to monitor the effectiveness of newly implemented control strategies. Here, we present DengueSeq, an amplicon sequencing protocol, which enables whole-genome sequencing of all four dengue virus serotypes. RESULTS We developed primer schemes for the four dengue virus serotypes, which can be combined into a pan-serotype approach. We validated both approaches using genetically diverse virus stocks and clinical specimens that contained a range of virus copies. High genome coverage (>95%) was achieved for all genotypes, except DENV2 (genotype VI) and DENV 4 (genotype IV) sylvatics, with similar performance of the serotype-specific and pan-serotype approaches. The limit of detection to reach 70% coverage was 10-100 RNA copies/μL for all four serotypes, which is similar to other commonly used primer schemes. DengueSeq facilitates the sequencing of samples without known serotypes, allows the detection of multiple serotypes in the same sample, and can be used with a variety of library prep kits and sequencing instruments. CONCLUSIONS DengueSeq was systematically evaluated with virus stocks and clinical specimens spanning the genetic diversity within each of the four dengue virus serotypes. The primer schemes can be plugged into existing amplicon sequencing workflows to facilitate the global need for expanded dengue virus genomic surveillance.
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Affiliation(s)
- Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, USA.
| | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, USA
| | - Lauren M Paul
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, USA
| | - Afeez Sodeinde
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Emma Taylor-Salmon
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut, USA
| | - Isabel M Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - Dennis Dijk
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC Location AMC, Amsterdam, The Netherlands
| | - Marcel Jonges
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC Location AMC, Amsterdam, The Netherlands
| | - Matthijs R A Welkers
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC Location AMC, Amsterdam, The Netherlands
- Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, The Netherlands
| | - Timothy Locksmith
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Yibo Dong
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, USA
| | - Namratha Tarigopula
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, USA
| | - Omer Tekin
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, USA
| | - Sarah Schmedes
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, USA
| | - Sylvia Bunch
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Natalia Cano
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Rayah Jaber
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Charles Panzera
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Ian Stryker
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Julieta Vergara
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Rebecca Zimler
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, USA
| | - Edgar Kopp
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Lea Heberlein
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Kaylee S Herzog
- Department of Epidemiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Joseph R Fauver
- Department of Epidemiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Andrea M Morrison
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, USA
| | - Scott F Michael
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, USA.
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.
- Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, USA.
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Kissler SM, Hay JA, Fauver JR, Mack C, Tai CG, Anderson DJ, Ho DD, Grubaugh ND, Grad YH. Viral kinetics of sequential SARS-CoV-2 infections. Nat Commun 2023; 14:6206. [PMID: 37798265 PMCID: PMC10556125 DOI: 10.1038/s41467-023-41941-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/22/2023] [Indexed: 10/07/2023] Open
Abstract
The impact of a prior SARS-CoV-2 infection on the progression of subsequent infections has been unclear. Using a convenience sample of 94,812 longitudinal RT-qPCR measurements from anterior nares and oropharyngeal swabs, we identified 71 individuals with two well-sampled SARS-CoV-2 infections between March 11th, 2020, and July 28th, 2022. We compared the SARS-CoV-2 viral kinetics of first vs. second infections in this group, adjusting for viral variant, vaccination status, and age. Relative to first infections, second infections usually featured a faster clearance time. Furthermore, a person's relative (rank-order) viral clearance time, compared to others infected with the same variant, was roughly conserved across first and second infections, so that individuals who had a relatively fast clearance time in their first infection also tended to have a relatively fast clearance time in their second infection (Spearman correlation coefficient: 0.30, 95% credible interval (0.12, 0.46)). These findings provide evidence that, like vaccination, immunity from a prior SARS-CoV-2 infection shortens the duration of subsequent acute SARS-CoV-2 infections principally by reducing viral clearance time. Additionally, there appears to be an inherent element of the immune response, or some other host factor, that shapes a person's relative ability to clear SARS-CoV-2 infection that persists across sequential infections.
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Affiliation(s)
- Stephen M Kissler
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - James A Hay
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Joseph R Fauver
- Department of Epidemiology, University of Nebraska Medical Center, Omaha, NE, USA
| | | | | | - Deverick J Anderson
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Durham, NC, USA
| | - David D Ho
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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3
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Petrone ME, Lucas C, Menasche B, Breban MI, Yildirim I, Campbell M, Omer SB, Holmes EC, Ko AI, Grubaugh ND, Iwasaki A, Wilen CB, Vogels CBF, Fauver JR. Nonsystematic Reporting Biases of the SARS-CoV-2 Variant Mu Could Impact Our Understanding of the Epidemiological Dynamics of Emerging Variants. Genome Biol Evol 2023; 15:evad052. [PMID: 36974986 PMCID: PMC10113931 DOI: 10.1093/gbe/evad052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/16/2023] [Accepted: 03/09/2023] [Indexed: 03/29/2023] Open
Abstract
Developing a timely and effective response to emerging SARS-CoV-2 variants of concern (VOCs) is of paramount public health importance. Global health surveillance does not rely on genomic data alone to identify concerning variants when they emerge. Instead, methods that utilize genomic data to estimate the epidemiological dynamics of emerging lineages have the potential to serve as an early warning system. However, these methods assume that genomic data are uniformly reported across circulating lineages. In this study, we analyze differences in reporting delays among SARS-CoV-2 VOCs as a plausible explanation for the timing of the global response to the former VOC Mu. Mu likely emerged in South America in mid-2020, where its circulation was largely confined. In this study, we demonstrate that Mu was designated as a VOC ∼1 year after it emerged and find that the reporting of genomic data for Mu differed significantly than that of other VOCs within countries, states, and individual laboratories. Our findings suggest that nonsystematic biases in the reporting of genomic data may have delayed the global response to Mu. Until they are resolved, the surveillance gaps that affected the global response to Mu could impede the rapid and accurate assessment of future emerging variants.
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Affiliation(s)
- Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, NSW, Australia
| | - Carolina Lucas
- Department of Immunobiology, Yale University School of Medicine
| | - Bridget Menasche
- Department of Laboratory Medicine, Yale University School of Medicine
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health
| | - Inci Yildirim
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health
- Department of Pediatric, Section of Infectious Diseases and Global Health, Yale University School of Medicine
- Yale Institute for Global Health, Yale University
| | - Melissa Campbell
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine
| | - Saad B Omer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health
- Yale Institute for Global Health, Yale University
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, NSW, Australia
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health
- Department of Ecology and Evolutionary Biology, Yale University
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine
- Howard Hughes Medical Institute
| | - Craig B Wilen
- Department of Immunobiology, Yale University School of Medicine
- Department of Laboratory Medicine, Yale University School of Medicine
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health
| | - Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health
- College of Public Health, University of Nebraska Medical Center
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Cheemarla NR, Hanron A, Fauver JR, Bishai J, Watkins TA, Brito AF, Zhao D, Alpert T, Vogels CBF, Ko AI, Schulz WL, Landry ML, Grubaugh ND, van Dijk D, Foxman EF. Nasal host response-based screening for undiagnosed respiratory viruses: a pathogen surveillance and detection study. The Lancet Microbe 2023; 4:e38-e46. [PMID: 36586415 PMCID: PMC9835789 DOI: 10.1016/s2666-5247(22)00296-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 09/24/2022] [Accepted: 10/06/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Symptomatic patients who test negative for common viruses are an important possible source of unrecognised or emerging pathogens, but metagenomic sequencing of all samples is inefficient because of the low likelihood of finding a pathogen in any given sample. We aimed to determine whether nasopharyngeal CXCL10 screening could be used as a strategy to enrich for samples containing undiagnosed viruses. METHODS In this pathogen surveillance and detection study, we measured CXCL10 concentrations from nasopharyngeal swabs from patients in the Yale New Haven health-care system, which had been tested at the Yale New Haven Hospital Clinical Virology Laboratory (New Haven, CT, USA). Patients who tested negative for a panel of respiratory viruses using multiplex PCR during Jan 23-29, 2017, or March 3-14, 2020, were included. We performed host and pathogen RNA sequencing (RNA-Seq) and analysis for viral reads on samples with CXCL10 higher than 1 ng/mL or CXCL10 testing and quantitative RT-PCR (RT-qPCR) for SARS-CoV-2. We used RNA-Seq and cytokine profiling to compare the host response to infection in samples that were virus positive (rhinovirus, seasonal coronavirus CoV-NL63, or SARS-CoV-2) and virus negative (controls). FINDINGS During Jan 23-29, 2017, 359 samples were tested for ten viruses on the multiplex PCR respiratory virus panel (RVP). 251 (70%) were RVP negative. 60 (24%) of 251 samples had CXCL10 higher than 150 pg/mL and were identified for further analysis. 28 (47%) of 60 CXCL10-high samples were positive for seasonal coronaviruses. 223 (89%) of 251 samples were PCR negative for 15 viruses and, of these, CXCL10-based screening identified 32 (13%) samples for further analysis. Of these 32 samples, eight (25%) with CXCL10 concentrations higher than 1 ng/mL and sufficient RNA were selected for RNA-Seq. Microbial RNA analysis showed the presence of influenza C virus in one sample and revealed RNA reads from bacterial pathobionts in four (50%) of eight samples. Between March 3 and March 14, 2020, 375 (59%) of 641 samples tested negative for 15 viruses on the RVP. 32 (9%) of 375 samples had CXCL10 concentrations ranging from 100 pg/mL to 1000 pg/mL and four of those were positive for SARS-CoV-2. CXCL10 elevation was statistically significant, and a distinguishing feature was found in 28 (8%) of 375 SARS-CoV-2-negative samples versus all four SARS-CoV-2-positive samples (p=4·4 × 10-5). Transcriptomic signatures showed an interferon response in virus-positive samples and an additional neutrophil-high hyperinflammatory signature in samples with high amounts of bacterial pathobionts. The CXCL10 cutoff for detecting a virus was 166·5 pg/mL for optimal sensitivity and 1091·0 pg/mL for specificity using a clinic-ready automated microfluidics-based immunoassay. INTERPRETATION These results confirm CXCL10 as a robust nasopharyngeal biomarker of viral respiratory infection and support host response-based screening followed by metagenomic sequencing of CXCL10-high samples as a practical approach to incorporate clinical samples into pathogen discovery and surveillance efforts. FUNDING National Institutes of Health, the Hartwell Foundation, the Gruber Foundation, Fast Grants for COVID-19 research from the Mercatus Center, and the Huffman Family Donor Advised Fund.
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Affiliation(s)
- Nagarjuna R Cheemarla
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Amelia Hanron
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Department of Pathology and Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Department of Epidemiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Jason Bishai
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Timothy A Watkins
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Anderson F Brito
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Instituto Todos pela Saúde, São Paulo, Brazil
| | - Dejian Zhao
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Albert I Ko
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Yale Institute of Global Health, Yale School of Public Health, New Haven, CT, USA
| | - Wade L Schulz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Marie L Landry
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Yale Institute of Global Health, Yale School of Public Health, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - David van Dijk
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Computer Science, Yale University, New Haven, CT, USA
| | - Ellen F Foxman
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
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5
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Hay JA, Kissler SM, Fauver JR, Mack C, Tai CG, Samant RM, Connolly S, Anderson DJ, Khullar G, MacKay M, Patel M, Kelly S, Manhertz A, Eiter I, Salgado D, Baker T, Howard B, Dudley JT, Mason CE, Nair M, Huang Y, DiFiori J, Ho DD, Grubaugh ND, Grad YH. Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: A retrospective cohort study. eLife 2022; 11:81849. [PMID: 36383192 PMCID: PMC9711520 DOI: 10.7554/elife.81849] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/15/2022] [Indexed: 11/17/2022] Open
Abstract
Background The combined impact of immunity and SARS-CoV-2 variants on viral kinetics during infections has been unclear. Methods We characterized 1,280 infections from the National Basketball Association occupational health cohort identified between June 2020 and January 2022 using serial RT-qPCR testing. Logistic regression and semi-mechanistic viral RNA kinetics models were used to quantify the effect of age, variant, symptom status, infection history, vaccination status and antibody titer to the founder SARS-CoV-2 strain on the duration of potential infectiousness and overall viral kinetics. The frequency of viral rebounds was quantified under multiple cycle threshold (Ct) value-based definitions. Results Among individuals detected partway through their infection, 51.0% (95% credible interval [CrI]: 48.3-53.6%) remained potentially infectious (Ct <30) 5 days post detection, with small differences across variants and vaccination status. Only seven viral rebounds (0.7%; N=999) were observed, with rebound defined as 3+days with Ct <30 following an initial clearance of 3+days with Ct ≥30. High antibody titers against the founder SARS-CoV-2 strain predicted lower peak viral loads and shorter durations of infection. Among Omicron BA.1 infections, boosted individuals had lower pre-booster antibody titers and longer clearance times than non-boosted individuals. Conclusions SARS-CoV-2 viral kinetics are partly determined by immunity and variant but dominated by individual-level variation. Since booster vaccination protects against infection, longer clearance times for BA.1-infected, boosted individuals may reflect a less effective immune response, more common in older individuals, that increases infection risk and reduces viral RNA clearance rate. The shifting landscape of viral kinetics underscores the need for continued monitoring to optimize isolation policies and to contextualize the health impacts of therapeutics and vaccines. Funding Supported in part by CDC contract #200-2016-91779, a sponsored research agreement to Yale University from the National Basketball Association contract #21-003529, and the National Basketball Players Association.
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Affiliation(s)
- James A Hay
- Harvard TH Chan School of Public HealthBostonUnited States
| | | | - Joseph R Fauver
- Yale School of Public HealthNew HavenUnited States
- University of Nebraska Medical CenterOmahaUnited States
| | | | | | | | | | - Deverick J Anderson
- Duke Center for Antimicrobial Stewardship and Infection PreventionDurhamUnited States
| | | | | | | | | | | | | | | | | | | | | | | | - Manoj Nair
- Vagelos College of Physicians and Surgeons, Columbia UniversityNew YorkUnited States
| | - Yaoxing Huang
- Vagelos College of Physicians and Surgeons, Columbia UniversityNew YorkUnited States
| | - John DiFiori
- Hospital for Special SurgeryNew YorkUnited States
- National Basketball AssociationNew YorkUnited States
| | - David D Ho
- Vagelos College of Physicians and Surgeons, Columbia UniversityNew YorkUnited States
| | | | - Yonatan H Grad
- Harvard TH Chan School of Public HealthBostonUnited States
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6
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Baaijens JA, Zulli A, Ott IM, Nika I, van der Lugt MJ, Petrone ME, Alpert T, Fauver JR, Kalinich CC, Vogels CBF, Breban MI, Duvallet C, McElroy KA, Ghaeli N, Imakaev M, Mckenzie-Bennett MF, Robison K, Plocik A, Schilling R, Pierson M, Littlefield R, Spencer ML, Simen BB, Hanage WP, Grubaugh ND, Peccia J, Baym M. Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques. Genome Biol 2022; 23:236. [PMID: 36348471 PMCID: PMC9643916 DOI: 10.1186/s13059-022-02805-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 10/25/2022] [Indexed: 11/09/2022] Open
Abstract
Effectively monitoring the spread of SARS-CoV-2 mutants is essential to efforts to counter the ongoing pandemic. Predicting lineage abundance from wastewater, however, is technically challenging. We show that by sequencing SARS-CoV-2 RNA in wastewater and applying algorithms initially used for transcriptome quantification, we can estimate lineage abundance in wastewater samples. We find high variability in signal among individual samples, but the overall trends match those observed from sequencing clinical samples. Thus, while clinical sequencing remains a more sensitive technique for population surveillance, wastewater sequencing can be used to monitor trends in mutant prevalence in situations where clinical sequencing is unavailable.
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Affiliation(s)
- Jasmijn A Baaijens
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Department of Intelligent Systems, Delft University of Technology, Delft, Netherlands.
| | - Alessandro Zulli
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA
| | - Isabel M Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Ioanna Nika
- Department of Intelligent Systems, Delft University of Technology, Delft, Netherlands
| | - Mart J van der Lugt
- Department of Intelligent Systems, Delft University of Technology, Delft, Netherlands
| | - Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Epidemiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Chaney C Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - William P Hanage
- Center for Communicable Disease Dynamics and Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Jordan Peccia
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA
| | - Michael Baym
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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7
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Chaguza C, Coppi A, Earnest R, Ferguson D, Kerantzas N, Warner F, Young HP, Breban MI, Billig K, Koch RT, Pham K, Kalinich CC, Ott IM, Fauver JR, Hahn AM, Tikhonova IR, Castaldi C, De Kumar B, Pettker CM, Warren JL, Weinberger DM, Landry ML, Peaper DR, Schulz W, Vogels CBF, Grubaugh ND. Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons. Med 2022; 3:325-334.e4. [PMID: 35399324 PMCID: PMC8983481 DOI: 10.1016/j.medj.2022.03.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/25/2021] [Accepted: 03/29/2022] [Indexed: 11/30/2022]
Abstract
Background The SARS-CoV-2 Omicron variant became a global concern due to its rapid spread and displacement of the dominant Delta variant. We hypothesized that part of Omicron's rapid rise was based on its increased ability to cause infections in persons that are vaccinated compared to Delta. Methods We analyzed nasal swab PCR tests for samples collected between December 12 and 16, 2021, in Connecticut when the proportion of Delta and Omicron variants was relatively equal. We used the spike gene target failure (SGTF) to classify probable Delta and Omicron infections. We fitted an exponential curve to the estimated infections to determine the doubling times for each variant. We compared the test positivity rates for each variant by vaccination status, number of doses, and vaccine manufacturer. Generalized linear models were used to assess factors associated with odds of infection with each variant among persons testing positive for SARS-CoV-2. Findings For infections with high virus copies (Ct < 30) among vaccinated persons, we found higher odds that they were infected with Omicron compared to Delta, and that the odds increased with increased number of vaccine doses. Compared to unvaccinated persons, we found significant reduction in Delta positivity rates after two (43.4%-49.1%) and three vaccine doses (81.1%), while we only found a significant reduction in Omicron positivity rates after three doses (62.3%). Conclusion The rapid rise in Omicron infections was likely driven by Omicron's escape from vaccine-induced immunity. Funding This work was supported by the Centers for Disease Control and Prevention (CDC).
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Andreas Coppi
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - David Ferguson
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Nicholas Kerantzas
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Frederick Warner
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - H Patrick Young
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kendall Billig
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Robert Tobias Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kien Pham
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chaney C Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Isabel M Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Irina R Tikhonova
- Yale Center for Genome Analysis, Yale University, New Haven, CT, USA
| | | | - Bony De Kumar
- Yale Center for Genome Analysis, Yale University, New Haven, CT, USA
| | - Christian M Pettker
- Quality and Safety, Yale New Haven Health, New Haven, CT, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Joshua L Warren
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Daniel M Weinberger
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Marie L Landry
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Section of Infectious Diseases, Department of Medicine, Yale School of Medicine, New Haven, CT, USA
- Clinical Virology Laboratory, Yale New Haven Hospital, New Haven, CT, USA
| | - David R Peaper
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Wade Schulz
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, 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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8
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Chaguza C, Coppi A, Earnest R, Ferguson D, Kerantzas N, Warner F, Young HP, Breban MI, Billig K, Koch RT, Pham K, Kalinich CC, Ott IM, Fauver JR, Hahn AM, Tikhonova IR, Castaldi C, De Kumar B, Pettker CM, Warren JL, Weinberger DM, Landry ML, Peaper DR, Schulz W, Vogels CBF, Grubaugh ND. Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons. Med 2022; 3:325-334.e4. [PMID: 35399324 DOI: 10.1101/2022.01.22.22269660] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/25/2021] [Accepted: 03/29/2022] [Indexed: 05/22/2023]
Abstract
BACKGROUND The SARS-CoV-2 Omicron variant became a global concern due to its rapid spread and displacement of the dominant Delta variant. We hypothesized that part of Omicron's rapid rise was based on its increased ability to cause infections in persons that are vaccinated compared to Delta. METHODS We analyzed nasal swab PCR tests for samples collected between December 12 and 16, 2021, in Connecticut when the proportion of Delta and Omicron variants was relatively equal. We used the spike gene target failure (SGTF) to classify probable Delta and Omicron infections. We fitted an exponential curve to the estimated infections to determine the doubling times for each variant. We compared the test positivity rates for each variant by vaccination status, number of doses, and vaccine manufacturer. Generalized linear models were used to assess factors associated with odds of infection with each variant among persons testing positive for SARS-CoV-2. FINDINGS For infections with high virus copies (Ct < 30) among vaccinated persons, we found higher odds that they were infected with Omicron compared to Delta, and that the odds increased with increased number of vaccine doses. Compared to unvaccinated persons, we found significant reduction in Delta positivity rates after two (43.4%-49.1%) and three vaccine doses (81.1%), while we only found a significant reduction in Omicron positivity rates after three doses (62.3%). CONCLUSION The rapid rise in Omicron infections was likely driven by Omicron's escape from vaccine-induced immunity. FUNDING This work was supported by the Centers for Disease Control and Prevention (CDC).
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Andreas Coppi
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - David Ferguson
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Nicholas Kerantzas
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Frederick Warner
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - H Patrick Young
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kendall Billig
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Robert Tobias Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kien Pham
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chaney C Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Isabel M Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Irina R Tikhonova
- Yale Center for Genome Analysis, Yale University, New Haven, CT, USA
| | | | - Bony De Kumar
- Yale Center for Genome Analysis, Yale University, New Haven, CT, USA
| | - Christian M Pettker
- Quality and Safety, Yale New Haven Health, New Haven, CT, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Joshua L Warren
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Daniel M Weinberger
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Marie L Landry
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Section of Infectious Diseases, Department of Medicine, Yale School of Medicine, New Haven, CT, USA
- Clinical Virology Laboratory, Yale New Haven Hospital, New Haven, CT, USA
| | - David R Peaper
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Wade Schulz
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, 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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9
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Earnest R, Uddin R, Matluk N, Renzette N, Turbett SE, Siddle KJ, Loreth C, Adams G, Tomkins-Tinch CH, Petrone ME, Rothman JE, Breban MI, Koch RT, Billig K, Fauver JR, Vogels CBF, Bilguvar K, De Kumar B, Landry ML, Peaper DR, Kelly K, Omerza G, Grieser H, Meak S, Martha J, Dewey HB, Kales S, Berenzy D, Carpenter-Azevedo K, King E, Huard RC, Novitsky V, Howison M, Darpolor J, Manne A, Kantor R, Smole SC, Brown CM, Fink T, Lang AS, Gallagher GR, Pitzer VE, Sabeti PC, Gabriel S, MacInnis BL, Tewhey R, Adams MD, Park DJ, Lemieux JE, Grubaugh ND. Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA. Cell Rep Med 2022; 3:100583. [PMID: 35480627 PMCID: PMC8913280 DOI: 10.1016/j.xcrm.2022.100583] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/30/2021] [Accepted: 03/01/2022] [Indexed: 12/11/2022]
Abstract
The SARS-CoV-2 Delta variant rose to dominance in mid-2021, likely propelled by an estimated 40%-80% increased transmissibility over Alpha. To investigate if this ostensible difference in transmissibility is uniform across populations, we partner with public health programs from all six states in New England in the United States. We compare logistic growth rates during each variant's respective emergence period, finding that Delta emerged 1.37-2.63 times faster than Alpha (range across states). We compute variant-specific effective reproductive numbers, estimating that Delta is 63%-167% more transmissible than Alpha (range across states). Finally, we estimate that Delta infections generate on average 6.2 (95% CI 3.1-10.9) times more viral RNA copies per milliliter than Alpha infections during their respective emergence. Overall, our evidence suggests that Delta's enhanced transmissibility can be attributed to its innate ability to increase infectiousness, but its epidemiological dynamics may vary depending on underlying population attributes and sequencing data availability.
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Affiliation(s)
- Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA.
| | - Rockib Uddin
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nicholas Matluk
- Maine Center for Disease Control and Prevention, Augusta, ME 04333, USA; Health and Environmental Testing Laboratory, Augusta, ME 04333, USA
| | - Nicholas Renzette
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Sarah E Turbett
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | | | - Gordon Adams
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Jessica E Rothman
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Robert Tobias Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Kendall Billig
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Kaya Bilguvar
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA; Departments of Neurosurgery and Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Medical Genetics, Acibadem University School of Medicine, Istanbul, Turkey
| | - Bony De Kumar
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
| | - Marie L Landry
- Departments of Laboratory Medicine and Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - David R Peaper
- Departments of Laboratory Medicine and Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Kevin Kelly
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Greg Omerza
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Heather Grieser
- Maine Center for Disease Control and Prevention, Augusta, ME 04333, USA; Health and Environmental Testing Laboratory, Augusta, ME 04333, USA
| | - Sim Meak
- Maine Center for Disease Control and Prevention, Augusta, ME 04333, USA; Health and Environmental Testing Laboratory, Augusta, ME 04333, USA
| | - John Martha
- Maine Center for Disease Control and Prevention, Augusta, ME 04333, USA; Health and Environmental Testing Laboratory, Augusta, ME 04333, USA
| | | | - Susan Kales
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | | | | | - Ewa King
- Rhode Island Department of Health, State Health Laboratories, Providence, RI 02904, USA
| | - Richard C Huard
- Rhode Island Department of Health, State Health Laboratories, Providence, RI 02904, USA
| | - Vlad Novitsky
- Division of Infectious Diseases, Brown University Alpert Medical School, Providence, RI 02906, USA
| | - Mark Howison
- Research Improving People's Lives, Providence, RI 02903, USA
| | - Josephine Darpolor
- Division of Infectious Diseases, Brown University Alpert Medical School, Providence, RI 02906, USA
| | - Akarsh Manne
- Division of Infectious Diseases, Brown University Alpert Medical School, Providence, RI 02906, USA
| | - Rami Kantor
- Division of Infectious Diseases, Brown University Alpert Medical School, Providence, RI 02906, USA
| | - Sandra C Smole
- Massachusetts Department of Public Health, Boston, MA 02130, USA
| | | | - Timelia Fink
- Massachusetts Department of Public Health, Boston, MA 02130, USA
| | - Andrew S Lang
- Massachusetts Department of Public Health, Boston, MA 02130, USA
| | - Glen R Gallagher
- Massachusetts Department of Public Health, Boston, MA 02130, USA
| | - Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Stacey Gabriel
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Ryan Tewhey
- Department of Medical Genetics, Acibadem University School of Medicine, Istanbul, Turkey; Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA; Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, USA
| | - Mark D Adams
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Daniel J Park
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jacob E Lemieux
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06510, USA.
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10
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Petrone ME, Lucas C, Menasche B, Breban MI, Yildirim I, Campbell M, Omer SB, Ko AI, Grubaugh ND, Iwasak A, Wilen CB, Vogels CBF, Fauver JR. Insights into the limited global spread of the immune evasive SARS-CoV-2 variant Mu. medRxiv 2022:2022.03.28.22273077. [PMID: 35378749 PMCID: PMC8978943 DOI: 10.1101/2022.03.28.22273077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
SARS-CoV-2 'Variants of Concern' (VOCs) continue to reshape the trajectory of the COVID-19 pandemic. However, why some VOCs, like Omicron, become globally dominant while the spread of others is limited is not fully understood. To address this question, we investigated the VOC Mu, which was first identified in Colombia in late 2020. Our study demonstrates that, although Mu is less sensitive to neutralization compared to variants that preceded it, it did not spread significantly outside of South and Central America. Additionally, we find evidence that the response to Mu was impeded by reporting delays and gaps in the global genomic surveillance system. Our findings suggest that immune evasion alone was not sufficient to outcompete highly transmissible variants that were circulating concurrently with Mu. Insights into the complex relationship between genomic and epidemiological characteristics of previous variants should inform our response to variants that are likely to emerge in the future.
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Affiliation(s)
- Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
- These authors contributed equally
| | - Carolina Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- These authors contributed equally
| | - Bridget Menasche
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
- These authors contributed equally
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Inci Yildirim
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Pediatric, Section of Infectious Diseases and Global Health, Yale University School of Medicine, New Haven, CT, USA
- Yale Institute for Global Health, Yale University, New Haven, CT, USA
| | - Melissa Campbell
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Saad B Omer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Yale Institute for Global Health, Yale University, New Haven, CT, USA
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Akiko Iwasak
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Craig B Wilen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- These authors contributed equally
| | - Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
- These authors contributed equally
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11
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Alpert T, Vogels CBF, Breban MI, Petrone ME, Wyllie AL, Grubaugh ND, Fauver JR. Sequencing SARS-CoV-2 Genomes from Saliva. Virus Evol 2022; 8:veab098. [PMID: 35542310 PMCID: PMC9074962 DOI: 10.1093/ve/veab098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 10/27/2021] [Accepted: 12/31/2021] [Indexed: 11/13/2022] Open
Abstract
Abstract
Genomic sequencing is crucial to understanding the epidemiology and evolution of SARS-CoV-2. Often, genomic studies rely on remnant diagnostic material, typically nasopharyngeal swabs, as input into whole genome SARS-CoV-2 next-generation sequencing pipelines. Saliva has proven to be a safe and stable specimen for the detection of SARS-CoV-2 RNA via traditional diagnostic assays, however saliva is not commonly used for SARS-CoV-2 sequencing. Using the ARTIC Network amplicon-generation approach with sequencing on the Oxford Nanopore MinION, we demonstrate that sequencing SARS-CoV-2 from saliva produces genomes comparable to those from nasopharyngeal swabs, and that RNA extraction is necessary to generate complete genomes from saliva. In this study, we show that saliva is a useful specimen type for genomic studies of SARS-CoV-2.
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Affiliation(s)
- Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06510, USA
| | - Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
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12
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Kissler SM, Fauver JR, Mack C, Tai CG, Breban MI, Watkins AE, Samant RM, Anderson DJ, Metti J, Khullar G, Baits R, MacKay M, Salgado D, Baker T, Dudley JT, Mason CE, Ho DD, Grubaugh ND, Grad YH. Viral Dynamics of SARS-CoV-2 Variants in Vaccinated and Unvaccinated Persons. N Engl J Med 2021; 385:2489-2491. [PMID: 34941024 PMCID: PMC8693673 DOI: 10.1056/nejmc2102507] [Citation(s) in RCA: 150] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Deverick J Anderson
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Durham, NC
| | | | | | | | | | | | | | | | | | - David D Ho
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY
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13
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Lucas C, Vogels CBF, Yildirim I, Rothman JE, Lu P, Monteiro V, Gehlhausen JR, Campbell M, Silva J, Tabachnikova A, Peña-Hernandez MA, Muenker MC, Breban MI, Fauver JR, Mohanty S, Huang J, Shaw AC, Ko AI, Omer SB, Grubaugh ND, Iwasaki A. Impact of circulating SARS-CoV-2 variants on mRNA vaccine-induced immunity. Nature 2021; 600:523-529. [PMID: 34634791 PMCID: PMC9348899 DOI: 10.1038/s41586-021-04085-y] [Citation(s) in RCA: 150] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 09/30/2021] [Indexed: 01/16/2023]
Abstract
The emergence of SARS-CoV-2 variants with mutations in major neutralizing antibody-binding sites can affect humoral immunity induced by infection or vaccination1-6. Here we analysed the development of anti-SARS-CoV-2 antibody and T cell responses in individuals who were previously infected (recovered) or uninfected (naive) and received mRNA vaccines to SARS-CoV-2. While individuals who were previously infected sustained higher antibody titres than individuals who were uninfected post-vaccination, the latter reached comparable levels of neutralization responses to the ancestral strain after the second vaccine dose. T cell activation markers measured upon spike or nucleocapsid peptide in vitro stimulation showed a progressive increase after vaccination. Comprehensive analysis of plasma neutralization using 16 authentic isolates of distinct locally circulating SARS-CoV-2 variants revealed a range of reduction in the neutralization capacity associated with specific mutations in the spike gene: lineages with E484K and N501Y/T (for example, B.1.351 and P.1) had the greatest reduction, followed by lineages with L452R (for example, B.1.617.2). While both groups retained neutralization capacity against all variants, plasma from individuals who were previously infected and vaccinated displayed overall better neutralization capacity than plasma from individuals who were uninfected and also received two vaccine doses, pointing to vaccine boosters as a relevant future strategy to alleviate the effect of emerging variants on antibody neutralizing activity.
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Affiliation(s)
- Carolina Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Inci Yildirim
- Department of Pediatric, Section of Infectious Diseases and Global Health, Yale University School of Medicine, New Haven, CT, USA
- Yale Institute for Global Health, Yale University, New Haven, CT, USA
| | - Jessica E Rothman
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Peiwen Lu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Valter Monteiro
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Jeff R Gehlhausen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
| | - Melissa Campbell
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Julio Silva
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | | | | | - M Catherine Muenker
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Subhasis Mohanty
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Jiefang Huang
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Albert C Shaw
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Saad B Omer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Yale Institute for Global Health, Yale University, New Haven, CT, USA
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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14
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Murrieta RA, Garcia-Luna SM, Murrieta DJ, Halladay G, Young MC, Fauver JR, Gendernalik A, Weger-Lucarelli J, Rückert C, Ebel GD. Impact of extrinsic incubation temperature on natural selection during Zika virus infection of Aedes aegypti and Aedes albopictus. PLoS Pathog 2021; 17:e1009433. [PMID: 34752502 PMCID: PMC8629396 DOI: 10.1371/journal.ppat.1009433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 11/29/2021] [Accepted: 10/18/2021] [Indexed: 01/10/2023] Open
Abstract
Arthropod-borne viruses (arboviruses) require replication across a wide range of temperatures to perpetuate. While vertebrate hosts tend to maintain temperatures of approximately 37°C—40°C, arthropods are subject to ambient temperatures which can have a daily fluctuation of > 10°C. Temperatures impact vector competence, extrinsic incubation period, and mosquito survival unimodally, with optimal conditions occurring at some intermediate temperature. In addition, the mean and range of daily temperature fluctuations influence arbovirus perpetuation and vector competence. The impact of temperature on arbovirus genetic diversity during systemic mosquito infection, however, is poorly understood. Therefore, we determined how constant extrinsic incubation temperatures of 25°C, 28°C, 32°C, and 35°C control Zika virus (ZIKV) vector competence and population dynamics within Aedes aegypti and Aedes albopictus mosquitoes. We also examined fluctuating temperatures which better mimic field conditions in the tropics. We found that vector competence varied in a unimodal manner for constant temperatures peaking between 28°C and 32°C for both Aedes species. Transmission peaked at 10 days post-infection for Aedes aegypti and 14 days for Aedes albopictus. Conversely, fluctuating temperature decreased vector competence. Using RNA-seq to characterize ZIKV population structure, we identified that temperature alters the selective environment in unexpected ways. During mosquito infection, constant temperatures more often elicited positive selection whereas fluctuating temperatures led to strong purifying selection in both Aedes species. These findings demonstrate that temperature has multiple impacts on ZIKV biology, including major effects on the selective environment within mosquitoes. Arthropod-borne viruses (arboviruses) have emerged in recent decades due to complex factors that include increases in international travel and trade, the breakdown of public health infrastructure, land use changes, and many others. Climate change also has the potential to shift the geographical ranges of arthropod vectors, consequently increasing the global risk of arbovirus infection. Changing temperatures may alter the virus-host interaction, ultimately resulting in the emergence of new viruses and virus genotypes in new areas. Therefore, we sought to characterize how temperature (both constant and fluctuating) alters the ability of Aedes aegypti and Aedes albopictus to transmit Zika virus, and how it influences virus populations within mosquitoes. We found that intermediate temperatures maximize virus transmission compared to more extreme and fluctuating temperatures. Constant temperatures increased positive selection on virus genomes, while fluctuating temperatures strengthened purifying selection. Our studies provide evidence that in addition to altering vector competence, temperature significantly influences natural selection within mosquitoes.
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Affiliation(s)
- Reyes A. Murrieta
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Selene M. Garcia-Luna
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
| | - Deedra J. Murrieta
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Gareth Halladay
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Michael C. Young
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Joseph R. Fauver
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, Laboratory of Epidemiology of Public Health, New Haven, Connecticut, United States of America
| | - Alex Gendernalik
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - James Weger-Lucarelli
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
- Department of Biomedical Sciences & Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Claudia Rückert
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
- Department of Biochemistry and Molecular Biology, College of Agriculture, Biotechnology & Natural Resources, University of Nevada, Reno, Nevada, United States of America
| | - Gregory D. Ebel
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
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15
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Santiago GA, Kalinich CC, Cruz-López F, González GL, Flores B, Hentoff A, Charriez KN, Fauver JR, Adams LE, Sharp TM, Black A, Bedford T, Ellis E, Ellis B, Waterman SH, Paz-Bailey G, Grubaugh ND, Muñoz-Jordán JL. Tracing the Origin, Spread, and Molecular Evolution of Zika Virus in Puerto Rico, 2016-2017. Emerg Infect Dis 2021; 27:2971-2973. [PMID: 34670646 PMCID: PMC8544999 DOI: 10.3201/eid2711.211575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We reconstructed the 2016-2017 Zika virus epidemic in Puerto Rico by using complete genomes to uncover the epidemic's origin, spread, and evolutionary dynamics. Our study revealed that the epidemic was propelled by multiple introductions that spread across the island, intricate evolutionary patterns, and ≈10 months of cryptic transmission.
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16
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Klein J, Brito AF, Trubin P, Lu P, Wong P, Alpert T, Peña-Hernández MA, Haynes W, Kamath K, Liu F, Vogels CBF, Fauver JR, Lucas C, Oh J, Mao T, Silva J, Wyllie AL, Muenker MC, Casanovas-Massana A, Moore AJ, Petrone ME, Kalinich CC, Dela Cruz C, Farhadian S, Ring A, Shon J, Ko AI, Grubaugh ND, Israelow B, Iwasaki A, Azar MM. Longitudinal immune profiling of a SARS-CoV-2 reinfection in a solid organ transplant recipient. J Infect Dis 2021; 225:374-384. [PMID: 34718647 DOI: 10.1093/infdis/jiab553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/28/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The underlying immunologic deficiencies enabling SARS-CoV-2 reinfection are currently unknown. We describe deep longitudinal immune profiling of a transplant recipient hospitalized twice for COVID-19. METHODS A 66-year-old male renal transplant recipient was hospitalized with COVID-19 March 2020 then readmitted to the hospital with COVID-19 233 days after initial diagnosis. Virologic and immunologic investigation were performed on samples from the primary and secondary infections. RESULTS Whole viral genome sequencing and phylogenic analysis revealed that viruses causing both infections were caused by distinct genetic lineages without evidence of immune escape mutations. Longitudinal comparison of cellular and humoral responses during primary SARS-CoV-2 infection revealed that this patient responded to the primary infection with low neutralization titer anti-SARS-CoV-2 antibodies that were likely present at the time of reinfection. DISCUSSION The development of neutralizing antibodies and humoral memory responses in this patient failed to confer protection against reinfection, suggesting that they were below a neutralizing titer threshold or that additional factors may be required for efficient prevention of SARS-CoV-2 reinfection. Development of poorly neutralizing antibodies may have been due to profound and relatively specific reduction in naïve CD4 T-cell pools. Seropositivity alone may not be a perfect correlate of protection in immunocompromised patients.
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Affiliation(s)
- Jonathan Klein
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Anderson F Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Paul Trubin
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Peiwen Lu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Patrick Wong
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mario A Peña-Hernández
- Department of Biological and Biomedical Sciences, Yale University School of Medicine, New Haven, CT, USA
| | | | | | - Feimei Liu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Carolina Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Jieun Oh
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Tianyang Mao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Julio Silva
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - M Catherine Muenker
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Adam J Moore
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chaney C Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Charles Dela Cruz
- Department of Medicine, Section of Pulmonary and Critical Care Medicine; Yale University School of Medicine, New Haven, CT, USA
| | - Shelli Farhadian
- Department of Internal Medicine, Section General Medicine; Yale University School of Medicine, New Haven, CT, USA
| | - Aaron Ring
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.,Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Benjamin Israelow
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.,Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Marwan M Azar
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
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17
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Earnest R, Uddin R, Matluk N, Renzette N, Siddle KJ, Loreth C, Adams G, Tomkins-Tinch CH, Petrone ME, Rothman JE, Breban MI, Koch RT, Billig K, Fauver JR, Vogels CB, Turbett S, Bilguvar K, De Kumar B, Landry ML, Peaper DR, Kelly K, Omerza G, Grieser H, Meak S, Martha J, Dewey HH, Kales S, Berenzy D, Carpenter-Azevedo K, King E, Huard RC, Smole SC, Brown CM, Fink T, Lang AS, Gallagher GR, Sabeti PC, Gabriel S, MacInnis BL, Tewhey R, Adams MD, Park DJ, Lemieux JE, Grubaugh ND. Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA. medRxiv 2021:2021.10.06.21264641. [PMID: 34642698 PMCID: PMC8509091 DOI: 10.1101/2021.10.06.21264641] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant quickly rose to dominance in mid-2021, displacing other variants, including Alpha. Studies using data from the United Kingdom and India estimated that Delta was 40-80% more transmissible than Alpha, allowing Delta to become the globally dominant variant. However, it was unclear if the ostensible difference in relative transmissibility was due mostly to innate properties of Delta's infectiousness or differences in the study populations. To investigate, we formed a partnership with SARS-CoV-2 genomic surveillance programs from all six New England US states. By comparing logistic growth rates, we found that Delta emerged 37-163% faster than Alpha in early 2021 (37% Massachusetts, 75% New Hampshire, 95% Maine, 98% Rhode Island, 151% Connecticut, and 163% Vermont). We next computed variant-specific effective reproductive numbers and estimated that Delta was 58-120% more transmissible than Alpha across New England (58% New Hampshire, 68% Massachusetts, 76% Connecticut, 85% Rhode Island, 98% Maine, and 120% Vermont). Finally, using RT-PCR data, we estimated that Delta infections generate on average ∼6 times more viral RNA copies per mL than Alpha infections. Overall, our evidence indicates that Delta's enhanced transmissibility could be attributed to its innate ability to increase infectiousness, but its epidemiological dynamics may vary depending on the underlying immunity and behavior of distinct populations.
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Affiliation(s)
- Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Rockib Uddin
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nicholas Matluk
- Maine Center for Disease Control and Prevention, Augusta, ME 04333
- Health and Environmental Testing Laboratory, Augusta, ME 04333
| | - Nicholas Renzette
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | | | | | - Gordon Adams
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Jessica E. Rothman
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Robert Tobias Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Kendall Billig
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Joseph R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Sarah Turbett
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kaya Bilguvar
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
- Departments of Neurosurgery and Genetics, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Medical Genetics, Acibadem University School of Medicine, Istanbul, Turkey
| | - Bony De Kumar
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
| | - Marie L. Landry
- Departments of Laboratory Medicine and Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - David R. Peaper
- Departments of Laboratory Medicine and Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Kevin Kelly
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Greg Omerza
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Heather Grieser
- Maine Center for Disease Control and Prevention, Augusta, ME 04333
- Health and Environmental Testing Laboratory, Augusta, ME 04333
| | - Sim Meak
- Maine Center for Disease Control and Prevention, Augusta, ME 04333
- Health and Environmental Testing Laboratory, Augusta, ME 04333
| | - John Martha
- Maine Center for Disease Control and Prevention, Augusta, ME 04333
- Health and Environmental Testing Laboratory, Augusta, ME 04333
| | | | - Susan Kales
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | | | | | - Ewa King
- Rhode Island Department of Health, State Health Laboratories, Providence, RI 02904, USA
| | - Richard C. Huard
- Rhode Island Department of Health, State Health Laboratories, Providence, RI 02904, USA
| | - Sandra C. Smole
- Massachusetts Department of Public Health, Boston MA 02130, USA
| | | | - Timelia Fink
- Massachusetts Department of Public Health, Boston MA 02130, USA
| | - Andrew S. Lang
- Massachusetts Department of Public Health, Boston MA 02130, USA
| | | | | | - Stacey Gabriel
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Ryan Tewhey
- Department of Medical Genetics, Acibadem University School of Medicine, Istanbul, Turkey
- Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, USA
| | - Mark D. Adams
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Daniel J. Park
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jacob E. Lemieux
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06510, USA
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18
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Lee M, Sallah YH, Petrone M, Ringer M, Cosentino D, Vogels CBF, Fauver JR, Alpert TD, Grubaugh ND, Gupta S. COVID-19 Outcomes and Genomic Characterization of SARS-CoV-2 Isolated From Veterans in New England States: Retrospective Analysis. JMIRx Med 2021; 2:e31503. [PMID: 35014989 PMCID: PMC8722526 DOI: 10.2196/31503] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/14/2021] [Accepted: 11/04/2021] [Indexed: 04/15/2023]
Abstract
BACKGROUND Clinical and virologic characteristics of COVID-19 infections in veterans in New England have not been described. The average US veteran is a male older than the general US population. SARS-CoV-2 infection is known to cause poorer outcomes among men and older adults, making the veteran population an especially vulnerable group for COVID-19. OBJECTIVE This study aims to evaluate clinical and virologic factors impacting COVID-19 outcomes. METHODS This retrospective chart review included 476 veterans in six New England states with confirmed SARS-CoV-2 infection between April and September 2020. Whole genome sequencing was performed on SARS-CoV-2 RNA isolated from these veterans, and the correlation of genomic data to clinical outcomes was evaluated. Clinical and demographic variables were collected by manual chart review and were correlated to the end points of peak disease severity (based on oxygenation requirements), hospitalization, and mortality using multivariate regression analyses. RESULTS Of 476 veterans, 274 had complete and accessible charts. Of the 274 veterans, 92.7% (n=254) were men and 83.2% (n=228) were White, and the mean age was 63 years. In the multivariate regression, significant predictors of hospitalization (C statistic 0.75) were age (odds ratio [OR] 1.05, 95% CI 1.03-1.08) and non-White race (OR 2.39, 95% CI 1.13-5.01). Peak severity (C statistic 0.70) also varied by age (OR 1.07, 95% CI 1.03-1.11) and O2 requirement on admission (OR 45.7, 95% CI 18.79-111). Mortality (C statistic 0.87) was predicted by age (OR 1.06, 95% CI 1.01-1.11), dementia (OR 3.44, 95% CI 1.07-11.1), and O2 requirement on admission (OR 6.74, 95% CI 1.74-26.1). Most (291/299, 97.3%) of our samples were dominated by the spike protein D614G substitution and were from SARS-CoV-2 B.1 lineage or one of 37 different B.1 sublineages, with none representing more than 8.7% (26/299) of the cases. CONCLUSIONS In a cohort of veterans from the six New England states with a mean age of 63 years and a high comorbidity burden, age was the largest predictor of hospitalization, peak disease severity, and mortality. Non-White veterans were more likely to be hospitalized, and patients who required oxygen on admission were more likely to have severe disease and higher rates of mortality. Multiple SARS-CoV-2 lineages were distributed in patients in New England early in the COVID-19 era, mostly related to viruses from New York State with D614G mutation.
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Affiliation(s)
- Megan Lee
- Yale School of Medicine West Haven, CT United States
| | | | - Mary Petrone
- Yale School of Public Health New Haven, CT United States
| | | | | | | | | | - Tara D Alpert
- Yale School of Public Health New Haven, CT United States
| | | | - Shaili Gupta
- Yale School of Medicine West Haven, CT United States
- VA Connecticut Healthcare System West Haven, CT United States
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19
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Baaijens JA, Zulli A, Ott IM, Petrone ME, Alpert T, Fauver JR, Kalinich CC, Vogels CBF, Breban MI, Duvallet C, McElroy K, Ghaeli N, Imakaev M, Mckenzie-Bennett M, Robison K, Plocik A, Schilling R, Pierson M, Littlefield R, Spencer M, Simen BB, Hanage WP, Grubaugh ND, Peccia J, Baym M. Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification. medRxiv 2021:2021.08.31.21262938. [PMID: 34494031 PMCID: PMC8423229 DOI: 10.1101/2021.08.31.21262938] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Effectively monitoring the spread of SARS-CoV-2 variants is essential to efforts to counter the ongoing pandemic. Wastewater monitoring of SARS-CoV-2 RNA has proven an effective and efficient technique to approximate COVID-19 case rates in the population. Predicting variant abundances from wastewater, however, is technically challenging. Here we show that by sequencing SARS-CoV-2 RNA in wastewater and applying computational techniques initially used for RNA-Seq quantification, we can estimate the abundance of variants in wastewater samples. We show by sequencing samples from wastewater and clinical isolates in Connecticut U.S.A. between January and April 2021 that the temporal dynamics of variant strains broadly correspond. We further show that this technique can be used with other wastewater sequencing techniques by expanding to samples taken across the United States in a similar timeframe. We find high variability in signal among individual samples, and limited ability to detect the presence of variants with clinical frequencies <10%; nevertheless, the overall trends match what we observed from sequencing clinical samples. Thus, while clinical sequencing remains a more sensitive technique for population surveillance, wastewater sequencing can be used to monitor trends in variant prevalence in situations where clinical sequencing is unavailable or impractical.
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Affiliation(s)
- Jasmijn A Baaijens
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Alessandro Zulli
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA
| | - Isabel M Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chaney C Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - William P Hanage
- Center for Communicable Disease Dynamics and Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Jordan Peccia
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA
| | - Michael Baym
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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20
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Mack CD, Tai C, Sikka R, Grad YH, Maragakis LL, Grubaugh ND, Anderson DJ, Ho D, Merson M, Samant RM, Fauver JR, Barrett J, Sims L, DiFiori J. SARS-CoV-2 Reinfection: A Case Series from a 12-Month Longitudinal Occupational Cohort. Clin Infect Dis 2021; 74:1682-1685. [PMID: 34453431 DOI: 10.1093/cid/ciab738] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Indexed: 12/28/2022] Open
Abstract
Seven cases of COVID-19 SARS-CoV-2 reinfection from the NBA 2020-2021 occupational testing cohort are described including clinical details, antibody test results, genomic sequencing, and longitudinal RT-PCR results. Reinfections were infrequent and varied in clinical presentation, viral dynamics, and immune response.
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Affiliation(s)
| | - Caroline Tai
- Real World Solutions, IQVIA Durham, North Carolina, USA
| | - Robby Sikka
- Minnesota Timberwolves, Minneapolis, Minnesota, USA
| | - Yonatan H Grad
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Lisa L Maragakis
- Johns Hopkins University School of Medicine, New Haven, Connecticut, USA
| | - Nathan D Grubaugh
- Yale School of Public Health, Yale University, New Haven, Connecticut, USA
| | - Deverick J Anderson
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Duke University School of Medicine, Durham, North Carolina, USA.,Infection Control Education for Major Sports, LLC, Chapel Hill, NC
| | - David Ho
- Aaron Diamond AIDS Research Center, Columbia University Department of Microbiology and Immunology, New York, New York, USA
| | - Michael Merson
- Global Health Institute, Duke University, Durham, North Carolina, USA
| | | | - Joseph R Fauver
- Yale School of Public Health, Yale University, New Haven, Connecticut, USA
| | - James Barrett
- Family and Preventive Medicine, University of Oklahoma College of Medicine, Oklahoma City, Oklahoma, USA
| | - Leroy Sims
- National Basketball Association, Hospital for Special Surgery, New York, New York, USA
| | - John DiFiori
- National Basketball Association, Hospital for Special Surgery, New York, New York, USA.,Primary Sports Medicine, Hospital for Special Surgery, New York, New York, USA
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21
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Petrone ME, Rothman JE, Breban MI, Ott IM, Russell A, Lasek-Nesselquist E, Kelly K, Omerza G, Renzette N, Watkins AE, Kalinich CC, Alpert T, Brito AF, Earnest R, Tikhonova IR, Castaldi C, Kelly JP, Shudt M, Plitnick J, Schneider E, Murphy S, Neal C, Laszlo E, Altajar A, Pearson C, Muyombwe A, Downing R, Razeq J, Niccolai L, Wilson MS, Anderson ML, Wang J, Liu C, Hui P, Mane S, Taylor BP, Hanage WP, Landry ML, Peaper DR, Bilguvar K, Fauver JR, Vogels CB, Gardner LM, Pitzer VE, St. George K, Adams MD, Grubaugh ND. Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 lineages. medRxiv 2021:2021.07.01.21259859. [PMID: 34230938 PMCID: PMC8259915 DOI: 10.1101/2021.07.01.21259859] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Emerging SARS-CoV-2 variants have shaped the second year of the COVID-19 pandemic and the public health discourse around effective control measures. Evaluating the public health threat posed by a new variant is essential for appropriately adapting response efforts when community transmission is detected. However, this assessment requires that a true comparison can be made between the new variant and its predecessors because factors other than the virus genotype may influence spread and transmission. In this study, we develop a framework that integrates genomic surveillance data to estimate the relative effective reproduction number (R t ) of co-circulating lineages. We use Connecticut, a state in the northeastern United States in which the SARS-CoV-2 variants B.1.1.7 and B.1.526 co-circulated in early 2021, as a case study for implementing this framework. We find that the R t of B.1.1.7 was 6-10% larger than that of B.1.526 in Connecticut in the midst of a COVID-19 vaccination campaign. To assess the generalizability of this framework, we apply it to genomic surveillance data from New York City and observe the same trend. Finally, we use discrete phylogeography to demonstrate that while both variants were introduced into Connecticut at comparable frequencies, clades that resulted from introductions of B.1.1.7 were larger than those resulting from B.1.526 introductions. Our framework, which uses open-source methods requiring minimal computational resources, may be used to monitor near real-time variant dynamics in a myriad of settings.
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Affiliation(s)
- Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Jessica E. Rothman
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Isabel M. Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Alexis Russell
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Erica Lasek-Nesselquist
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | - Kevin Kelly
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Greg Omerza
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Nicholas Renzette
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Anne E. Watkins
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Chaney C. Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Anderson F. Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Irina R. Tikhonova
- Yale Center for Genome Analysis, Yale University, New Haven, CT, 06510, USA
| | | | - John P. Kelly
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Matthew Shudt
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Jonathan Plitnick
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | - Erasmus Schneider
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | | | - Caleb Neal
- Murphy Medical Associates, Greenwich, CT 06830, USA
| | - Eva Laszlo
- Murphy Medical Associates, Greenwich, CT 06830, USA
| | | | - Claire Pearson
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Anthony Muyombwe
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Randy Downing
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Jafar Razeq
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Linda Niccolai
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | | | - Margaret L. Anderson
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Jianhui Wang
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Chen Liu
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Pei Hui
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Shrikant Mane
- Yale Center for Genome Analysis, Yale University, New Haven, CT, 06510, USA
| | - Bradford P. Taylor
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - William P. Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Marie L. Landry
- Departments of Laboratory Medicine and Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - David R. Peaper
- Departments of Laboratory Medicine and Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Kaya Bilguvar
- Yale Center for Genome Analysis, Yale University, New Haven, CT, 06510, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Joseph R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Lauren M. Gardner
- Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore 21218, MD, USA
| | - Virginia E. Pitzer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Kirsten St. George
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | - Mark D. Adams
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06510, USA
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22
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Kupritz J, Martin J, Fischer K, Curtis KC, Fauver JR, Huang Y, Choi YJ, Beatty WL, Mitreva M, Fischer PU. Isolation and characterization of a novel bacteriophage WO from Allonemobius socius crickets in Missouri. PLoS One 2021; 16:e0250051. [PMID: 34197460 PMCID: PMC8248633 DOI: 10.1371/journal.pone.0250051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/15/2021] [Indexed: 11/19/2022] Open
Abstract
Wolbachia are endosymbionts of numerous arthropod and some nematode species, are important for their development and if present can cause distinct phenotypes of their hosts. Prophage DNA has been frequently detected in Wolbachia, but particles of Wolbachia bacteriophages (phage WO) have been only occasionally isolated. Here, we report the characterization and isolation of a phage WO of the southern ground cricket, Allonemobius socius, and provided the first whole-genome sequence of phage WO from this arthropod family outside of Asia. We screened A. socius abdomen DNA extracts from a cricket population in eastern Missouri by quantitative PCR for Wolbachia surface protein and phage WO capsid protein and found a prevalence of 55% and 50%, respectively, with many crickets positive for both. Immunohistochemistry using antibodies against Wolbachia surface protein showed many Wolbachia clusters in the reproductive system of female crickets. Whole-genome sequencing using Oxford Nanopore MinION and Illumina technology allowed for the assembly of a high-quality, 55 kb phage genome containing 63 open reading frames (ORF) encoding for phage WO structural proteins and host lysis and transcriptional manipulation. Taxonomically important regions of the assembled phage genome were validated by Sanger sequencing of PCR amplicons. Analysis of the nucleotides sequences of the ORFs encoding the large terminase subunit (ORF2) and minor capsid (ORF7) frequently used for phage WO phylogenetics showed highest homology to phage WOAu of Drosophila simulans (94.46% identity) and WOCin2USA1 of the cherry fruit fly, Rhagoletis cingulata (99.33% identity), respectively. Transmission electron microscopy examination of cricket ovaries showed a high density of phage particles within Wolbachia cells. Isolation of phage WO revealed particles characterized by 40–62 nm diameter heads and up to 190 nm long tails. This study provides the first detailed description and genomic characterization of phage WO from North America that is easily accessible in a widely distributed cricket species.
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Affiliation(s)
- Jonah Kupritz
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - John Martin
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kerstin Fischer
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kurt C. Curtis
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Joseph R. Fauver
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Yuefang Huang
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Young-Jun Choi
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Wandy L. Beatty
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Makedonka Mitreva
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Peter U. Fischer
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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23
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Kissler SM, Fauver JR, Mack C, Olesen SW, Tai C, Shiue KY, Kalinich CC, Jednak S, Ott IM, Vogels CBF, Wohlgemuth J, Weisberger J, DiFiori J, Anderson DJ, Mancell J, Ho DD, Grubaugh ND, Grad YH. Viral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategies. PLoS Biol 2021; 19:e3001333. [PMID: 34252080 PMCID: PMC8297933 DOI: 10.1371/journal.pbio.3001333] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 07/22/2021] [Accepted: 06/21/2021] [Indexed: 02/04/2023] Open
Abstract
SARS-CoV-2 infections are characterized by viral proliferation and clearance phases and can be followed by low-level persistent viral RNA shedding. The dynamics of viral RNA concentration, particularly in the early stages of infection, can inform clinical measures and interventions such as test-based screening. We used prospective longitudinal quantitative reverse transcription PCR testing to measure the viral RNA trajectories for 68 individuals during the resumption of the 2019-2020 National Basketball Association season. For 46 individuals with acute infections, we inferred the peak viral concentration and the duration of the viral proliferation and clearance phases. According to our mathematical model, we found that viral RNA concentrations peaked an average of 3.3 days (95% credible interval [CI] 2.5, 4.2) after first possible detectability at a cycle threshold value of 22.3 (95% CI 20.5, 23.9). The viral clearance phase lasted longer for symptomatic individuals (10.9 days [95% CI 7.9, 14.4]) than for asymptomatic individuals (7.8 days [95% CI 6.1, 9.7]). A second test within 2 days after an initial positive PCR test substantially improves certainty about a patient's infection stage. The effective sensitivity of a test intended to identify infectious individuals declines substantially with test turnaround time. These findings indicate that SARS-CoV-2 viral concentrations peak rapidly regardless of symptoms. Sequential tests can help reveal a patient's progress through infection stages. Frequent, rapid-turnaround testing is needed to effectively screen individuals before they become infectious.
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Affiliation(s)
- Stephen M. Kissler
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Joseph R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Christina Mack
- Real World Solutions, IQVIA, Durham, North Carolina, United States of America
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Scott W. Olesen
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Caroline Tai
- Real World Solutions, IQVIA, Durham, North Carolina, United States of America
| | - Kristin Y. Shiue
- Real World Solutions, IQVIA, Durham, North Carolina, United States of America
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Chaney C. Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Sarah Jednak
- Department of Health Management and Policy, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Isabel M. Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Chantal B. F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Jay Wohlgemuth
- Quest Diagnostics, San Juan Capistrano, California, United States of America
| | - James Weisberger
- Bioreference Laboratories, Elmwood Park, New Jersey, United States of America
| | - John DiFiori
- Hospital for Special Surgery, New York, New York, United States of America
- National Basketball Association, New York, New York, United States of America
| | - Deverick J. Anderson
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Durham, North Carolina, United States of America
| | - Jimmie Mancell
- Department of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - David D. Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, United States of America
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Yonatan H. Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
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24
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Abstract
Genomic sequencing is crucial to understanding the epidemiology and evolution of SARS-CoV-2. Often, genomic studies rely on remnant diagnostic material, typically nasopharyngeal swabs, as input into whole genome SARS-CoV-2 next-generation sequencing pipelines. Saliva has proven to be a safe and stable specimen for the detection of SARS-CoV-2 RNA via traditional diagnostic assays, however saliva is not commonly used for SARS-CoV-2 sequencing. Using the ARTIC Network amplicon-generation approach with sequencing on the Oxford Nanopore MinION, we demonstrate that sequencing SARS-CoV-2 from saliva produces genomes comparable to those from nasopharyngeal swabs, and that RNA extraction is necessary to generate complete genomes from saliva. In this study, we show that saliva is a useful specimen type for genomic studies of SARS-CoV-2.
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Affiliation(s)
- Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | | | - Anne L. Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06510, USA
| | - Joseph R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
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25
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Vogels CBF, Breban MI, Ott IM, Alpert T, Petrone ME, Watkins AE, Kalinich CC, Earnest R, Rothman JE, Goes de Jesus J, Morales Claro I, Magalhães Ferreira G, Crispim MAE, Singh L, Tegally H, Anyaneji UJ, Hodcroft EB, Mason CE, Khullar G, Metti J, Dudley JT, MacKay MJ, Nash M, Wang J, Liu C, Hui P, Murphy S, Neal C, Laszlo E, Landry ML, Muyombwe A, Downing R, Razeq J, de Oliveira T, Faria NR, Sabino EC, Neher RA, Fauver JR, Grubaugh ND. Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2. PLoS Biol 2021; 19:e3001236. [PMID: 33961632 PMCID: PMC8133773 DOI: 10.1371/journal.pbio.3001236] [Citation(s) in RCA: 156] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/19/2021] [Accepted: 04/16/2021] [Indexed: 12/25/2022] Open
Abstract
With the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants that may increase transmissibility and/or cause escape from immune responses, there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) variant, first detected in the United Kingdom, could be serendipitously detected by the Thermo Fisher TaqPath COVID-19 PCR assay because a key deletion in these viruses, spike Δ69-70, would cause a "spike gene target failure" (SGTF) result. However, a SGTF result is not definitive for B.1.1.7, and this assay cannot detect other variants of concern (VOC) that lack spike Δ69-70, such as B.1.351 (also 501Y.V2), detected in South Africa, and P.1 (also 501Y.V3), recently detected in Brazil. We identified a deletion in the ORF1a gene (ORF1a Δ3675-3677) in all 3 variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Δ3675-3677 as the primary target and spike Δ69-70 to differentiate, we designed and validated an open-source PCR assay to detect SARS-CoV-2 VOC. Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence and spread of B.1.1.7, B.1.351, and P.1.
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Affiliation(s)
- Chantal B. F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Isabel M. Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Anne E. Watkins
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Chaney C. Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Jessica E. Rothman
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Jaqueline Goes de Jesus
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ingra Morales Claro
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Giulia Magalhães Ferreira
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Virologia, Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Myuki A. E. Crispim
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | | | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ugochukwu J. Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | - Emma B. Hodcroft
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | | | - Gaurav Khullar
- Tempus Labs, Chicago, Illinois, United States of America
| | - Jessica Metti
- Tempus Labs, Chicago, Illinois, United States of America
| | - Joel T. Dudley
- Tempus Labs, Chicago, Illinois, United States of America
| | | | - Megan Nash
- Tempus Labs, Chicago, Illinois, United States of America
| | - Jianhui Wang
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Chen Liu
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Pei Hui
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Steven Murphy
- Murphy Medical Associates, Greenwich, Connecticut, United States of America
| | - Caleb Neal
- Murphy Medical Associates, Greenwich, Connecticut, United States of America
| | - Eva Laszlo
- Murphy Medical Associates, Greenwich, Connecticut, United States of America
| | - Marie L. Landry
- Departments of Laboratory Medicine and Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Anthony Muyombwe
- Connecticut State Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Randy Downing
- Connecticut State Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Jafar Razeq
- Connecticut State Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nuno R. Faria
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Ester C. Sabino
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Richard A. Neher
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joseph R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
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26
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Alpert T, Brito AF, Lasek-Nesselquist E, Rothman J, Valesano AL, MacKay MJ, Petrone ME, Breban MI, Watkins AE, Vogels CBF, Kalinich CC, Dellicour S, Russell A, Kelly JP, Shudt M, Plitnick J, Schneider E, Fitzsimmons WJ, Khullar G, Metti J, Dudley JT, Nash M, Beaubier N, Wang J, Liu C, Hui P, Muyombwe A, Downing R, Razeq J, Bart SM, Grills A, Morrison SM, Murphy S, Neal C, Laszlo E, Rennert H, Cushing M, Westblade L, Velu P, Craney A, Cong L, Peaper DR, Landry ML, Cook PW, Fauver JR, Mason CE, Lauring AS, St George K, MacCannell DR, Grubaugh ND. Early introductions and transmission of SARS-CoV-2 variant B.1.1.7 in the United States. Cell 2021; 184:2595-2604.e13. [PMID: 33891875 PMCID: PMC8018830 DOI: 10.1016/j.cell.2021.03.061] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/10/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023]
Abstract
The emergence and spread of SARS-CoV-2 lineage B.1.1.7, first detected in the United Kingdom, has become a global public health concern because of its increased transmissibility. Over 2,500 COVID-19 cases associated with this variant have been detected in the United States (US) since December 2020, but the extent of establishment is relatively unknown. Using travel, genomic, and diagnostic data, we highlight that the primary ports of entry for B.1.1.7 in the US were in New York, California, and Florida. Furthermore, we found evidence for many independent B.1.1.7 establishments starting in early December 2020, followed by interstate spread by the end of the month. Finally, we project that B.1.1.7 will be the dominant lineage in many states by mid- to late March. Thus, genomic surveillance for B.1.1.7 and other variants urgently needs to be enhanced to better inform the public health response.
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Affiliation(s)
- Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Anderson F Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Erica Lasek-Nesselquist
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA; Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | - Jessica Rothman
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Andrew L Valesano
- Department of Internal Medicine, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Anne E Watkins
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Chaney C Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium; Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Alexis Russell
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - John P Kelly
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Matthew Shudt
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA; Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | - Jonathan Plitnick
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA; Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | - Erasmus Schneider
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA; Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | - William J Fitzsimmons
- Department of Internal Medicine, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | | | | | | | | | - Jianhui Wang
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Chen Liu
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Pei Hui
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Anthony Muyombwe
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Randy Downing
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Jafar Razeq
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Stephen M Bart
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA; Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Ardath Grills
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | | | | | - Caleb Neal
- Murphy Medical Associates, Greenwich, CT 06830, USA
| | - Eva Laszlo
- Murphy Medical Associates, Greenwich, CT 06830, USA
| | - Hanna Rennert
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA
| | - Melissa Cushing
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA
| | - Lars Westblade
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA
| | - Priya Velu
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA
| | - Arryn Craney
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA
| | - Lin Cong
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA
| | - David R Peaper
- Departments of Laboratory Medicine and of Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Marie L Landry
- Departments of Laboratory Medicine and of Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Peter W Cook
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Christopher E Mason
- Tempus Labs, Chicago, IL 60654, USA; Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA
| | - Adam S Lauring
- Department of Internal Medicine, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kirsten St George
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA; Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, USA.
| | | | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06510, USA.
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27
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Klein J, Brito AF, Trubin P, Lu P, Wong P, Alpert T, Peña-Hernández MA, Haynes W, Kamath K, Liu F, Vogels CBF, Fauver JR, Lucas C, Oh J, Mao T, Silva J, Wyllie AL, Muenker MC, Casanovas-Massana A, Moore AJ, Petrone ME, Kalinich CC, Cruz CD, Farhadian S, Ring A, Shon J, Ko AI, Grubaugh ND, Israelow B, Iwasaki A, Azar MM. Case Study: Longitudinal immune profiling of a SARS-CoV-2 reinfection in a solid organ transplant recipient. medRxiv 2021. [PMID: 33791729 DOI: 10.1101/2021.03.24.21253992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Prior to the emergence of antigenically distinct SARS-CoV-2 variants, reinfections were reported infrequently - presumably due to the generation of durable and protective immune responses. However, case reports also suggested that rare, repeated infections may occur as soon as 48 days following initial disease onset. The underlying immunologic deficiencies enabling SARS-CoV-2 reinfections are currently unknown. Here we describe a renal transplant recipient who developed recurrent, symptomatic SARS-CoV-2 infection - confirmed by whole virus genome sequencing - 7 months after primary infection. To elucidate the immunological mechanisms responsible for SARS-CoV-2 reinfection, we performed longitudinal profiling of cellular and humoral responses during both primary and recurrent SARS-CoV-2 infection. We found that the patient responded to the primary infection with transient, poor-quality adaptive immune responses. The patient's immune system was further compromised by intervening treatment for acute rejection of the renal allograft prior to reinfection. Importantly, we also identified the development of neutralizing antibodies and the formation of humoral memory responses prior to SARS-CoV-2 reinfection. However, these neutralizing antibodies failed to confer protection against reinfection, suggesting that additional factors are required for efficient prevention of SARS-CoV-2 reinfection. Further, we found no evidence supporting viral evasion of primary adaptive immune responses, suggesting that susceptibility to reinfection may be determined by host factors rather than pathogen adaptation in this patient. In summary, our study suggests that a low neutralizing antibody presence alone is not sufficient to confer resistance against reinfection. Thus, patients with solid organ transplantation, or patients who are otherwise immunosuppressed, who recover from infection with SARS-CoV-2 may not develop sufficient protective immunity and are at risk of reinfection.
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28
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Vogels CB, Breban MI, Alpert T, Petrone ME, Watkins AE, Ott IM, de Jesus JG, Claro IM, Ferreira GM, Crispim MA, Singh L, Tegally H, Anyaneji UJ, Hodcroft EB, Mason CE, Khullar G, Metti J, Dudley JT, MacKay MJ, Nash M, Wang J, Liu C, Hui P, Murphy S, Neal C, Laszlo E, Landry ML, Muyombwe A, Downing R, Razeq J, de Oliveira T, Faria NR, Sabino EC, Neher RA, Fauver JR, Grubaugh ND. PCR assay to enhance global surveillance for SARS-CoV-2 variants of concern. medRxiv 2021:2021.01.28.21250486. [PMID: 33758901 PMCID: PMC7987060 DOI: 10.1101/2021.01.28.21250486] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
With the emergence of SARS-CoV-2 variants that may increase transmissibility and/or cause escape from immune responses 1-3 , there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) variant first detected in the UK 4,5 could be serendipitously detected by the ThermoFisher TaqPath COVID-19 PCR assay because a key deletion in these viruses, spike Δ69-70, would cause a "spike gene target failure" (SGTF) result. However, a SGTF result is not definitive for B.1.1.7, and this assay cannot detect other variants of concern that lack spike Δ69-70, such as B.1.351 (also 501Y.V2) detected in South Africa 6 and P.1 (also 501Y.V3) recently detected in Brazil 7 . We identified a deletion in the ORF1a gene (ORF1a Δ3675-3677) in all three variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Δ3675-3677 as the primary target and spike Δ69-70 to differentiate, we designed and validated an open source PCR assay to detect SARS-CoV-2 variants of concern 8 . Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence spread of B.1.1.7, B.1.351, and P.1.
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Affiliation(s)
- Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Anne E. Watkins
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Isabel M. Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Jaqueline Goes de Jesus
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP 05403–000, Brazil
| | - Ingra Morales Claro
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP 05403–000, Brazil
| | - Giulia Magalhães Ferreira
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP 05403–000, Brazil
- Laboratório de Virologia, Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Myuki A.E. Crispim
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | | | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ugochukwu J. Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | - Emma B. Hodcroft
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | | | | | | | | | | | | | - Jianhui Wang
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Chen Liu
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Pei Hui
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | | | - Caleb Neal
- Murphy Medical Associates, Greenwich, CT 06614, USA
| | - Eva Laszlo
- Murphy Medical Associates, Greenwich, CT 06614, USA
| | - Marie L. Landry
- Departments of Laboratory Medicine and Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Anthony Muyombwe
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Randy Downing
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Jafar Razeq
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nuno R. Faria
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP 05403–000, Brazil
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
- Department of Zoology, University of Oxford, Oxford, UK
| | - Ester C. Sabino
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP 05403–000, Brazil
| | - Richard A. Neher
- Biozentrum, University of Basel, 4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Joseph R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06510, USA
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29
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Alpert T, Brito AF, Lasek-Nesselquist E, Rothman J, Valesano AL, MacKay MJ, Petrone ME, Breban MI, Watkins AE, Vogels CB, Kalinich CC, Dellicour S, Russell A, Kelly JP, Shudt M, Plitnick J, Schneider E, Fitzsimmons WJ, Khullar G, Metti J, Dudley JT, Nash M, Beaubier N, Wang J, Liu C, Hui P, Muyombwe A, Downing R, Razeq J, Bart SM, Grills A, Morrison SM, Murphy S, Neal C, Laszlo E, Rennert H, Cushing M, Westblade L, Velu P, Craney A, Fauntleroy KA, Peaper DR, Landry ML, Cook PW, Fauver JR, Mason CE, Lauring AS, George KS, MacCannell DR, Grubaugh ND. Early introductions and community transmission of SARS-CoV-2 variant B.1.1.7 in the United States. medRxiv 2021:2021.02.10.21251540. [PMID: 33594373 PMCID: PMC7885932 DOI: 10.1101/2021.02.10.21251540] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The emergence and spread of SARS-CoV-2 lineage B.1.1.7, first detected in the United Kingdom, has become a global public health concern because of its increased transmissibility. Over 2500 COVID-19 cases associated with this variant have been detected in the US since December 2020, but the extent of establishment is relatively unknown. Using travel, genomic, and diagnostic data, we highlight the primary ports of entry for B.1.1.7 in the US and locations of possible underreporting of B.1.1.7 cases. Furthermore, we found evidence for many independent B.1.1.7 establishments starting in early December 2020, followed by interstate spread by the end of the month. Finally, we project that B.1.1.7 will be the dominant lineage in many states by mid to late March. Thus, genomic surveillance for B.1.1.7 and other variants urgently needs to be enhanced to better inform the public health response.
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Affiliation(s)
- Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Anderson F. Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Erica Lasek-Nesselquist
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | - Jessica Rothman
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Andrew L. Valesano
- Department of Internal Medicine, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Anne E. Watkins
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Chaney C. Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Alexis Russell
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - John P. Kelly
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Matthew Shudt
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | - Jonathan Plitnick
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | - Erasmus Schneider
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | - William J. Fitzsimmons
- Department of Internal Medicine, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | | | | | | | | | - Jianhui Wang
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Chen Liu
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Pei Hui
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Anthony Muyombwe
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Randy Downing
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Jafar Razeq
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Stephen M. Bart
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Ardath Grills
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | | | | | - Caleb Neal
- Murphy Medical Associates, Greenwich, CT 06830, USA
| | - Eva Laszlo
- Murphy Medical Associates, Greenwich, CT 06830, USA
| | - Hanna Rennert
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA
| | - Melissa Cushing
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA
| | - Lars Westblade
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA
| | - Priya Velu
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA
| | - Arryn Craney
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA
| | - Kathy A. Fauntleroy
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA
| | - David R. Peaper
- Departments of Laboratory Medicine and Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Marie L. Landry
- Departments of Laboratory Medicine and Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Peter W. Cook
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Joseph R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Christopher E. Mason
- Tempus Labs, Chicago, IL 60654, USA
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA
| | - Adam S. Lauring
- Department of Internal Medicine, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kirsten St. George
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | | | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06510, USA
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30
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Pollett S, Fauver JR, Maljkovic Berry I, Melendrez M, Morrison A, Gillis LD, Johansson MA, Jarman RG, Grubaugh ND. Genomic Epidemiology as a Public Health Tool to Combat Mosquito-Borne Virus Outbreaks. J Infect Dis 2021; 221:S308-S318. [PMID: 31711190 DOI: 10.1093/infdis/jiz302] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing technologies, exponential increases in the availability of virus genomic data, and ongoing advances in phylogenomic methods have made genomic epidemiology an increasingly powerful tool for public health response to a range of mosquito-borne virus outbreaks. In this review, we offer a brief primer on the scope and methods of phylogenomic analyses that can answer key epidemiological questions during mosquito-borne virus public health emergencies. We then focus on case examples of outbreaks, including those caused by dengue, Zika, yellow fever, West Nile, and chikungunya viruses, to demonstrate the utility of genomic epidemiology to support the prevention and control of mosquito-borne virus threats. We extend these case studies with operational perspectives on how to best incorporate genomic epidemiology into structured surveillance and response programs for mosquito-borne virus control. Many tools for genomic epidemiology already exist, but so do technical and nontechnical challenges to advancing their use. Frameworks to support the rapid sharing of multidimensional data and increased cross-sector partnerships, networks, and collaborations can support advancement on all scales, from research and development to implementation by public health agencies.
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Affiliation(s)
- S Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland.,Department of Preventive Medicine and Biostatistics, Uniformed Services University, Bethesda, Maryland.,Marie Bashir Institute, University of Sydney, Camperdown, New South Wales, Australia
| | - J R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut.,Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | | | | | - L D Gillis
- Bureau of Public Health Laboratories-Miami, Florida Department of Health, San Juan, Puerto Rico
| | - M A Johansson
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - R G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - N D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut
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31
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Abstract
Recent reports suggest that some SARS-CoV-2 genetic variants, such as B.1.1.7, might be more transmissible and are quickly spreading around the world. As the emergence of more transmissible variants could exacerbate the pandemic, we provide public health guidance for increased surveillance and measures to reduce community transmission.
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Affiliation(s)
- Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA; Yale Institute for Global Health, Yale University, New Haven, CT, USA
| | - Emma B Hodcroft
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
| | - Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
| | - Alexandra L Phelan
- Center for Global Health Science and Security, Georgetown University, Washington, DC, USA; O'Neill Institute for National and Global Health Law, Georgetown University Law Center, Washington, DC, USA.
| | - Muge Cevik
- Division of Infection and Global Health Research, School of Medicine, University of St Andrews, Fife, UK
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32
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Vogels CBF, Watkins AE, Harden CA, Brackney DE, Shafer J, Wang J, Caraballo C, Kalinich CC, Ott IM, Fauver JR, Kudo E, Lu P, Venkataraman A, Tokuyama M, Moore AJ, Muenker MC, Casanovas-Massana A, Fournier J, Bermejo S, Campbell M, Datta R, Nelson A, Dela Cruz CS, Ko AI, Iwasaki A, Krumholz HM, Matheus JD, Hui P, Liu C, Farhadian SF, Sikka R, Wyllie AL, Grubaugh ND. SalivaDirect: A simplified and flexible platform to enhance SARS-CoV-2 testing capacity. Med (N Y) 2020; 2:263-280.e6. [PMID: 33521748 PMCID: PMC7836249 DOI: 10.1016/j.medj.2020.12.010] [Citation(s) in RCA: 192] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/14/2020] [Accepted: 12/21/2020] [Indexed: 01/15/2023]
Abstract
Background Scaling SARS-CoV-2 testing to meet demands of safe reopenings continues to be plagued by assay costs and supply chain shortages. In response, we developed SalivaDirect, which received Emergency Use Authorization (EUA) from the U.S. Food and Drug Administration (FDA). Methods We simplified our saliva-based diagnostic test by (1) not requiring collection tubes with preservatives, (2) replacing nucleic acid extraction with a simple enzymatic and heating step, and (3) testing specimens with a dualplex qRT-PCR assay. Moreover, we validated SalivaDirect with reagents and instruments from multiple vendors to minimize supply chain issues. Findings From our hospital cohort, we show a high positive agreement (94%) between saliva tested with SalivaDirect and nasopharyngeal swabs tested with a commercial qRT-PCR kit. In partnership with the National Basketball Association (NBA) and National Basketball Players Association (NBPA), we tested 3,779 saliva specimens from healthy individuals and detected low rates of invalid (0.3%) and false-positive (<0.05%) results. Conclusions We demonstrate that saliva is a valid alternative to swabs for SARS-CoV-2 screening and that SalivaDirect can make large-scale testing more accessible and affordable. Uniquely, we can designate other laboratories to use our sensitive, flexible, and simplified platform under our EUA (https://publichealth.yale.edu/salivadirect/). Funding This study was funded by the NBA and NBPA (N.D.G.), the Huffman Family Donor Advised Fund (N.D.G.), a Fast Grant from Emergent Ventures at the Mercatus Center at George Mason University (N.D.G.), the Yale Institute for Global Health (N.D.G.), and the Beatrice Kleinberg Neuwirth Fund (A.I.K.). C.B.F.V. is supported by NWO Rubicon 019.181EN.004. Frequent testing is critical to limit SARS-CoV-2 transmission. In response to this need, we developed SalivaDirect, a sensitive, simplified, and flexible testing framework, which received Emergency Use Authorization (EUA) from the U.S. Food and Drug Administration (FDA). We tested saliva collected from a hospital cohort and showed a high positive agreement (94%) as compared to paired nasopharyngeal swabs tested with a commercial diagnostic kit. Then, we partnered with the National Basketball Association (NBA) to test a large cohort of mostly healthy individuals, and we detected low rates of invalid (0.3%) and false-positive (0.03%–0.05%) results. Our study shows that SalivaDirect can help to increase testing capacity by providing access to an affordable framework that is less prone to supply chain shortages.
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Affiliation(s)
- Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Anne E Watkins
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Christina A Harden
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Doug E Brackney
- Connecticut Agricultural Experimental Station, State of Connecticut, New Haven, CT 06511, USA
| | - Jared Shafer
- Drug Free Sport International, Kansas City, MO 64108, USA
| | - Jianhui Wang
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - César Caraballo
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, CT 06510, USA.,Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Chaney C Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Isabel M Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Eriko Kudo
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Peiwen Lu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Arvind Venkataraman
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Maria Tokuyama
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Adam J Moore
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - M Catherine Muenker
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - John Fournier
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Santos Bermejo
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Melissa Campbell
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Rupak Datta
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Allison Nelson
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | | | - Charles S Dela Cruz
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Harlan M Krumholz
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, CT 06510, USA.,Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - J D Matheus
- Drug Free Sport International, Kansas City, MO 64108, USA
| | - Pei Hui
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Chen Liu
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Shelli F Farhadian
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Robby Sikka
- Minnesota Timberwolves, Minneapolis, MN 55403, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
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Vogels CBF, Brito AF, Wyllie AL, Fauver JR, Ott IM, Kalinich CC, Petrone ME, Casanovas-Massana A, Catherine Muenker M, Moore AJ, Klein J, Lu P, Lu-Culligan A, Jiang X, Kim DJ, Kudo E, Mao T, Moriyama M, Oh JE, Park A, Silva J, Song E, Takahashi T, Taura M, Tokuyama M, Venkataraman A, Weizman OE, Wong P, Yang Y, Cheemarla NR, White EB, Lapidus S, Earnest R, Geng B, Vijayakumar P, Odio C, Fournier J, Bermejo S, Farhadian S, Dela Cruz CS, Iwasaki A, Ko AI, Landry ML, Foxman EF, Grubaugh ND. Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT-qPCR primer-probe sets. Nat Microbiol 2020. [PMID: 32651556 DOI: 10.1101/2020.03.30.20048108] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The recent spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exemplifies the critical need for accurate and rapid diagnostic assays to prompt clinical and public health interventions. Currently, several quantitative reverse transcription-PCR (RT-qPCR) assays are being used by clinical, research and public health laboratories. However, it is currently unclear whether results from different tests are comparable. Our goal was to make independent evaluations of primer-probe sets used in four common SARS-CoV-2 diagnostic assays. From our comparisons of RT-qPCR analytical efficiency and sensitivity, we show that all primer-probe sets can be used to detect SARS-CoV-2 at 500 viral RNA copies per reaction. The exception for this is the RdRp-SARSr (Charité) confirmatory primer-probe set which has low sensitivity, probably due to a mismatch to circulating SARS-CoV-2 in the reverse primer. We did not find evidence for background amplification with pre-COVID-19 samples or recent SARS-CoV-2 evolution decreasing sensitivity. Our recommendation for SARS-CoV-2 diagnostic testing is to select an assay with high sensitivity and that is regionally used, to ease comparability between outcomes.
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Affiliation(s)
- Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
| | - Anderson F Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Isabel M Ott
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Chaney C Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - M Catherine Muenker
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Adam J Moore
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Jonathan Klein
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Peiwen Lu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Alice Lu-Culligan
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Xiaodong Jiang
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Daniel J Kim
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Eriko Kudo
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Tianyang Mao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Miyu Moriyama
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Ji Eun Oh
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Annsea Park
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Julio Silva
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Eric Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Takehiro Takahashi
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Manabu Taura
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Maria Tokuyama
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Arvind Venkataraman
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Orr-El Weizman
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Patrick Wong
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Yexin Yang
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Nagarjuna R Cheemarla
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Elizabeth B White
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Sarah Lapidus
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Bertie Geng
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA
| | - Pavithra Vijayakumar
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA
| | - Camila Odio
- Department of Medicine, Northeast Medical Group, Yale-New Haven Health, New Haven, CT, USA
| | - John Fournier
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Santos Bermejo
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Shelli Farhadian
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Charles S Dela Cruz
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Marie L Landry
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
- Clinical Virology Laboratory, Yale-New Haven Hospital, New Haven, CT, USA
| | - Ellen F Foxman
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
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Hosier H, Farhadian SF, Morotti RA, Deshmukh U, Lu-Culligan A, Campbell KH, Yasumoto Y, Vogels CB, Casanovas-Massana A, Vijayakumar P, Geng B, Odio CD, Fournier J, Brito AF, Fauver JR, Liu F, Alpert T, Tal R, Szigeti-Buck K, Perincheri S, Larsen C, Gariepy AM, Aguilar G, Fardelmann KL, Harigopal M, Taylor HS, Pettker CM, Wyllie AL, Cruz CD, Ring AM, Grubaugh ND, Ko AI, Horvath TL, Iwasaki A, Reddy UM, Lipkind HS. SARS-CoV-2 infection of the placenta. J Clin Invest 2020; 130:4947-4953. [PMID: 32573498 PMCID: PMC7456249 DOI: 10.1172/jci139569] [Citation(s) in RCA: 318] [Impact Index Per Article: 79.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/10/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUNDThe effects of the novel coronavirus disease 2019 (COVID-19) in pregnancy remain relatively unknown. We present a case of second trimester pregnancy with symptomatic COVID-19 complicated by severe preeclampsia and placental abruption.METHODSWe analyzed the placenta for the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through molecular and immunohistochemical assays and by and electron microscopy and measured the maternal antibody response in the blood to this infection.RESULTSSARS-CoV-2 localized predominantly to syncytiotrophoblast cells at the materno-fetal interface of the placenta. Histological examination of the placenta revealed a dense macrophage infiltrate, but no evidence for the vasculopathy typically associated with preeclampsia.CONCLUSIONThis case demonstrates SARS-CoV-2 invasion of the placenta, highlighting the potential for severe morbidity among pregnant women with COVID-19.FUNDINGBeatrice Kleinberg Neuwirth Fund and Fast Grant Emergent Ventures funding from the Mercatus Center at George Mason University. The funding bodies did not have roles in the design of the study or data collection, analysis, and interpretation and played no role in writing the manuscript.
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MESH Headings
- Abortion, Therapeutic
- Abruptio Placentae/etiology
- Abruptio Placentae/pathology
- Abruptio Placentae/virology
- Adult
- Betacoronavirus/genetics
- Betacoronavirus/isolation & purification
- Betacoronavirus/pathogenicity
- COVID-19
- Coronavirus Infections/complications
- Coronavirus Infections/pathology
- Coronavirus Infections/virology
- Female
- Humans
- Microscopy, Electron, Transmission
- Pandemics
- Phylogeny
- Placenta/pathology
- Placenta/virology
- Pneumonia, Viral/complications
- Pneumonia, Viral/pathology
- Pneumonia, Viral/virology
- Pre-Eclampsia/etiology
- Pre-Eclampsia/pathology
- Pre-Eclampsia/virology
- Pregnancy
- Pregnancy Complications, Infectious/etiology
- Pregnancy Complications, Infectious/pathology
- Pregnancy Complications, Infectious/virology
- Pregnancy Trimester, Second
- RNA, Viral/genetics
- RNA, Viral/isolation & purification
- SARS-CoV-2
- Viral Load
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Affiliation(s)
- Hillary Hosier
- Department of Obstetrics, Gynecology, and Reproductive Sciences
| | | | | | - Uma Deshmukh
- Department of Obstetrics, Gynecology, and Reproductive Sciences
| | | | | | - Yuki Yasumoto
- Department of Comparative Medicine, Yale School of Medicine
| | - Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, and
| | | | | | - Bertie Geng
- Department of Obstetrics, Gynecology, and Reproductive Sciences
| | | | - John Fournier
- Section of Infectious Diseases, Department of Medicine
| | - Anderson F. Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, and
| | - Joseph R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, and
| | | | - Tara Alpert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Reshef Tal
- Department of Obstetrics, Gynecology, and Reproductive Sciences
| | | | | | | | | | | | | | | | - Hugh S. Taylor
- Department of Obstetrics, Gynecology, and Reproductive Sciences
| | | | - Anne L. Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, and
| | - Charles Dela Cruz
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | | | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, and
| | - Albert I. Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, and
| | | | | | - Uma M. Reddy
- Department of Obstetrics, Gynecology, and Reproductive Sciences
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35
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Kalinich CC, Jensen CG, Neugebauer P, Petrone ME, Peña-Hernández M, Ott IM, Wyllie AL, Alpert T, Vogels CBF, Fauver JR, Grubaugh ND, Brito AF. Real-time public health communication of local SARS-CoV-2 genomic epidemiology. PLoS Biol 2020; 18:e3000869. [PMID: 32822393 PMCID: PMC7467297 DOI: 10.1371/journal.pbio.3000869] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/02/2020] [Indexed: 01/20/2023] Open
Abstract
Genomic epidemiology can provide a unique, real-time understanding of SARS-CoV-2 transmission patterns. Yet the potential for genomic analyses to guide local policy and community-based behavioral decisions is limited because they are often oriented towards specially trained scientists and conducted on a national or global scale. Here, we propose a new paradigm: Phylogenetic analyses performed on a local level (municipal, county, or state), with results communicated in a clear, timely, and actionable manner to strengthen public health responses. We believe that presenting results rapidly, and tailored to a non-expert audience, can serve as a template for effective public health response to COVID-19 and other emerging viral diseases.
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Affiliation(s)
- Chaney C. Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Cole G. Jensen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Peter Neugebauer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Mario Peña-Hernández
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Isabel M. Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Anne L. Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Chantal B. F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Joseph R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Anderson F. Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
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36
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Farhadian S, Glick LR, Vogels CBF, Thomas J, Chiarella J, Casanovas-Massana A, Zhou J, Odio C, Vijayakumar P, Geng B, Fournier J, Bermejo S, Fauver JR, Alpert T, Wyllie AL, Turcotte C, Steinle M, Paczkowski P, Dela Cruz C, Wilen C, Ko AI, MacKay S, Grubaugh ND, Spudich S, Barakat LA. Acute encephalopathy with elevated CSF inflammatory markers as the initial presentation of COVID-19. BMC Neurol 2020; 20:248. [PMID: 32552792 PMCID: PMC7301053 DOI: 10.1186/s12883-020-01812-2] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/01/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND COVID-19 is caused by the severe acute respiratory syndrome virus SARS-CoV-2. It is widely recognized as a respiratory pathogen, but neurologic complications can be the presenting manifestation in a subset of infected patients. CASE PRESENTATION We describe a 78-year old immunocompromised woman who presented with altered mental status after witnessed seizure-like activity at home. She was found to have SARS-CoV-2 infection and associated neuroinflammation. In this case, we undertake the first detailed analysis of cerebrospinal fluid (CSF) cytokines during COVID-19 infection and find a unique pattern of inflammation in CSF, but no evidence of viral neuroinvasion. CONCLUSION Our findings suggest that neurologic symptoms such as encephalopathy and seizures may be the initial presentation of COVID-19. Central nervous system inflammation may associate with neurologic manifestations of disease.
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Affiliation(s)
- Shelli Farhadian
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA.
- Department of Neurology, Yale School of Medicine, New Haven, CT, 06510, USA.
| | - Laura R Glick
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Jared Thomas
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Jennifer Chiarella
- Department of Neurology, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | | | - Camila Odio
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Pavithra Vijayakumar
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Bertie Geng
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06510, USA
| | - John Fournier
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Santos Bermejo
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | | | | | | | - Charles Dela Cruz
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Craig Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Albert I Ko
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | | | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Serena Spudich
- Department of Neurology, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Lydia Aoun Barakat
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA
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Cheemarla NR, Brito AF, Fauver JR, Alpert T, Vogels CB, Omer SB, Ko A, Grubaugh ND, Landry ML, Foxman EF. Host response-based screening to identify undiagnosed cases of COVID-19 and expand testing capacity. medRxiv 2020:2020.06.04.20109306. [PMID: 32577694 PMCID: PMC7302303 DOI: 10.1101/2020.06.04.20109306] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The COVID-19 pandemic has created unprecedented challenges in diagnostic testing. At the beginning of the epidemic, a confluence of factors resulted in delayed deployment of PCR-based diagnostic tests, resulting in lack of testing of individuals with symptoms of the disease. Although these tests are now more widely available, it is estimated that a three- to ten-fold increase in testing capacity will be required to ensure adequate surveillance as communities reopen(1). In response to these challenges, we evaluated potential roles of host-response based screening in the diagnosis of COVID-19. Previous work from our group showed that the nasopharyngeal (NP) level of CXCL10, a protein produced as part of the host response to viral infection, is a sensitive predictor of respiratory virus infection across a wide spectrum of viruses(2). Here, we show that NP CXCL10 is elevated during SARS-CoV-2 infection and use a CXCL10-based screening strategy to identify four undiagnosed cases of COVID-19 in Connecticut in early March. In a second set of samples tested at the Yale New Haven Hospital, we show that NP CXCL10 had excellent performance as a rule-out test (NPV 0.99, 95% C.I. 0.985-0.997). Our results demonstrate how biomarker-based screening could be used to leverage existing PCR testing capacity to rapidly enable widespread testing for COVID-19.
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Farhadian S, Glick LR, Vogels CBF, Thomas J, Chiarella J, Casanovas-Massana A, Zhou J, Odio C, Vijayakumar P, Geng B, Fournier J, Bermejo S, Fauver JR, Alpert T, Wyllie AL, Turcotte C, Steinle M, Paczkowski P, Cruz CD, Wilen C, Ko AI, MacKay S, Grubaugh ND, Spudich S, Aoun Barakat L. Acute encephalopathy with elevated CSF inflammatory markers as the initial presentation of COVID-19. Res Sq 2020:rs.3.rs-28583. [PMID: 32702723 PMCID: PMC7336693 DOI: 10.21203/rs.3.rs-28583/v1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
BACKGROUND COVID-19 is caused by the severe acute respiratory syndrome virus SARS-CoV-2. It is widely recognized as a respiratory pathogen, but neurologic complications can be the presenting manifestation in a subset of infected patients. CASE PRESENTATION We describe a 78-year old immunocompromised woman who presented with altered mental status after witnessed seizure-like activity at home. She was found to have SARS-CoV-2 infection and associated neuroinflammation. In this case, we undertake the first detailed analysis of cerebrospinal fluid (CSF) cytokines during COVID-19 infection and find a unique pattern of inflammation in CSF, but no evidence of viral neuroinvasion. CONCLUSION Our findings suggest that neurologic symptoms such as encephalopathy and seizures may be the initial presentation of COVID-19. Central nervous system inflammation may associate with neurologic manifestations of disease.
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Fauver JR, Petrone ME, Hodcroft EB, Shioda K, Ehrlich HY, Watts AG, Vogels CBF, Brito AF, Alpert T, Muyombwe A, Razeq J, Downing R, Cheemarla NR, Wyllie AL, Kalinich CC, Ott IM, Quick J, Loman NJ, Neugebauer KM, Greninger AL, Jerome KR, Roychoudhury P, Xie H, Shrestha L, Huang ML, Pitzer VE, Iwasaki A, Omer SB, Khan K, Bogoch II, Martinello RA, Foxman EF, Landry ML, Neher RA, Ko AI, Grubaugh ND. Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States. Cell 2020; 181:990-996.e5. [PMID: 32386545 PMCID: PMC7204677 DOI: 10.1016/j.cell.2020.04.021] [Citation(s) in RCA: 240] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/05/2020] [Accepted: 04/14/2020] [Indexed: 12/15/2022]
Abstract
The novel coronavirus SARS-CoV-2 was first detected in the Pacific Northwest region of the United States in January 2020, with subsequent COVID-19 outbreaks detected in all 50 states by early March. To uncover the sources of SARS-CoV-2 introductions and patterns of spread within the United States, we sequenced nine viral genomes from early reported COVID-19 patients in Connecticut. Our phylogenetic analysis places the majority of these genomes with viruses sequenced from Washington state. By coupling our genomic data with domestic and international travel patterns, we show that early SARS-CoV-2 transmission in Connecticut was likely driven by domestic introductions. Moreover, the risk of domestic importation to Connecticut exceeded that of international importation by mid-March regardless of our estimated effects of federal travel restrictions. This study provides evidence of widespread sustained transmission of SARS-CoV-2 within the United States and highlights the critical need for local surveillance. Connecticut’s COVID-19 outbreak resulted from multiple domestic virus introductions SARS-CoV-2 genomic data indicate that coast-to-coast spread occurred in the United States Risk of introduction by domestic air travel exceeded international travel in March Restrictions on international travel did not significantly alter risk estimates
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Affiliation(s)
- Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA.
| | - Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Emma B Hodcroft
- Biozentrum, University of Basel, 4056 Basel, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Kayoko Shioda
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Hanna Y Ehrlich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | | | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Anderson F Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Tara Alpert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Anthony Muyombwe
- Connecticut State Department of Public Health, Hartford, CT 06510, USA
| | - Jafar Razeq
- Connecticut State Department of Public Health, Hartford, CT 06510, USA
| | - Randy Downing
- Connecticut State Department of Public Health, Hartford, CT 06510, USA
| | - Nagarjuna R Cheemarla
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Chaney C Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Isabel M Ott
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06510, USA
| | - Joshua Quick
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA; Vaccine & Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Keith R Jerome
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA; Vaccine & Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA; Vaccine & Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Hong Xie
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Lasata Shrestha
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA; Vaccine & Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University, New Haven, CT 06510, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Saad B Omer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA; Yale Institute of Global Health, Yale University, New Haven, CT 06510, USA; Section of Infectious Diseases, Department of Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Yale School of Nursing, Yale University, New Haven, CT 06510, USA
| | - Kamran Khan
- BlueDot, Toronto, ON M5J 1A7, Canada; Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON M5B 1A6, Canada; Section of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON M5S 3H2, Canada
| | - Isaac I Bogoch
- Section of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON M5S 3H2, Canada
| | - Richard A Martinello
- Section of Infectious Diseases, Department of Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Department of Pediatrics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Infection Prevention, Yale New Haven Health, New Haven, CT 06510, USA
| | - Ellen F Foxman
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Department of Immunobiology, Yale University, New Haven, CT 06510, USA
| | - Marie L Landry
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Section of Infectious Diseases, Department of Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Clinical Virology Laboratory, Yale New Haven Health, New Haven, CT 06510, USA
| | - Richard A Neher
- Biozentrum, University of Basel, 4056 Basel, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA.
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Fauver JR, Petrone ME, Hodcroft EB, Shioda K, Ehrlich HY, Watts AG, Vogels CBF, Brito AF, Alpert T, Muyombwe A, Razeq J, Downing R, Cheemarla NR, Wyllie AL, Kalinich CC, Ott I, Quick J, Loman NJ, Neugebauer KM, Greninger AL, Jerome KR, Roychoudhury P, Xie H, Shrestha L, Huang ML, Pitzer VE, Iwasaki A, Omer SB, Khan K, Bogoch II, Martinello RA, Foxman EF, Landry ML, Neher RA, Ko AI, Grubaugh ND. Coast-to-coast spread of SARS-CoV-2 in the United States revealed by genomic epidemiology. medRxiv 2020:2020.03.25.20043828. [PMID: 32511630 PMCID: PMC7276058 DOI: 10.1101/2020.03.25.20043828] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Since its emergence and detection in Wuhan, China in late 2019, the novel coronavirus SARS-CoV-2 has spread to nearly every country around the world, resulting in hundreds of thousands of infections to date. The virus was first detected in the Pacific Northwest region of the United States in January, 2020, with subsequent COVID-19 outbreaks detected in all 50 states by early March. To uncover the sources of SARS-CoV-2 introductions and patterns of spread within the U.S., we sequenced nine viral genomes from early reported COVID-19 patients in Connecticut. Our phylogenetic analysis places the majority of these genomes with viruses sequenced from Washington state. By coupling our genomic data with domestic and international travel patterns, we show that early SARS-CoV-2 transmission in Connecticut was likely driven by domestic introductions. Moreover, the risk of domestic importation to Connecticut exceeded that of international importation by mid-March regardless of our estimated impacts of federal travel restrictions. This study provides evidence for widespread, sustained transmission of SARS-CoV-2 within the U.S. and highlights the critical need for local surveillance.
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Affiliation(s)
- Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
- These authors contributed equally
| | - Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
- These authors contributed equally
| | - Emma B Hodcroft
- Biozentrum, University of Basel, 4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- These authors contributed equally
| | - Kayoko Shioda
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Hanna Y Ehrlich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | | | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Anderson F Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Tara Alpert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06510, USA
| | - Anthony Muyombwe
- Connecticut State Department of Public Health, Hartford, CT, 06510, USA
| | - Jafar Razeq
- Connecticut State Department of Public Health, Hartford, CT, 06510, USA
| | - Randy Downing
- Connecticut State Department of Public Health, Hartford, CT, 06510, USA
| | - Nagarjuna R Cheemarla
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Chaney C Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Isabel Ott
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, 06510, USA
| | - Joshua Quick
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06510, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine, University of Washington, Seattle, WA, 98195, USA
- Vaccine & Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Keith R Jerome
- Department of Laboratory Medicine, University of Washington, Seattle, WA, 98195, USA
- Vaccine & Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine, University of Washington, Seattle, WA, 98195, USA
- Vaccine & Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Hong Xie
- Department of Laboratory Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Lasata Shrestha
- Department of Laboratory Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington, Seattle, WA, 98195, USA
- Vaccine & Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University, New Haven, CT, 06510, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Saad B Omer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
- Yale Institute of Global Health, Yale University, New Haven, CT, 06510, USA
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06510, USA
- Yale School of Nursing, Yale University, New Haven, CT, 06510, USA
| | - Kamran Khan
- BlueDot, Toronto, ON, M5J 1A7, Canada
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, M5B 1A6,Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, ON, M5S 3H2, Canada
| | - Isaac I Bogoch
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, ON, M5S 3H2, Canada
| | - Richard A Martinello
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, 06510, USA
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, 06510, USA
- Yale New Haven Health, Department of Infection Prevention, New Haven, CT, 06510, USA
| | - Ellen F Foxman
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, 06510, USA
- Department of Immunobiology, Yale University, New Haven, CT, 06510, USA
| | - Marie L Landry
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, 06510, USA
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Richard A Neher
- Biozentrum, University of Basel, 4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
- Senior author
- Lead contact
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41
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Fauver JR, Martin J, Weil GJ, Mitreva M, Fischer PU. De novo Assembly of the Brugia malayi Genome Using Long Reads from a Single MinION Flowcell. Sci Rep 2019; 9:19521. [PMID: 31863009 PMCID: PMC6925183 DOI: 10.1038/s41598-019-55908-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/28/2019] [Indexed: 11/15/2022] Open
Abstract
Filarial nematode infections cause a substantial global disease burden. Genomic studies of filarial worms can improve our understanding of their biology and epidemiology. However, genomic information from field isolates is limited and available reference genomes are often discontinuous. Single molecule sequencing technologies can reduce the cost of genome sequencing and long reads produced from these devices can improve the contiguity and completeness of genome assemblies. In addition, these new technologies can make generation and analysis of large numbers of field isolates feasible. In this study, we assessed the performance of the Oxford Nanopore Technologies MinION for sequencing and assembling the genome of Brugia malayi, a human parasite widely used in filariasis research. Using data from a single MinION flowcell, a 90.3 Mb nuclear genome was assembled into 202 contigs with an N50 of 2.4 Mb. This assembly covered 96.9% of the well-defined B. malayi reference genome with 99.2% identity. The complete mitochondrial genome was obtained with individual reads and the nearly complete genome of the endosymbiotic bacteria Wolbachia was assembled alongside the nuclear genome. Long-read data from the MinION produced an assembly that approached the quality of a well-established reference genome using comparably fewer resources.
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Affiliation(s)
- Joseph R Fauver
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States.
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States.
| | - John Martin
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, United States
| | - Gary J Weil
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Makedonka Mitreva
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, United States
| | - Peter U Fischer
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
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Wanji S, Esum ME, Njouendou AJ, Mbeng AA, Chounna Ndongmo PW, Abong RA, Fru J, Fombad FF, Nchanji GT, Ngongeh G, Ngandjui NV, Enyong PI, Storey H, Curtis KC, Fischer K, Fauver JR, Lew D, Goss CW, Fischer PU. Mapping of lymphatic filariasis in loiasis areas: A new strategy shows no evidence for Wuchereria bancrofti endemicity in Cameroon. PLoS Negl Trop Dis 2019; 13:e0007192. [PMID: 30849120 PMCID: PMC6436748 DOI: 10.1371/journal.pntd.0007192] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 03/27/2019] [Accepted: 01/28/2019] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Mapping of lymphatic filariasis (LF) caused by Wuchereria bancrofti largely relies on the detection of circulating antigen using ICT cards. Several studies have recently shown that this test can be cross-reactive with sera of subjects heavily infected with Loa loa and thus mapping results in loiasis endemic areas may be inaccurate. METHODOLOGY/PRINCIPAL FINDINGS In order to develop an LF mapping strategy for areas with high loiasis prevalence, we collected day blood samples from 5,001 subjects residing in 50 villages that make up 6 health districts throughout Cameroon. Antigen testing using Filarial Test Strip (FTS, a novel platform that uses the same reagents as ICT) revealed an overall positivity rate of 1.1% and L. loa microfilaria (Mf) rates of up to 46%. Among the subjects with 0 to 8,000 Mf/ml in day blood, only 0.4% were FTS positive, while 22.2% of subjects with >8,000 Mf/ml were FTS positive. A Mf density of >8,200 Mf/ml was determined as the cut point at which positive FTS results should be excluded from the analysis. No FTS positive samples were also positive for W. bancrofti antibodies as measured by two different point of care tests that use the Wb123 antigen not found in L. loa. Night blood examination of the FTS positive subjects showed a high prevalence of L. loa Mf with densities up to 12,710 Mf/ml. No W. bancrofti Mf were identified, as confirmed by qPCR. Our results show that high loads of L. loa Mf in day blood are a reliable indicator of FTS positivity, and Wb123 rapid test proved to be relatively specific. CONCLUSIONS/SIGNIFICANCE Our study provides a simple day blood-based algorithm for LF mapping in loiasis areas. The results indicate that many districts that were formerly classified as endemic for LF in Cameroon are non-endemic and do not require mass drug administration for elimination of LF.
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Affiliation(s)
- Samuel Wanji
- Parasites and Vector Biology research unit (PAVBRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea, Cameroon
- * E-mail:
| | - Mathias Eyong Esum
- Parasites and Vector Biology research unit (PAVBRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea, Cameroon
| | - Abdel Jelil Njouendou
- Parasites and Vector Biology research unit (PAVBRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea, Cameroon
| | - Amuam Andrew Mbeng
- Parasites and Vector Biology research unit (PAVBRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea, Cameroon
| | - Patrick W. Chounna Ndongmo
- Parasites and Vector Biology research unit (PAVBRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea, Cameroon
| | - Raphael Awah Abong
- Parasites and Vector Biology research unit (PAVBRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea, Cameroon
| | - Jerome Fru
- Parasites and Vector Biology research unit (PAVBRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea, Cameroon
| | - Fanny F. Fombad
- Parasites and Vector Biology research unit (PAVBRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea, Cameroon
| | - Gordon Takop Nchanji
- Parasites and Vector Biology research unit (PAVBRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea, Cameroon
| | - Glory Ngongeh
- Parasites and Vector Biology research unit (PAVBRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea, Cameroon
| | - Narcisse V. Ngandjui
- Parasites and Vector Biology research unit (PAVBRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea, Cameroon
| | - Peter Ivo Enyong
- Parasites and Vector Biology research unit (PAVBRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea, Cameroon
| | - Helen Storey
- Diagnostics Program, PATH, Seattle, Washington, United States of America
| | - Kurt C. Curtis
- Infectious Diseases Division, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kerstin Fischer
- Infectious Diseases Division, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Joseph R. Fauver
- Infectious Diseases Division, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Daphne Lew
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Charles W. Goss
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Peter U. Fischer
- Infectious Diseases Division, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
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43
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Fauver JR, Akter S, Morales AIO, Black WC, Rodriguez AD, Stenglein MD, Ebel GD, Weger-Lucarelli J. A reverse-transcription/RNase H based protocol for depletion of mosquito ribosomal RNA facilitates viral intrahost evolution analysis, transcriptomics and pathogen discovery. Virology 2018; 528:181-197. [PMID: 30616207 DOI: 10.1016/j.virol.2018.12.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/28/2018] [Accepted: 12/28/2018] [Indexed: 11/17/2022]
Abstract
Identifying novel viruses or assessing viral variation by NGS requires high sequencing coverage. More than 90% of total RNA is ribosomal (rRNA), making variant calling, virus discovery or transcriptomic profiling difficult. Current methods to increase informative reads suffer from drawbacks, either they cannot be used for some viruses, are optimized for a single species, or introduce bias. We describe a two-part approach combining reverse-transcription to create RNA/DNA hybrids which are then degraded with RNaseH/DNase sequentially that works for three medically relevant mosquito genera; Aedes, Anopheles, and Culex. We demonstrate depletion of rRNA from different samples, including whole mosquitoes and midgut contents from FTA cards. We describe novel insect-specific virus genomes from field collected mosquitoes. The protocol requires only common laboratory reagents and small oligonucleotides specific to rRNA. This approach can be adapted for other organisms, aiding virus diversity analyses, virus discovery and transcriptomics in both laboratory and field samples.
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Affiliation(s)
- Joseph R Fauver
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Shamima Akter
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, 360 W Campus Drive, Blacksburg, VA, USA
| | - Aldo Ivan Ortega Morales
- Departamento de Parasitología, Universidad Autónoma Agraria Antonio Narro, Torreón, Coahuila, Mexico
| | - William C Black
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Americo D Rodriguez
- Centro Regional de Investigación en Salud Publica, Instituto Nacional de Salud Pública, Tapachula, Chiapas, Mexico
| | - Mark D Stenglein
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Gregory D Ebel
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA.
| | - James Weger-Lucarelli
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA.
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Garcia-Luna SM, Weger-Lucarelli J, Rückert C, Murrieta RA, Young MC, Byas AD, Fauver JR, Perera R, Flores-Suarez AE, Ponce-Garcia G, Rodriguez AD, Ebel GD, Black WC. Variation in competence for ZIKV transmission by Aedes aegypti and Aedes albopictus in Mexico. PLoS Negl Trop Dis 2018; 12:e0006599. [PMID: 29965958 PMCID: PMC6044546 DOI: 10.1371/journal.pntd.0006599] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/13/2018] [Accepted: 06/08/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND ZIKV is a new addition to the arboviruses circulating in the New World, with more than 1 million cases since its introduction in 2015. A growing number of studies have reported vector competence (VC) of Aedes mosquitoes from several areas of the world for ZIKV transmission. Some studies have used New World mosquitoes from disparate regions and concluded that these have a variable but relatively low competence for the Asian lineage of ZIKV. METHODOLOGY/PRINCIPAL FINDINGS Ten Aedes aegypti (L) and three Ae. albopictus (Skuse) collections made in 2016 from throughout Mexico were analyzed for ZIKV (PRVABC59-Asian lineage) VC. Mexican Ae. aegypti had high rates of midgut infection (MIR), dissemination (DIR) and salivary gland infection (SGIR) but low to moderate transmission rates (TR). It is unclear whether this low TR was due to heritable salivary gland escape barriers or to underestimating the amount of virus in saliva due to the loss of virus during filtering and random losses on surfaces when working with small volumes. VC varied among collections, geographic regions and whether the collection was made north or south of the Neovolcanic axis (NVA). The four rates were consistently lower in northeastern Mexico, highest in collections along the Pacific coast and intermediate in the Yucatan. All rates were lowest north of the NVA. It was difficult to assess VC in Ae. albopictus because rates varied depending upon the number of generations in the laboratory. CONCLUSIONS/SIGNIFICANCE Mexican Ae. aegypti and Ae. albopictus are competent vectors of ZIKV. There is however large variance in vector competence among geographic sites and regions. At 14 days post infection, TR varied from 8-51% in Ae. aegypti and from 2-26% in Ae. albopictus.
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Affiliation(s)
- Selene M. Garcia-Luna
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - James Weger-Lucarelli
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Claudia Rückert
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Reyes A. Murrieta
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Michael C. Young
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Alex D. Byas
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Joseph R. Fauver
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Rushika Perera
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Adriana E. Flores-Suarez
- Universidad Autonoma de Nuevo Leon, Facultad de Ciencias Biologicas, San Nicolas de los Garza, Nuevo Leon, México
| | - Gustavo Ponce-Garcia
- Universidad Autonoma de Nuevo Leon, Facultad de Ciencias Biologicas, San Nicolas de los Garza, Nuevo Leon, México
| | - Americo D. Rodriguez
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Centro Regional de Investigación en Salud Publica, Instituto Nacional de Salud Publica, Tapachula, Chiapas, México
| | - Gregory D. Ebel
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - William C. Black
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
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Fauver JR, Weger-Lucarelli J, Fakoli LS, Bolay K, Bolay FK, Diclaro JW, Brackney DE, Foy BD, Stenglein MD, Ebel GD. Xenosurveillance reflects traditional sampling techniques for the identification of human pathogens: A comparative study in West Africa. PLoS Negl Trop Dis 2018; 12:e0006348. [PMID: 29561834 PMCID: PMC5880402 DOI: 10.1371/journal.pntd.0006348] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 04/02/2018] [Accepted: 02/26/2018] [Indexed: 01/05/2023] Open
Abstract
Background Novel surveillance strategies are needed to detect the rapid and continuous emergence of infectious disease agents. Ideally, new sampling strategies should be simple to implement, technologically uncomplicated, and applicable to areas where emergence events are known to occur. To this end, xenosurveillance is a technique that makes use of blood collected by hematophagous arthropods to monitor and identify vertebrate pathogens. Mosquitoes are largely ubiquitous animals that often exist in sizable populations. As well, many domestic or peridomestic species of mosquitoes will preferentially take blood-meals from humans, making them a unique and largely untapped reservoir to collect human blood. Methodology/Principal findings We sought to take advantage of this phenomenon by systematically collecting blood-fed mosquitoes during a field trail in Northern Liberia to determine whether pathogen sequences from blood engorged mosquitoes accurately mirror those obtained directly from humans. Specifically, blood was collected from humans via finger-stick and by aspirating bloodfed mosquitoes from the inside of houses. Shotgun metagenomic sequencing of RNA and DNA derived from these specimens was performed to detect pathogen sequences. Samples obtained from xenosurveillance and from finger-stick blood collection produced a similar number and quality of reads aligning to two human viruses, GB virus C and hepatitis B virus. Conclusions/Significance This study represents the first systematic comparison between xenosurveillance and more traditional sampling methodologies, while also demonstrating the viability of xenosurveillance as a tool to sample human blood for circulating pathogens. Infectious diseases continue to be a burden on mankind, particularly in the developing countries of the tropics. Recognition of pathogen transmission in humans is a crucial step to thwarting epidemics of these pathogens. However, sampling human blood or tissue is invasive and logistically difficult. Xenosurveillance takes advantage of the blood-feeding behavior of mosquitoes to sample human blood for the presence of infectious disease agents. In this study, we aimed to compare xenosurveillance to a more traditional sampling method to assess the usefulness of this technique in field settings where it could potentially be beneficial. DNA and RNA next generation sequencing followed by an in-house bioinformatic pipeline identified viruses and parasites of human origin in blood collected by either mosquitoes or finger-stick. Xenosurveillance produces samples of comparable quality to finger-stick blood collections while alleviating many of the difficulties of direct human sampling. This study suggests xenosurveillance can be a complimentary strategy for infectious disease surveillance in low-resource areas.
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Affiliation(s)
- Joseph R. Fauver
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
| | - James Weger-Lucarelli
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | | | - Kpehe Bolay
- Liberian Institute for Biomedical Research, Charlesville, Liberia
| | - Fatorma K. Bolay
- Liberian Institute for Biomedical Research, Charlesville, Liberia
| | | | - Doug E. Brackney
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Brian D. Foy
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Mark D. Stenglein
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Gregory D. Ebel
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
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Gendernalik A, Weger-Lucarelli J, Garcia Luna SM, Fauver JR, Rückert C, Murrieta RA, Bergren N, Samaras D, Nguyen C, Kading RC, Ebel GD. American Aedes vexans Mosquitoes are Competent Vectors of Zika Virus. Am J Trop Med Hyg 2017; 96:1338-1340. [PMID: 28719283 PMCID: PMC5462567 DOI: 10.4269/ajtmh.16-0963] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Starting in 2013–2014, the Americas have experienced a massive outbreak of Zika virus (ZIKV) which has now reached at least 49 countries. Although most cases have occurred in South America and the Caribbean, imported and autochthonous cases have occurred in the United States. Aedes aegypti and Aedes albopictus mosquitoes are known vectors of ZIKV. Little is known about the potential for temperate Aedes mosquitoes to transmit ZIKV. Aedes vexans has a worldwide distribution, is highly abundant in particular localities, aggressively bites humans, and is a competent vector of several arboviruses. However, it is not clear whether Ae. vexans mosquitoes are competent to transmit ZIKV. To determine the vector competence of Ae. vexans for ZIKV, wild-caught mosquitoes were exposed to an infectious bloodmeal containing a ZIKV strain isolated during the current outbreak. Approximately 80% of 148 mosquitoes tested became infected by ZIKV, and approximately 5% transmitted infectious virus after 14 days of extrinsic incubation. These results establish that Ae. vexans are competent ZIKV vectors. Their relative importance as vectors (i.e., their vectorial capacity) depends on feeding behavior, longevity, and other factors that are likely to vary in ecologically distinct environments.
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Affiliation(s)
- Alex Gendernalik
- Arthropod-Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - James Weger-Lucarelli
- Arthropod-Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Selene M Garcia Luna
- Arthropod-Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Joseph R Fauver
- Arthropod-Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Claudia Rückert
- Arthropod-Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Reyes A Murrieta
- Arthropod-Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Nicholas Bergren
- Arthropod-Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Demitrios Samaras
- Arthropod-Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Chilinh Nguyen
- Arthropod-Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Rebekah C Kading
- Arthropod-Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Gregory D Ebel
- Arthropod-Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
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Fauver JR, Gendernalik A, Weger-Lucarelli J, Grubaugh ND, Brackney DE, Foy BD, Ebel GD. The Use of Xenosurveillance to Detect Human Bacteria, Parasites, and Viruses in Mosquito Bloodmeals. Am J Trop Med Hyg 2017; 97:324-329. [PMID: 28722623 DOI: 10.4269/ajtmh.17-0063] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Infectious disease surveillance is hindered by several factors, including limited infrastructure and geographic isolation of many resource-poor regions. In addition, the complexities of sample acquisition, processing, and analysis, even in developed regions, can be rate limiting. Therefore, new strategies to survey human populations for emerging pathogens are necessary. Xenosurveillance is a method that utilizes mosquitoes as sampling devices to search for genetic signatures of pathogens in vertebrates. Previously we demonstrated that xenosurveillance can detect viral RNA in both laboratory and field settings. However, its ability to detect bacteria and parasites remains to be assessed. Accordingly, we fed Anopheles gambiae mosquitoes blood that contained Trypanosoma brucei gambiense and Bacillus anthracis. In addition, we determined whether two additional emerging viruses, Middle East Respiratory Syndrome Coronavirus and Zika virus could be detected by this method. Pathogen-specific real-time reverse transcription polymerase chain reaction was used to evaluate the sensitivity of xenosurveillance across multiple pathogen taxa and over time. We detected RNA from all pathogens at clinically relevant concentrations from mosquitoes processed up to 1 day postbloodfeeding. These results demonstrate that xenosurveillance may be used as a tool to expand surveillance for viral, parasitic, and bacterial pathogens in resource-limited areas.
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Affiliation(s)
- Joseph R Fauver
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado
| | - Alex Gendernalik
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado
| | - James Weger-Lucarelli
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado
| | - Nathan D Grubaugh
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California.,Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado
| | - Doug E Brackney
- Center for Vector Biology and Zoonotic Diseases, Connecticut Agricultural Experiment Station, New Haven, Connecticut
| | - Brian D Foy
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado
| | - Gregory D Ebel
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado
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Grubaugh ND, Ladner JT, Kraemer MUG, Dudas G, Tan AL, Gangavarapu K, Wiley MR, White S, Thézé J, Magnani DM, Prieto K, Reyes D, Bingham AM, Paul LM, Robles-Sikisaka R, Oliveira G, Pronty D, Barcellona CM, Metsky HC, Baniecki ML, Barnes KG, Chak B, Freije CA, Gladden-Young A, Gnirke A, Luo C, MacInnis B, Matranga CB, Park DJ, Qu J, Schaffner SF, Tomkins-Tinch C, West KL, Winnicki SM, Wohl S, Yozwiak NL, Quick J, Fauver JR, Khan K, Brent SE, Reiner RC, Lichtenberger PN, Ricciardi MJ, Bailey VK, Watkins DI, Cone MR, Kopp EW, Hogan KN, Cannons AC, Jean R, Monaghan AJ, Garry RF, Loman NJ, Faria NR, Porcelli MC, Vasquez C, Nagle ER, Cummings DAT, Stanek D, Rambaut A, Sanchez-Lockhart M, Sabeti PC, Gillis LD, Michael SF, Bedford T, Pybus OG, Isern S, Palacios G, Andersen KG. Genomic epidemiology reveals multiple introductions of Zika virus into the United States. Nature 2017; 546:401-405. [PMID: 28538723 PMCID: PMC5536180 DOI: 10.1038/nature22400] [Citation(s) in RCA: 232] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/28/2017] [Indexed: 12/23/2022]
Abstract
Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital abnormalities. In July 2016, mosquito-borne ZIKV transmission was reported in the continental United States; since then, hundreds of locally acquired infections have been reported in Florida. To gain insights into the timing, source, and likely route(s) of ZIKV introduction, we tracked the virus from its first detection in Florida by sequencing ZIKV genomes from infected patients and Aedes aegypti mosquitoes. We show that at least 4 introductions, but potentially as many as 40, contributed to the outbreak in Florida and that local transmission is likely to have started in the spring of 2016-several months before its initial detection. By analysing surveillance and genetic data, we show that ZIKV moved among transmission zones in Miami. Our analyses show that most introductions were linked to the Caribbean, a finding corroborated by the high incidence rates and traffic volumes from the region into the Miami area. Our study provides an understanding of how ZIKV initiates transmission in new regions.
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Affiliation(s)
- Nathan D Grubaugh
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Jason T Ladner
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
- Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Gytis Dudas
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Amanda L Tan
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida 33965, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Michael R Wiley
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
- College of Public Health, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | - Stephen White
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Miami, Florida 33125, USA
| | - Julien Thézé
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | - Diogo M Magnani
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Karla Prieto
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
- College of Public Health, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | - Daniel Reyes
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | - Andrea M Bingham
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, Florida 32399, USA
| | - Lauren M Paul
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida 33965, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Glenn Oliveira
- Scripps Translational Science Institute, La Jolla, California 92037, USA
| | - Darryl Pronty
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Miami, Florida 33125, USA
| | - Carolyn M Barcellona
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida 33965, USA
| | - Hayden C Metsky
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Mary Lynn Baniecki
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kayla G Barnes
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Bridget Chak
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Catherine A Freije
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | | | - Andreas Gnirke
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Cynthia Luo
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Bronwyn MacInnis
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | | | - Daniel J Park
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - James Qu
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | | | | | - Kendra L West
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Sarah M Winnicki
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Shirlee Wohl
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Nathan L Yozwiak
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Joshua Quick
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Joseph R Fauver
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, Ontario M5B 1T8, Canada
- Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Shannon E Brent
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, Ontario M5B 1T8, Canada
| | - Robert C Reiner
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington 98121, USA
| | - Paola N Lichtenberger
- Division of Infectious Diseases, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Michael J Ricciardi
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Varian K Bailey
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - David I Watkins
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Marshall R Cone
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida 33612, USA
| | - Edgar W Kopp
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida 33612, USA
| | - Kelly N Hogan
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida 33612, USA
| | - Andrew C Cannons
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida 33612, USA
| | - Reynald Jean
- Florida Department of Health in Miami-Dade County, Miami, Florida 33125, USA
| | - Andrew J Monaghan
- National Center for Atmospheric Research, Boulder, Colorado 80307, USA
| | - Robert F Garry
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana 70112, USA
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | | | | | - Elyse R Nagle
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | - Derek A T Cummings
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32610, USA
| | - Danielle Stanek
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, Florida 32399, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Mariano Sanchez-Lockhart
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | - Pardis C Sabeti
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Leah D Gillis
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Miami, Florida 33125, USA
| | - Scott F Michael
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida 33965, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | - Sharon Isern
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida 33965, USA
| | - Gustavo Palacios
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
| | - Kristian G Andersen
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA
- Scripps Translational Science Institute, La Jolla, California 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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Chotiwan N, Brewster CD, Magalhaes T, Weger-Lucarelli J, Duggal NK, Rückert C, Nguyen C, Garcia Luna SM, Fauver JR, Andre B, Gray M, Black WC, Kading RC, Ebel GD, Kuan G, Balmaseda A, Jaenisch T, Marques ETA, Brault AC, Harris E, Foy BD, Quackenbush SL, Perera R, Rovnak J. Rapid and specific detection of Asian- and African-lineage Zika viruses. Sci Transl Med 2017; 9:eaag0538. [PMID: 28469032 PMCID: PMC5654541 DOI: 10.1126/scitranslmed.aag0538] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 08/12/2016] [Accepted: 02/15/2017] [Indexed: 01/23/2023]
Abstract
Understanding the dynamics of Zika virus transmission and formulating rational strategies for its control require precise diagnostic tools that are also appropriate for resource-poor environments. We have developed a rapid and sensitive loop-mediated isothermal amplification (LAMP) assay that distinguishes Zika viruses of Asian and African lineages. The assay does not detect chikungunya virus or flaviviruses such as dengue, yellow fever, or West Nile viruses. The assay conditions allowed direct detection of Zika virus RNA in cultured infected cells; in mosquitoes; in virus-spiked samples of human blood, plasma, saliva, urine, and semen; and in infected patient serum, plasma, and semen samples without the need for RNA isolation or reverse transcription. The assay offers rapid, specific, sensitive, and inexpensive detection of the Asian-lineage Zika virus strain that is currently circulating in the Western hemisphere, and can also detect the African-lineage Zika virus strain using separate, specific primers.
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Affiliation(s)
- Nunya Chotiwan
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Connie D Brewster
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Tereza Magalhaes
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Laboratory of Virology and Experimental Therapeutics, Centro de Pesquisas Aggeu Magalhaes, Fundacao Oswaldo Cruz, Recife-PE, Brazil
| | - James Weger-Lucarelli
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Nisha K Duggal
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Claudia Rückert
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Chilinh Nguyen
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Selene M Garcia Luna
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Joseph R Fauver
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Barb Andre
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Meg Gray
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - William C Black
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Rebekah C Kading
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Gregory D Ebel
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Guillermina Kuan
- Centro de Salud Sócrates Flores Vivas, Ministry of Health, Managua, Nicaragua
| | - Angel Balmaseda
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Thomas Jaenisch
- Section Clinical Tropical Medicine, Department for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
- German Centre for Infection Research (DZIF), partner site Heidelberg, Heidelberg, Germany
| | - Ernesto T A Marques
- Laboratory of Virology and Experimental Therapeutics, Centro de Pesquisas Aggeu Magalhaes, Fundacao Oswaldo Cruz, Recife-PE, Brazil
- Center for Vaccine Research, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Aaron C Brault
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720-7360, USA
| | - Brian D Foy
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Sandra L Quackenbush
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Rushika Perera
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Joel Rovnak
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA.
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Weger-Lucarelli J, Rückert C, Chotiwan N, Nguyen C, Garcia Luna SM, Fauver JR, Foy BD, Perera R, Black WC, Kading RC, Ebel GD. Vector Competence of American Mosquitoes for Three Strains of Zika Virus. PLoS Negl Trop Dis 2016; 10:e0005101. [PMID: 27783679 PMCID: PMC5081193 DOI: 10.1371/journal.pntd.0005101] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 10/09/2016] [Indexed: 11/18/2022] Open
Abstract
In 2015, Zika virus (ZIKV; Flaviviridae; Flavivirus) emerged in the Americas, causing millions of infections in dozens of countries. The rapid spread of the virus and the association with disease outcomes such as Guillain-Barré syndrome and microcephaly make understanding transmission dynamics essential. Currently, there are no reports of vector competence (VC) of American mosquitoes for ZIKV isolates from the Americas. Further, it is not clear whether ZIKV strains from other genetic lineages can be transmitted by American Aedes aegypti populations, and whether the scope of the current epidemic is in part facilitated by viral factors such as enhanced replicative fitness or increased vector competence. Therefore, we characterized replication of three ZIKV strains, one from each of the three phylogenetic clades in several cell lines and assessed their abilities to be transmitted by Ae. aegypti mosquitoes. Additionally, laboratory colonies of different Culex spp. were infected with an American outbreak strain of ZIKV to assess VC. Replication rates were variable and depended on virus strain, cell line and MOI. African strains used in this study outcompeted the American strain in vitro in both mammalian and mosquito cell culture. West and East African strains of ZIKV tested here were more efficiently transmitted by Ae. aegypti from Mexico than was the currently circulating American strain of the Asian lineage. Long-established laboratory colonies of Culex mosquitoes were not efficient ZIKV vectors. These data demonstrate the capacity for additional ZIKV strains to infect and replicate in American Aedes mosquitoes and suggest that neither enhanced virus replicative fitness nor virus adaptation to local vector mosquitoes seems likely to explain the extent and intensity of ZIKV transmission in the Americas. The mechanisms contributing to the explosive nature of the current ZIKV outbreak in the Americas are poorly understood. Therefore, we characterized the replication of three strains, one from each phylogenetic clade of ZIKV and evaluated virus strain differences in transmission efficiency by American mosquitoes. Our results suggest that the strain currently circulating in the Americas does not have unusually high infectivity for American Ae. aegypti as compared to the African strains used in this study. Colonized Culex mosquitoes were inefficient vectors. In vitro data suggested slower replication and decreased fitness for the currently circulating American strain compared to African strains isolated decades ago. Therefore, viral adaptation to local mosquitoes does not appear, at present, to be driving the current ZIKV outbreak in the Americas.
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Affiliation(s)
- James Weger-Lucarelli
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Claudia Rückert
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Nunya Chotiwan
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Chilinh Nguyen
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Selene M. Garcia Luna
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Joseph R. Fauver
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Brian D. Foy
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Rushika Perera
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - William C. Black
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Rebekah C. Kading
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Gregory D. Ebel
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
- * E-mail:
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