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Koch RT, Erazo D, Folly AJ, Johnson N, Dellicour S, Grubaugh ND, Vogels CBF. Genomic epidemiology of West Nile virus in Europe. One Health 2024; 18:100664. [PMID: 38193029 PMCID: PMC10772404 DOI: 10.1016/j.onehlt.2023.100664] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/12/2023] [Indexed: 01/10/2024] Open
Abstract
West Nile virus is one of the most widespread mosquito-borne zoonotic viruses, with unique transmission dynamics in various parts of the world. Genomic surveillance has provided important insights in the global patterns of West Nile virus emergence and spread. In Europe, multiple West Nile virus lineages have been isolated, with lineage 1a and 2 being the main lineages responsible for human infections. In contrast to North America, where a single introduction of lineage 1a resulted in the virus establishing itself in a new continent, at least 13 introductions of lineages 1a and 2 have occurred into Europe, which is likely a vast underestimation of the true number of introductions. Historically, lineage 1a was the main lineage circulating in Europe, but since the emergence of lineage 2 in the early 2000s, the latter has become the predominant lineage. This shift in West Nile virus lineage prevalence has been broadly linked to the expansion of the virus into northerly temperate regions, where autochthonous cases in animals and humans have been reported in Germany and The Netherlands. Here, we discuss how genomic analysis has increased our understanding of the epidemiology of West Nile virus in Europe, and we present a global Nextstrain build consisting of publicly available West Nile virus genomes (https://nextstrain.org/community/grubaughlab/WNV-Global). Our results elucidate recent insights in West Nile virus lineage dynamics in Europe, and discuss how expanded programs can fill current genomic surveillance gaps.
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Affiliation(s)
- R Tobias Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Diana Erazo
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium
| | - Arran J Folly
- Vector-Borne Diseases, Virology Department, Animal and Plant Health Agency, Woodham Lane, Addlestone, Surrey, UK
| | - Nicholas Johnson
- Vector-Borne Diseases, Virology Department, Animal and Plant Health Agency, Woodham Lane, Addlestone, Surrey, UK
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - 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
- Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, United States of America
| | - Chantal B F Vogels
- 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
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2
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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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3
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Taylor-Salmon E, Hill V, Paul LM, Koch RT, Breban MI, Chaguza C, Sodeinde A, Warren JL, Bunch S, Cano N, Cone M, Eysoldt S, Garcia A, Gilles N, Hagy A, Heberlein L, Jaber R, Kassens E, Colarusso P, Davis A, Baudin S, Rico E, Mejía-Echeverri Á, Scott B, Stanek D, Zimler R, Muñoz-Jordán JL, Santiago GA, Adams LE, Paz-Bailey G, Spillane M, Katebi V, Paulino-Ramírez R, Mueses S, Peguero A, Sánchez N, Norman FF, Galán JC, Huits R, Hamer DH, Vogels CBF, Morrison A, Michael SF, Grubaugh ND. Travel surveillance uncovers dengue virus dynamics and introductions in the Caribbean. Nat Commun 2024; 15:3508. [PMID: 38664380 PMCID: PMC11045810 DOI: 10.1038/s41467-024-47774-8] [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: 11/11/2023] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Dengue is the most prevalent mosquito-borne viral disease in humans, and cases are continuing to rise globally. In particular, islands in the Caribbean have experienced more frequent outbreaks, and all four dengue virus (DENV) serotypes have been reported in the region, leading to hyperendemicity and increased rates of severe disease. However, there is significant variability regarding virus surveillance and reporting between islands, making it difficult to obtain an accurate understanding of the epidemiological patterns in the Caribbean. To investigate this, we used travel surveillance and genomic epidemiology to reconstruct outbreak dynamics, DENV serotype turnover, and patterns of spread within the region from 2009-2022. We uncovered two recent DENV-3 introductions from Asia, one of which resulted in a large outbreak in Cuba, which was previously under-reported. We also show that while outbreaks can be synchronized between islands, they are often caused by different serotypes. Our study highlights the importance of surveillance of infected travelers to provide a snapshot of local introductions and transmission in areas with limited local surveillance and suggests that the recent DENV-3 introductions may pose a major public health threat in the region.
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Affiliation(s)
- Emma Taylor-Salmon
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA.
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
| | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Lauren M Paul
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Robert T Koch
- 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
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Afeez Sodeinde
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Joshua L Warren
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
- Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, 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
| | - Marshall Cone
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Sarah Eysoldt
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Alezaundra Garcia
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Nicadia Gilles
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Andrew Hagy
- 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
| | - Rayah Jaber
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Elizabeth Kassens
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Pamela Colarusso
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, USA
| | - Amanda Davis
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, USA
| | - Samantha Baudin
- Florida Department of Health in Miami-Dade County, Miami, FL, USA
| | - Edhelene Rico
- Florida Department of Health in Miami-Dade County, Miami, FL, USA
| | | | - Blake Scott
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, USA
| | - Danielle Stanek
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, USA
| | - Rebecca Zimler
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, USA
| | - Jorge L Muñoz-Jordán
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Gilberto A Santiago
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Laura E Adams
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Gabriela Paz-Bailey
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Melanie Spillane
- Office of Data, Analytics, and Technology, Division of Global Migration Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Bureau for Global Health, United States Agency for International Development, Arlington, VA, USA
| | - Volha Katebi
- Office of Data, Analytics, and Technology, Division of Global Migration Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Robert Paulino-Ramírez
- Instituto de Medicina Tropical & Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
| | - Sayira Mueses
- Instituto de Medicina Tropical & Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
| | - Armando Peguero
- Instituto de Medicina Tropical & Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
| | - Nelissa Sánchez
- Instituto de Medicina Tropical & Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
| | - Francesca F Norman
- National Referral Unit for Tropical Diseases, Infectious Diseases Department, CIBER de Enfermedades Infecciosas, IRYCIS, Hospital Ramón y Cajal, Universidad de Alcalá, Madrid, Spain
| | - Juan-Carlos Galán
- Microbiology Department, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), CIBER de Epidemiologia y Salud Publica (CIBERESP), Madrid, Spain
| | - Ralph Huits
- Department of Infectious Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar, Verona, Italy
| | - Davidson H Hamer
- Department of Global Health, Boston University School of Public Health, Section of Infectious Diseases, Boston University School of Medicine, Center for Emerging Infectious Disease Policy and Research, Boston University, and National Emerging Infectious Disease Laboratory, Boston, MA, USA
| | - Chantal B F Vogels
- 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
| | - Andrea 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, FL, USA.
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
- Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA.
- Yale Institute for Global Health, Yale University, New Haven, CT, USA.
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
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4
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Erazo D, Grant L, Ghisbain G, Marini G, Colón-González FJ, Wint W, Rizzoli A, Van Bortel W, Vogels CBF, Grubaugh ND, Mengel M, Frieler K, Thiery W, Dellicour S. Contribution of climate change to the spatial expansion of West Nile virus in Europe. Nat Commun 2024; 15:1196. [PMID: 38331945 PMCID: PMC10853512 DOI: 10.1038/s41467-024-45290-3] [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: 06/27/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024] Open
Abstract
West Nile virus (WNV) is an emerging mosquito-borne pathogen in Europe where it represents a new public health threat. While climate change has been cited as a potential driver of its spatial expansion on the continent, a formal evaluation of this causal relationship is lacking. Here, we investigate the extent to which WNV spatial expansion in Europe can be attributed to climate change while accounting for other direct human influences such as land-use and human population changes. To this end, we trained ecological niche models to predict the risk of local WNV circulation leading to human cases to then unravel the isolated effect of climate change by comparing factual simulations to a counterfactual based on the same environmental changes but a counterfactual climate where long-term trends have been removed. Our findings demonstrate a notable increase in the area ecologically suitable for WNV circulation during the period 1901-2019, whereas this area remains largely unchanged in a no-climate-change counterfactual. We show that the drastic increase in the human population at risk of exposure is partly due to historical changes in population density, but that climate change has also been a critical driver behind the heightened risk of WNV circulation in Europe.
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Affiliation(s)
- Diana Erazo
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium.
| | - Luke Grant
- Department of Water and Climate, Vrije Universiteit Brussel, Brussels, Belgium
| | - Guillaume Ghisbain
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium
- Laboratory of Zoology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Giovanni Marini
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
| | | | - William Wint
- Environmental Research Group Oxford Ltd, Department of Biology, Mansfield Road, Oxford, OX1 3SZ, UK
| | - Annapaola Rizzoli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Wim Van Bortel
- Unit Entomology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Outbreak Research team, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - 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
| | - Matthias Mengel
- Department Transformation Pathways, Potsdam Institute for Climate Impact Research (PIK), Potsdam, Germany
| | - Katja Frieler
- Department Transformation Pathways, Potsdam Institute for Climate Impact Research (PIK), Potsdam, Germany
| | - Wim Thiery
- Department of Water and Climate, Vrije Universiteit Brussel, Brussels, Belgium
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium.
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium.
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5
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Jones FK, Morrison AM, Santiago GA, Rysava K, Zimler RA, Heberlein LA, Kopp E, Saunders KE, Baudin S, Rico E, Mejía-Echeverri Á, Taylor-Salmon E, Hill V, Breban MI, Vogels CBF, Grubaugh ND, Paul LM, Michael SF, Johansson MA, Adams LE, Munoz-Jordan J, Paz-Bailey G, Stanek DR. Introduction and Spread of Dengue Virus 3, Florida, USA, May 2022-April 2023. Emerg Infect Dis 2024; 30:376-379. [PMID: 38232709 PMCID: PMC10826764 DOI: 10.3201/eid3002.231615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024] Open
Abstract
During May 2022-April 2023, dengue virus serotype 3 was identified among 601 travel-associated and 61 locally acquired dengue cases in Florida, USA. All 203 sequenced genomes belonged to the same genotype III lineage and revealed potential transmission chains in which most locally acquired cases occurred shortly after introduction, with little sustained transmission.
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6
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Lange RE, Dupuis Ii AP, Prusinski MA, Maffei JG, Koetzner CA, Ngo K, Backenson B, Oliver J, Vogels CBF, Grubaugh ND, Kramer LD, Ciota AT. Identification and characterization of novel lineage 1 Powassan virus strains in New York State. Emerg Microbes Infect 2023; 12:2155585. [PMID: 36503411 PMCID: PMC9788702 DOI: 10.1080/22221751.2022.2155585] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/01/2022] [Indexed: 12/14/2022]
Abstract
Powassan virus (POWV, family Flaviviridae) is a reemerging tick-borne virus endemic in North America and Russia. In 1997, a POWV-like agent was isolated from Ixodes scapularis in New England and determined to be genetically distinct from the original POWV isolate. This revealed the existence of two lineages: lineage 1, prototype Powassan virus (POWV-1) and lineage 2, deer tick virus (DTV). POWV-1 is thought to be primarily maintained in a cycle between I. cookei and woodchucks and I. marxi and squirrels, while DTV is primarily maintained in a cycle between I. scapularis and small mammal hosts. Recent tick, mammalian, and human isolates from New York State (NYS) have been identified as DTV, but for the first time in 45 years, we detected four POWV-1 isolates, including the first reported isolation of POWV-1 from I. scapularis. We aimed to investigate genotypic and phenotypic characteristics of recent NYS isolates through sequence analysis and evaluation of replication kinetics in vitro and in vivo. Our sequencing revealed genetic divergence between NYS POWV-1 isolates, with two distinct foci. We found that POWV-1 isolates displayed variable replication kinetics in nymphal ticks but not in cell culture. POWV-1 isolated from I. scapularis displayed increased fitness in experimentally infected I. scapularis as compared to historic and recent POWV-1 isolates from I. cookei. These data suggest the emergence of divergent POWV-1 strains in alternate tick hosts and maintenance of genetically and phenotypically discrete POWV-1 foci.
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Affiliation(s)
- Rachel E Lange
- Department of Biomedical Sciences, State University of New York University at Albany School of Public Health, Albany, NY, USA
- New York State Department of Health, The Arbovirus Laboratory, Wadsworth Center, Slingerlands, NY, USA
| | - Alan P Dupuis Ii
- New York State Department of Health, The Arbovirus Laboratory, Wadsworth Center, Slingerlands, NY, USA
| | - Melissa A Prusinski
- New York State Department of Health, Bureau of Communicable Disease Control, Vector Ecology Laboratory, Albany, NY, USA
| | - Joseph G Maffei
- New York State Department of Health, The Arbovirus Laboratory, Wadsworth Center, Slingerlands, NY, USA
| | - Cheri A Koetzner
- New York State Department of Health, The Arbovirus Laboratory, Wadsworth Center, Slingerlands, NY, USA
| | - Kiet Ngo
- New York State Department of Health, The Arbovirus Laboratory, Wadsworth Center, Slingerlands, NY, USA
| | - Bryon Backenson
- New York State Department of Health, Bureau of Communicable Disease Control, Vector Ecology Laboratory, Albany, NY, USA
| | - JoAnne Oliver
- New York State Department of Health, Bureau of Communicable Disease Control, Syracuse, NY, 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
| | - Laura D Kramer
- Department of Biomedical Sciences, State University of New York University at Albany School of Public Health, Albany, NY, USA
- New York State Department of Health, The Arbovirus Laboratory, Wadsworth Center, Slingerlands, NY, USA
| | - Alexander T Ciota
- Department of Biomedical Sciences, State University of New York University at Albany School of Public Health, Albany, NY, USA
- New York State Department of Health, The Arbovirus Laboratory, Wadsworth Center, Slingerlands, NY, USA
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7
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Brackney DE, Vogels CBF. The known unknowns of Powassan virus ecology. J Med Entomol 2023; 60:1142-1148. [PMID: 37862099 PMCID: PMC10645372 DOI: 10.1093/jme/tjad095] [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] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/14/2023] [Accepted: 07/05/2023] [Indexed: 10/21/2023]
Abstract
Powassan virus (POWV; Family: Flaviviridae, Genus: Flavivirus) is the sole North American member of the tick-borne encephalitis sero-complex. While associated with high rates of morbidity and mortality, POWV has historically been of little public health concern due to low incidence rates. However, over the last 20 yr, incidence rates have increased highlighting the growing epidemiological threat. Currently, there are no vaccines or therapeutics with tick habitat reduction, acaricide application, and public awareness programs being our primary means of intervention. The effectiveness of these control strategies is dependent on having a sound understanding of the virus's ecology. In this Forum, we review what is currently known about POWV ecology, identify gaps in our knowledge, and discuss prevailing and alternative hypotheses about transmission dynamics, reservoir hosts, and spatial focality.
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Affiliation(s)
- Doug E Brackney
- Department of Entomology, Center for Vector Biology and Zoonotic Diseases, The Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
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8
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Earnest R, Hahn AM, Feriancek NM, Brandt M, Filler RB, Zhao Z, Breban MI, Vogels CBF, Chen NFG, Koch RT, Porzucek AJ, Sodeinde A, Garbiel A, Keanna C, Litwak H, Stuber HR, Cantoni JL, Pitzer VE, Olarte Castillo XA, Goodman LB, Wilen CB, Linske MA, Williams SC, Grubaugh ND. Survey of white-footed mice in Connecticut, USA reveals low SARS-CoV-2 seroprevalence and infection with divergent betacoronaviruses. bioRxiv 2023:2023.09.22.559030. [PMID: 37808797 PMCID: PMC10557615 DOI: 10.1101/2023.09.22.559030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Diverse mammalian species display susceptibility to and infection with SARS-CoV-2. Potential SARS-CoV-2 spillback into rodents is understudied despite their host role for numerous zoonoses and human proximity. We assessed exposure and infection among white-footed mice (Peromyscus leucopus) in Connecticut, USA. We observed 1% (6/540) wild-type neutralizing antibody seroprevalence among 2020-2022 residential mice with no cross-neutralization of variants. We detected no SARS-CoV-2 infections via RT-qPCR, but identified non-SARS-CoV-2 betacoronavirus infections via pan-coronavirus PCR among 1% (5/468) of residential mice. Sequencing revealed two divergent betacoronaviruses, preliminarily named Peromyscus coronavirus-1 and -2. Both belong to the Betacoronavirus 1 species and are ~90% identical to the closest known relative, Porcine hemagglutinating encephalomyelitis virus. Low SARS-CoV-2 seroprevalence suggests white-footed mice may not be sufficiently susceptible or exposed to SARS-CoV-2 to present a long-term human health risk. However, the discovery of divergent, non-SARS-CoV-2 betacoronaviruses expands the diversity of known rodent coronaviruses and further investigation is required to understand their transmission extent.
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Affiliation(s)
- Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Nicole M Feriancek
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Matthew Brandt
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Renata B Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Zhe Zhao
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Mallery I Breban
- 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
| | - Nicholas F G Chen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Robert T Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Abbey J Porzucek
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Afeez Sodeinde
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Alexa Garbiel
- Department of Environmental Science and Forestry, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - Claire Keanna
- Department of Environmental Science and Forestry, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - Hannah Litwak
- Department of Environmental Science and Forestry, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - Heidi R Stuber
- Department of Entomology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - Jamie L Cantoni
- Department of Entomology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Ximena A Olarte Castillo
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY 14853
| | - Laura B Goodman
- Department of Public & Ecosystem Health, Cornell University College of Veterinary Medicine, Ithaca, NY 14853
| | - Craig B Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Megan A Linske
- Department of Entomology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - Scott C Williams
- Department of Environmental Science and Forestry, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, 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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9
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Abstract
The COVID-19 pandemic galvanized the field of virus genomic surveillance, demonstrating its utility for public health. Now, we must harness the momentum that led to increased infrastructure, training, and political will to build a sustainable global genomic surveillance network for other epidemic and endemic viruses. We suggest a generalizable modular sequencing framework wherein users can easily switch between virus targets to maximize cost-effectiveness and maintain readiness for new threats. We also highlight challenges associated with genomic surveillance and when global inequalities persist. We propose solutions to mitigate some of these issues, including training and multilateral partnerships. Exploring alternatives to clinical sequencing can also reduce the cost of surveillance programs. Finally, we discuss how establishing genomic surveillance would aid control programs and potentially provide a warning system for outbreaks, using a global respiratory virus (RSV), an arbovirus (dengue virus), and a regional zoonotic virus (Lassa virus) as examples.
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Affiliation(s)
- Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Chantal B F Vogels
- 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
| | - Ana I Bento
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Bloomington, IN, USA; The Rockefeller Foundation, New York, NY, USA
| | - Chrispin Chaguza
- 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
| | - Christine V F Carrington
- Department of Preclinical Sciences, The University of the West Indies, St. Augustine Campus, St. Augustine, Trinidad and Tobago
| | - Nathan D Grubaugh
- 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 Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA; Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA.
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10
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Chen NFG, Chaguza C, Gagne L, Doucette M, Smole S, Buzby E, Hall J, Ash S, Harrington R, Cofsky S, Clancy S, Kapsak CJ, Sevinsky J, Libuit K, Park DJ, Hemarajata P, Garrigues JM, Green NM, Sierra-Patev S, Carpenter-Azevedo K, Huard RC, Pearson C, Incekara K, Nishimura C, Huang JP, Gagnon E, Reever E, Razeq J, Muyombwe A, Borges V, Ferreira R, Sobral D, Duarte S, Santos D, Vieira L, Gomes JP, Aquino C, Savino IM, Felton K, Bajwa M, Hayward N, Miller H, Naumann A, Allman R, Greer N, Fall A, Mostafa HH, McHugh MP, Maloney DM, Dewar R, Kenicer J, Parker A, Mathers K, Wild J, Cotton S, Templeton KE, Churchwell G, Lee PA, Pedrosa M, McGruder B, Schmedes S, Plumb MR, Wang X, Barcellos RB, Godinho FMS, Salvato RS, Ceniseros A, Breban MI, Grubaugh ND, Gallagher GR, Vogels CBF. Development of an amplicon-based sequencing approach in response to the global emergence of mpox. PLoS Biol 2023; 21:e3002151. [PMID: 37310918 PMCID: PMC10263305 DOI: 10.1371/journal.pbio.3002151] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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: 01/12/2023] [Accepted: 05/05/2023] [Indexed: 06/15/2023] Open
Abstract
The 2022 multicountry mpox outbreak concurrent with the ongoing Coronavirus Disease 2019 (COVID-19) pandemic further highlighted the need for genomic surveillance and rapid pathogen whole-genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, these methods are resource intensive and require samples with high viral DNA concentrations. Given the atypical clinical presentation of cases associated with the outbreak and uncertainty regarding viral load across both the course of infection and anatomical body sites, there was an urgent need for a more sensitive and broadly applicable sequencing approach. Highly multiplexed amplicon-based sequencing (PrimalSeq) was initially developed for sequencing of Zika virus, and later adapted as the main sequencing approach for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Here, we used PrimalScheme to develop a primer scheme for human monkeypox virus that can be used with many sequencing and bioinformatics pipelines implemented in public health laboratories during the COVID-19 pandemic. We sequenced clinical specimens that tested presumptively positive for human monkeypox virus with amplicon-based and metagenomic sequencing approaches. We found notably higher genome coverage across the virus genome, with minimal amplicon drop-outs, in using the amplicon-based sequencing approach, particularly in higher PCR cycle threshold (Ct) (lower DNA titer) samples. Further testing demonstrated that Ct value correlated with the number of sequencing reads and influenced the percent genome coverage. To maximize genome coverage when resources are limited, we recommend selecting samples with a PCR Ct below 31 Ct and generating 1 million sequencing reads per sample. To support national and international public health genomic surveillance efforts, we sent out primer pool aliquots to 10 laboratories across the United States, United Kingdom, Brazil, and Portugal. These public health laboratories successfully implemented the human monkeypox virus primer scheme in various amplicon sequencing workflows and with different sample types across a range of Ct values. Thus, we show that amplicon-based sequencing can provide a rapidly deployable, cost-effective, and flexible approach to pathogen whole-genome sequencing in response to newly emerging pathogens. Importantly, through the implementation of our primer scheme into existing SARS-CoV-2 workflows and across a range of sample types and sequencing platforms, we further demonstrate the potential of this approach for rapid outbreak response.
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Affiliation(s)
- Nicholas F. G. Chen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Luc Gagne
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Matthew Doucette
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Sandra Smole
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Erika Buzby
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Joshua Hall
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Stephanie Ash
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Rachel Harrington
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Seana Cofsky
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Selina Clancy
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Curtis J. Kapsak
- Theiagen Genomics, Highlands Ranch, Colorado, United States of America
| | - Joel Sevinsky
- Theiagen Genomics, Highlands Ranch, Colorado, United States of America
| | - Kevin Libuit
- Theiagen Genomics, Highlands Ranch, Colorado, United States of America
| | - Daniel J. Park
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Peera Hemarajata
- Los Angeles County Public Health Laboratories, Downey, California, United States of America
| | - Jacob M. Garrigues
- Los Angeles County Public Health Laboratories, Downey, California, United States of America
| | - Nicole M. Green
- Los Angeles County Public Health Laboratories, Downey, California, United States of America
| | - Sean Sierra-Patev
- Rhode Island Department of Health, Rhode Island State Health Laboratory, Providence, Rhode Island, United States of America
| | - Kristin Carpenter-Azevedo
- Rhode Island Department of Health, Rhode Island State Health Laboratory, Providence, Rhode Island, United States of America
| | - Richard C. Huard
- Rhode Island Department of Health, Rhode Island State Health Laboratory, Providence, Rhode Island, United States of America
| | - Claire Pearson
- Connecticut Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Kutluhan Incekara
- Connecticut Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Christina Nishimura
- Connecticut Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Jian Ping Huang
- Connecticut Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Emily Gagnon
- Connecticut Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Ethan Reever
- Connecticut Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Jafar Razeq
- Connecticut Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Anthony Muyombwe
- Connecticut Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Rita Ferreira
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniel Sobral
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Silvia Duarte
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniela Santos
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Luís Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Carly Aquino
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Isabella M. Savino
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Karinda Felton
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Moneeb Bajwa
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Nyjil Hayward
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Holly Miller
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Allison Naumann
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Ria Allman
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Neel Greer
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Amary Fall
- Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Heba H. Mostafa
- Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Martin P. McHugh
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
- School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | - Daniel M. Maloney
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Rebecca Dewar
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Juliet Kenicer
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Abby Parker
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Katharine Mathers
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Jonathan Wild
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Seb Cotton
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Kate E. Templeton
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - George Churchwell
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, Florida, United States of America
| | - Philip A. Lee
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, Florida, United States of America
| | - Maria Pedrosa
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, Florida, United States of America
| | - Brenna McGruder
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, Florida, United States of America
| | - Sarah Schmedes
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, Florida, United States of America
| | - Matthew R. Plumb
- Minnesota Department of Health, Public Health Laboratory, St. Paul, Minnesota, United States of America
| | - Xiong Wang
- Minnesota Department of Health, Public Health Laboratory, St. Paul, Minnesota, United States of America
| | - Regina Bones Barcellos
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Fernanda M. S. Godinho
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Richard Steiner Salvato
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Aimee Ceniseros
- Idaho Bureau of Laboratories, Boise, Idaho, 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
| | - 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
| | - Glen R. Gallagher
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
- Rhode Island Department of Health, Rhode Island State Health Laboratory, Providence, Rhode Island, 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
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11
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Hill V, Koch RT, Bialosuknia SM, Ngo K, Zink SD, Koetzner CA, Maffei JG, Dupuis AP, Backenson PB, Oliver J, Bransfield AB, Misencik MJ, Petruff TA, Shepard JJ, Warren JL, Gill MS, Baele G, Vogels CBF, Gallagher G, Burns P, Hentoff A, Smole S, Brown C, Osborne M, Kramer LD, Armstrong PM, Ciota AT, Grubaugh ND. Dynamics of eastern equine encephalitis virus during the 2019 outbreak in the Northeast United States. Curr Biol 2023:S0960-9822(23)00679-6. [PMID: 37295427 DOI: 10.1016/j.cub.2023.05.047] [Citation(s) in RCA: 1] [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: 03/09/2023] [Revised: 05/04/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023]
Abstract
Eastern equine encephalitis virus (EEEV) causes a rare but severe disease in horses and humans and is maintained in an enzootic transmission cycle between songbirds and Culiseta melanura mosquitoes. In 2019, the largest EEEV outbreak in the United States for more than 50 years occurred, centered in the Northeast. To explore the dynamics of the outbreak, we sequenced 80 isolates of EEEV and combined them with existing genomic data. We found that, similar to previous years, cases were driven by multiple independent but short-lived virus introductions into the Northeast from Florida. Once in the Northeast, we found that Massachusetts was important for regional spread. We found no evidence of any changes in viral, human, or bird factors which would explain the increase in cases in 2019, although the ecology of EEEV is complex and further data is required to explore these in more detail. By using detailed mosquito surveillance data collected by Massachusetts and Connecticut, however, we found that the abundance of Cs. melanura was exceptionally high in 2019, as was the EEEV infection rate. We employed these mosquito data to build a negative binomial regression model and applied it to estimate early season risks of human or horse cases. We found that the month of first detection of EEEV in mosquito surveillance data and vector index (abundance multiplied by infection rate) were predictive of cases later in the season. We therefore highlight the importance of mosquito surveillance programs as an integral part of public health and disease control.
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Affiliation(s)
- Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA.
| | - Robert T Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Sean M Bialosuknia
- The Arbovirus Laboratory, New York State Department of Health, Wadsworth Center, Slingerlands, NY 12159, USA
| | - Kiet Ngo
- The Arbovirus Laboratory, New York State Department of Health, Wadsworth Center, Slingerlands, NY 12159, USA
| | - Steven D Zink
- The Arbovirus Laboratory, New York State Department of Health, Wadsworth Center, Slingerlands, NY 12159, USA
| | - Cheri A Koetzner
- The Arbovirus Laboratory, New York State Department of Health, Wadsworth Center, Slingerlands, NY 12159, USA
| | - Joseph G Maffei
- The Arbovirus Laboratory, New York State Department of Health, Wadsworth Center, Slingerlands, NY 12159, USA
| | - Alan P Dupuis
- The Arbovirus Laboratory, New York State Department of Health, Wadsworth Center, Slingerlands, NY 12159, USA
| | - P Bryon Backenson
- New York State Department of Health, Bureau of Communicable Disease Control, Albany, NY 12237, USA
| | - JoAnne Oliver
- New York State Department of Health, Bureau of Communicable Disease Control, Syracuse, NY 13202, USA; Division of Environmental and Renewable Resources, State University of New York at Morrisville - School of Agriculture, Business and Technology, Morrisville, NY 13408, USA
| | - Angela B Bransfield
- Center for Vector Biology and Zoonotic Diseases, Department of Entomology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - Michael J Misencik
- Center for Vector Biology and Zoonotic Diseases, Department of Entomology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - Tanya A Petruff
- Center for Vector Biology and Zoonotic Diseases, Department of Entomology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - John J Shepard
- Center for Vector Biology and Zoonotic Diseases, Department of Entomology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| | - Joshua L Warren
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA; Public Health Modeling Unit, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mandev S Gill
- Department of Statistics, University of Georgia, Athens, GA 30602, USA
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven BE-3000, Belgium
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Glen Gallagher
- Massachusetts Department of Public Health, Boston, MA 02108, USA; Rhode Island State Health Laboratory, Rhode Island Department of Health, Providence, RI 02904, USA
| | - Paul Burns
- Massachusetts Department of Public Health, Boston, MA 02108, USA
| | - Aaron Hentoff
- Massachusetts Department of Public Health, Boston, MA 02108, USA
| | - Sandra Smole
- Massachusetts Department of Public Health, Boston, MA 02108, USA
| | - Catherine Brown
- Massachusetts Department of Public Health, Boston, MA 02108, USA
| | - Matthew Osborne
- Massachusetts Department of Public Health, Boston, MA 02108, USA
| | - Laura D Kramer
- The Arbovirus Laboratory, New York State Department of Health, Wadsworth Center, Slingerlands, NY 12159, USA; Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Albany, NY 12237, USA
| | - Philip M Armstrong
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA; Division of Environmental and Renewable Resources, State University of New York at Morrisville - School of Agriculture, Business and Technology, Morrisville, NY 13408, USA.
| | - Alexander T Ciota
- The Arbovirus Laboratory, New York State Department of Health, Wadsworth Center, Slingerlands, NY 12159, USA; Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Albany, NY 12237, USA.
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA; Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
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12
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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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13
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Hill V, Koch RT, Bialosuknia SM, Ngo K, Zink SD, Koetzner CA, Maffei JG, Dupuis AP, Backenson PB, Oliver J, Bransfield AB, Misencik MJ, Petruff TA, Shepard JJ, Warren JL, Gill MS, Baele G, Vogels CBF, Gallagher G, Burns P, Hentoff A, Smole S, Brown C, Osborne M, Kramer LD, Armstrong PM, Ciota AT, Grubaugh ND. Dynamics of Eastern equine encephalitis virus during the 2019 outbreak in the Northeast United States. medRxiv 2023:2023.03.06.23286851. [PMID: 36945576 PMCID: PMC10029029 DOI: 10.1101/2023.03.06.23286851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Eastern equine encephalitis virus (EEEV) causes a rare but severe disease in horses and humans, and is maintained in an enzootic transmission cycle between songbirds and Culiseta melanura mosquitoes. In 2019, the largest EEEV outbreak in the United States for more than 50 years occurred, centered in the Northeast. To explore the dynamics of the outbreak, we sequenced 80 isolates of EEEV and combined them with existing genomic data. We found that, like previous years, cases were driven by frequent short-lived virus introductions into the Northeast from Florida. Once in the Northeast, we found that Massachusetts was important for regional spread. We found no evidence of any changes in viral, human, or bird factors which would explain the increase in cases in 2019. By using detailed mosquito surveillance data collected by Massachusetts and Connecticut, however, we found that the abundance of Cs. melanura was exceptionally high in 2019, as was the EEEV infection rate. We employed these mosquito data to build a negative binomial regression model and applied it to estimate early season risks of human or horse cases. We found that the month of first detection of EEEV in mosquito surveillance data and vector index (abundance multiplied by infection rate) were predictive of cases later in the season. We therefore highlight the importance of mosquito surveillance programs as an integral part of public health and disease control.
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14
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Filardi BA, Monteiro VS, Schwartzmann PV, do Prado Martins V, Zucca LER, Baiocchi GC, Malik AA, Silva J, Hahn AM, Chen NFG, Pham K, Pérez-Then E, Miric M, Brache V, Cochon L, Larocca RA, Mendez RDR, Bardini Silveira D, Pinto AR, Croda J, Yildirim I, Omer SB, Ko AI, Vermund SH, Grubaugh ND, Iwasaki A, Lucas C, Vogels CBF, Breban M, Koch TR, Chaguza C, Tikhonova I, Castaldi C, Mane S, De Kumar B, Ferguson D, Kerantzas N, Peaper D, Landry ML, Schulz W. Age-dependent impairment in antibody responses elicited by a homologous CoronaVac booster dose. Sci Transl Med 2023; 15:eade6023. [PMID: 36791210 DOI: 10.1126/scitranslmed.ade6023] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The emergence of the SARS-CoV-2 Omicron sublineages resulted in increased transmission rates and reduced protection from vaccines. To counteract these effects, multiple booster strategies were used in different countries, although data comparing their efficiency in improving protective immunity remain sparse, especially among vulnerable populations, including older adults. The inactivated CoronaVac vaccine was among the most widely distributed vaccine worldwide and was essential in the early control of SARS-CoV-2-related hospitalizations and deaths. However, it is not well understood whether homologous versus heterologous booster doses in those fully vaccinated with CoronaVac induce distinct humoral responses or whether these responses vary across age groups. We analyzed plasma antibody responses from CoronaVac-vaccinated younger or older individuals who received a homologous CoronaVac or heterologous BNT162b2 or ChAdOx1 booster vaccine. All three evaluated boosters resulted in increased virus-specific IgG titers 28 days after the booster dose. However, we found that both IgG titers against SARS-CoV-2 Spike or RBD and neutralization titers against Omicron sublineages were substantially reduced in participants who received homologous CoronaVac compared with the heterologous BNT162b2 or ChAdOx1 booster. This effect was specifically prominent in recipients >50 years of age. In this group, the CoronaVac booster induced low virus-specific IgG titers and failed to elevate neutralization titers against any Omicron sublineage. Our results point to the notable inefficiency of CoronaVac immunization and boosting in mounting protective antiviral humoral immunity, particularly among older adults, during the Omicron wave. These observations also point to benefits of heterologous regimens in high-risk populations fully vaccinated with CoronaVac.
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Affiliation(s)
- Bruno Andraus Filardi
- Instituto do Cancer Brasil - Unidade de Ribeirão Preto, São Paulo, São Paulo, Brazil.,Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, São Paulo, São Paulo, Brazil
| | | | - Pedro Vellosa Schwartzmann
- Intensive Cardiac Unit, Hospital Unimed Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil.,Advanced Research Center - CAPED, Centro Médico Ribeirão Shopping, Ribeirão Preto, São Paulo, Brazil
| | | | | | - Gabriela Crispim Baiocchi
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Amyn A Malik
- 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
| | - Julio Silva
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Nicholas F G Chen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kien Pham
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Eddy Pérez-Then
- Ministry of Health, Santo Domingo, Dominican Republic.,Two Oceans in Health, Santo Domingo, Dominican Republic
| | - Marija Miric
- Two Oceans in Health, Santo Domingo, Dominican Republic
| | - Vivian Brache
- Profamilia, Biomedical Research Department, Santo Domingo, Dominican Republic
| | - Leila Cochon
- Intensive Cardiac Unit, Hospital Unimed Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Rafael A Larocca
- Center of Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | - Douglas Bardini Silveira
- Laboratório de Imunologia Aplicada, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Aguinaldo Roberto Pinto
- Laboratório de Imunologia Aplicada, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Julio Croda
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.,Oswaldo Cruz Foundation Mato Grosso do Sul, Campo Grande, Brazil.,Federal University of Mato Grosso do Sul, Campo Grande, Brazil
| | - Inci Yildirim
- Yale Institute for Global Health, Yale University, New Haven, CT, USA.,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
| | - Saad B Omer
- 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.,Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Albert I Ko
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA.,Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.,Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, BA, Brazil
| | - Sten H Vermund
- Department of Pediatric, Section of Infectious Diseases and Global Health, Yale University School of Medicine, New Haven, CT, USA.,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
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.,Center for Infection and Immunity, Yale University, New Haven, CT, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Carolina Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.,Center for Infection and Immunity, Yale University, New Haven, CT, USA
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15
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Oliveira G, Vogels CBF, Zolfaghari A, Saraf S, Klitting R, Weger-Lucarelli J, P. Leon K, Ontiveros CO, Agarwal R, Tsetsarkin KA, Harris E, Ebel GD, Wohl S, Grubaugh ND, Andersen KG. Genomic and phenotypic analyses suggest moderate fitness differences among Zika virus lineages. PLoS Negl Trop Dis 2023; 17:e0011055. [PMID: 36753510 PMCID: PMC9907835 DOI: 10.1371/journal.pntd.0011055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 12/22/2022] [Indexed: 02/09/2023] Open
Abstract
RNA viruses have short generation times and high mutation rates, allowing them to undergo rapid molecular evolution during epidemics. However, the extent of RNA virus phenotypic evolution within epidemics and the resulting effects on fitness and virulence remain mostly unknown. Here, we screened the 2015-2016 Zika epidemic in the Americas for lineage-specific fitness differences. We engineered a library of recombinant viruses representing twelve major Zika virus lineages and used them to measure replicative fitness within disease-relevant human primary cells and live mosquitoes. We found that two of these lineages conferred significant in vitro replicative fitness changes among human primary cells, but we did not find fitness changes in Aedes aegypti mosquitoes. Additionally, we found evidence for elevated levels of positive selection among five amino acid sites that define major Zika virus lineages. While our work suggests that Zika virus may have acquired several phenotypic changes during a short time scale, these changes were relatively moderate and do not appear to have enhanced transmission during the epidemic.
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Affiliation(s)
- Glenn Oliveira
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 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
| | - Ashley Zolfaghari
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Sharada Saraf
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Raphaelle Klitting
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Karla P. Leon
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Carlos O. Ontiveros
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Rimjhim Agarwal
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Konstantin A. Tsetsarkin
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, 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
| | - Shirlee Wohl
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 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
- * E-mail: (NDG); (KGA)
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail: (NDG); (KGA)
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16
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Hart C, Hassett E, Vogels CBF, Shapley D, Grubaugh ND, Thangamani S. Powassan Virus Lineage I in Field-Collected Dermacentor variabilis Ticks, New York, USA. Emerg Infect Dis 2023; 29:415-417. [PMID: 36692472 PMCID: PMC9881768 DOI: 10.3201/eid2902.220410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Powassan virus is a tickborne flavivirus that can cause lethal or debilitating neurologic illness. It is canonically transmitted by Ixodes spp. ticks but might spill over to sympatric Dermacentor species. We detected Powassan virus lineage I from a pool of field-collected D. variabilis ticks in New York, USA.
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17
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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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18
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Garrigues JM, Hemarajata P, Lucero B, Alarcón J, Ransohoff H, Marutani AN, Kim M, Marlowe EM, Realegeno SE, Kagan RM, Montero CI, Chen NFG, Grubaugh ND, Vogels CBF, Green NM. Identification of Human Monkeypox Virus Genome Deletions That Impact Diagnostic Assays. J Clin Microbiol 2022; 60:e0165522. [PMID: 36445125 PMCID: PMC9769645 DOI: 10.1128/jcm.01655-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Affiliation(s)
| | - Peera Hemarajata
- Los Angeles County Department of Public Health, Downey, California, USA
| | - Briar Lucero
- Los Angeles County Department of Public Health, Downey, California, USA
| | - Jemma Alarcón
- Los Angeles County Department of Public Health, Downey, California, USA
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Heidi Ransohoff
- Los Angeles County Department of Public Health, Downey, California, USA
| | - Amy N. Marutani
- Los Angeles County Department of Public Health, Downey, California, USA
| | - Moon Kim
- Los Angeles County Department of Public Health, Downey, California, USA
| | | | - Susan E. Realegeno
- Infectious Diseases, Quest Diagnostics, San Juan Capistrano, California, USA
| | - Ron M. Kagan
- Infectious Diseases, Quest Diagnostics, San Juan Capistrano, California, USA
| | - Clemente I. Montero
- Infectious Diseases, Quest Diagnostics, San Juan Capistrano, California, USA
| | - Nicholas F. G. Chen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Chantal B. F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Nicole M. Green
- Los Angeles County Department of Public Health, Downey, California, USA
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19
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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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20
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Poterek ML, Vogels CBF, Grubaugh ND, Ebel GD, Alex Perkins T, Cavany SM. Interactions between seasonal temperature variation and temporal synchrony drive increased arbovirus co-infection incidence. R Soc Open Sci 2022; 9:220829. [PMID: 36277835 PMCID: PMC9579765 DOI: 10.1098/rsos.220829] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/27/2022] [Indexed: 05/11/2023]
Abstract
Though instances of arthropod-borne (arbo)virus co-infection have been documented clinically, the overall incidence of arbovirus co-infection and its drivers are not well understood. Now that dengue, Zika and chikungunya viruses are all in circulation across tropical and subtropical regions of the Americas, it is important to understand the environmental and biological conditions that make co-infections more likely to occur. To understand this, we developed a mathematical model of co-circulation of two arboviruses, with transmission parameters approximating dengue, Zika and/or chikungunya viruses, and co-infection possible in both humans and mosquitoes. We examined the influence of seasonal timing of arbovirus co-circulation on the extent of co-infection. By undertaking a sensitivity analysis of this model, we examined how biological factors interact with seasonality to determine arbovirus co-infection transmission and prevalence. We found that temporal synchrony of the co-infecting viruses and average temperature were the most influential drivers of co-infection incidence. Our model highlights the synergistic effect of co-transmission from mosquitoes, which leads to more than double the number of co-infections than would be expected in a scenario without co-transmission. Our results suggest that appreciable numbers of co-infections are unlikely to occur except in tropical climates when the viruses co-occur in time and space.
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Affiliation(s)
- Marya L. Poterek
- Eck Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Chantal B. F. Vogels
- 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
| | - Gregory D. Ebel
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - T. Alex Perkins
- Eck Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Sean M. Cavany
- Eck Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
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21
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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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22
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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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23
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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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24
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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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25
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Pérez-Then E, Lucas C, Monteiro VS, Miric M, Brache V, Cochon L, Vogels CBF, Malik AA, De la Cruz E, Jorge A, De Los Santos M, Leon P, Breban MI, Billig K, Yildirim I, Pearson C, Downing R, Gagnon E, Muyombwe A, Razeq J, Campbell M, Ko AI, Omer SB, Grubaugh ND, Vermund SH, Iwasaki A. Neutralizing antibodies against the SARS-CoV-2 Delta and Omicron variants following heterologous CoronaVac plus BNT162b2 booster vaccination. Nat Med 2022; 28:481-485. [PMID: 35051990 PMCID: PMC8938264 DOI: 10.1038/s41591-022-01705-6] [Citation(s) in RCA: 261] [Impact Index Per Article: 130.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 01/18/2022] [Indexed: 11/15/2022]
Abstract
The recent emergence of the SARS-CoV-2 Omicron variant is raising concerns because of its increased transmissibility and its numerous spike mutations, which have the potential to evade neutralizing antibodies elicited by COVID-19 vaccines. Here we evaluated the effects of a heterologous BNT162b2 mRNA vaccine booster on the humoral immunity of participants who had received a two-dose regimen of CoronaVac, an inactivated vaccine used globally. We found that a heterologous CoronaVac prime vaccination of two doses followed by a BNT162b2 booster induces elevated virus-specific antibody levels and potent neutralization activity against the ancestral virus and the Delta variant, resembling the titers obtained after two doses of mRNA vaccines. Although neutralization of Omicron was undetectable in participants who had received a two-dose regimen of CoronaVac, the BNT162b2 booster resulted in a 1.4-fold increase in neutralization activity against Omicron compared with the two-dose mRNA vaccine. Despite this increase, neutralizing antibody titers were reduced by 7.1-fold and 3.6-fold for Omicron compared with the ancestral strain and the Delta variant, respectively. These findings have immediate implications for multiple countries that previously used a CoronaVac regimen and reinforce the idea that the Omicron variant is associated with immune escape from vaccines or infection-induced immunity, highlighting the global need for vaccine boosters to combat the impact of emerging variants.
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Affiliation(s)
| | - Carolina Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
| | | | - Marija Miric
- Two Oceans in Health, Santo Domingo, Dominican Republic
| | - Vivian Brache
- Biomedical Research Department, Profamilia, Santo Domingo, Dominican Republic
| | - Leila Cochon
- Biomedical Research Department, Profamilia, Santo Domingo, Dominican Republic
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Amyn A Malik
- Yale Institute for Global Health, Yale University, New Haven, CT, USA
- Section of Infectious Diseases, Department of Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Elena De la Cruz
- Biomedical Research Department, Profamilia, Santo Domingo, Dominican Republic
| | - Aidelis Jorge
- Biomedical Research Department, Profamilia, Santo Domingo, Dominican Republic
| | | | - Patricia Leon
- Laboratorio de Referencia, Santo Domingo, Dominican Republic
| | - 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
| | - Inci Yildirim
- 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
- Section of Infectious Diseases and Global Health, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Claire Pearson
- Connecticut State Department of Public Health, Rocky Hill, CT, USA
| | - Randy Downing
- Connecticut State Department of Public Health, Rocky Hill, CT, USA
| | - Emily Gagnon
- Connecticut State Department of Public Health, Rocky Hill, CT, USA
| | - Anthony Muyombwe
- Connecticut State Department of Public Health, Rocky Hill, CT, USA
| | - Jafar Razeq
- Connecticut State Department of Public Health, Rocky Hill, CT, USA
| | - Melissa Campbell
- Section of Infectious Diseases and Global Health, Department of Pediatrics, 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
- Section of Infectious Diseases, Department of Medicine, Yale University School of Medicine, New Haven, CT, USA
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - 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
- Section of Infectious Diseases, Department of 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
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | | | - Akiko Iwasaki
- Ministry of Health, Santo Domingo, Dominican Republic.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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26
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Unterman A, Sumida TS, Nouri N, Yan X, Zhao AY, Gasque V, Schupp JC, Asashima H, Liu Y, Cosme C, Deng W, Chen M, Raredon MSB, Hoehn KB, Wang G, Wang Z, DeIuliis G, Ravindra NG, Li N, Castaldi C, Wong P, Fournier J, Bermejo S, Sharma L, Casanovas-Massana A, Vogels CBF, Wyllie AL, Grubaugh ND, Melillo A, Meng H, Stein Y, Minasyan M, Mohanty S, Ruff WE, Cohen I, Raddassi K, Niklason LE, Ko AI, Montgomery RR, Farhadian SF, Iwasaki A, Shaw AC, van Dijk D, Zhao H, Kleinstein SH, Hafler DA, Kaminski N, Dela Cruz CS. Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19. Nat Commun 2022; 13:440. [PMID: 35064122 PMCID: PMC8782894 DOI: 10.1038/s41467-021-27716-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [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: 07/28/2020] [Accepted: 12/03/2021] [Indexed: 02/06/2023] Open
Abstract
Dysregulated immune responses against the SARS-CoV-2 virus are instrumental in severe COVID-19. However, the immune signatures associated with immunopathology are poorly understood. Here we use multi-omics single-cell analysis to probe the dynamic immune responses in hospitalized patients with stable or progressive course of COVID-19, explore V(D)J repertoires, and assess the cellular effects of tocilizumab. Coordinated profiling of gene expression and cell lineage protein markers shows that S100Ahi/HLA-DRlo classical monocytes and activated LAG-3hi T cells are hallmarks of progressive disease and highlights the abnormal MHC-II/LAG-3 interaction on myeloid and T cells, respectively. We also find skewed T cell receptor repertories in expanded effector CD8+ clones, unmutated IGHG+ B cell clones, and mutated B cell clones with stable somatic hypermutation frequency over time. In conclusion, our in-depth immune profiling reveals dyssynchrony of the innate and adaptive immune interaction in progressive COVID-19.
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MESH Headings
- Adaptive Immunity/drug effects
- Adaptive Immunity/genetics
- Adaptive Immunity/immunology
- Aged
- Antibodies, Monoclonal, Humanized/therapeutic use
- CD4-Positive T-Lymphocytes/drug effects
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/metabolism
- CD8-Positive T-Lymphocytes/drug effects
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- COVID-19/genetics
- COVID-19/immunology
- Cells, Cultured
- Female
- Gene Expression Profiling/methods
- Gene Expression Regulation/drug effects
- Gene Expression Regulation/immunology
- Humans
- Immunity, Innate/drug effects
- Immunity, Innate/genetics
- Immunity, Innate/immunology
- Male
- RNA-Seq/methods
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/immunology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- SARS-CoV-2/drug effects
- SARS-CoV-2/immunology
- SARS-CoV-2/physiology
- Single-Cell Analysis/methods
- COVID-19 Drug Treatment
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Affiliation(s)
- Avraham Unterman
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA.
- Pulmonary Institute, Tel Aviv Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel.
| | - Tomokazu S Sumida
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA.
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA.
| | - Nima Nouri
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Center for Medical Informatics, Yale School of Medicine, New Haven, CT, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Xiting Yan
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Amy Y Zhao
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Victor Gasque
- Department of Computer Science, Yale University, New Haven, CT, USA
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jonas C Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
- Department of Respiratory Medicine, Hannover Medical School and Biomedical Research in End-stage and Obstructive Lung Disease Hannover, German Lung Research Center (DZL), Hannover, Germany
| | - Hiromitsu Asashima
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
| | - Yunqing Liu
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Carlos Cosme
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Wenxuan Deng
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Ming Chen
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Micha Sam Brickman Raredon
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Medical Scientist Training Program, Yale School of Medicine, New Haven, CT, USA
| | - Kenneth B Hoehn
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Guilin Wang
- Yale Center for Genome Analysis/Keck Biotechnology Resource Laboratory, Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Giuseppe DeIuliis
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Neal G Ravindra
- Department of Computer Science, Yale University, New Haven, CT, USA
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Ningshan Li
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
- SJTU-Yale Joint Center for Biostatistics and Data Science, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | | | - Patrick Wong
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
| | - John Fournier
- School of Medicine, Yale University, New Haven, CT, USA
| | - Santos Bermejo
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Lokesh Sharma
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Arnau Casanovas-Massana
- 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
| | - Anne L Wyllie
- 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
| | - Anthony Melillo
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Hailong Meng
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Yan Stein
- Pulmonary Institute, Tel Aviv Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel
| | - Maksym Minasyan
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Subhasis Mohanty
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - William E Ruff
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
| | - Inessa Cohen
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
| | - Khadir Raddassi
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
| | - Laura E Niklason
- Departments of Anesthesiology & Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Ruth R Montgomery
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Shelli F Farhadian
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Albert C Shaw
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - David van Dijk
- Department of Computer Science, Yale University, New Haven, CT, USA
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- SJTU-Yale Joint Center for Biostatistics and Data Science, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Inter-Departmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Steven H Kleinstein
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Inter-Departmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - David A Hafler
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Charles S Dela Cruz
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
- West Haven Veterans Affair Medical Center, West Haven, CT, USA
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27
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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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28
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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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29
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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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30
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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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31
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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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32
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Takahashi T, Ellingson MK, Wong P, Israelow B, Lucas C, Klein J, Silva J, Mao T, Oh JE, Tokuyama M, Lu P, Venkataraman A, Park A, Liu F, Meir A, Sun J, Wang EY, Casanovas-Massana A, Wyllie AL, Vogels CBF, Earnest R, Lapidus S, Ott IM, Moore AJ, Shaw A, Fournier JB, Odio CD, Farhadian S, Dela Cruz C, Grubaugh ND, Schulz WL, Ring AM, Ko AI, Omer SB, Iwasaki A. Reply to: A finding of sex similarities rather than differences in COVID-19 outcomes. Nature 2021; 597:E10-E11. [PMID: 34552250 DOI: 10.1038/s41586-021-03645-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Takehiro Takahashi
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
| | - Mallory K Ellingson
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
| | - Patrick Wong
- Department of Immunobiology, Yale University School of Medicine, 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
| | - Carolina Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Jon Klein
- 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
| | - Tianyang Mao
- 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
| | - Maria Tokuyama
- 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
| | - Arvind Venkataraman
- 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
| | - Feimei Liu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Biomedical Engineering, Yale School of Engineering and Applied Science, New Haven, CT, USA
| | - Amit Meir
- Boyer Center for Molecular Medicine, Department of Microbial Pathogenesis, Yale University, New Haven, CT, USA
| | - Jonathan Sun
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Eric Y Wang
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Arnau Casanovas-Massana
- 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
| | - Chantal B F Vogels
- 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
| | - Sarah Lapidus
- 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
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Adam J Moore
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Albert Shaw
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - John B Fournier
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Camila D Odio
- Department of Medicine, Section of Infectious Diseases, 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 Dela Cruz
- Department of Medicine, Section of Pulmonary and Critical Care 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
| | - Wade L Schulz
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, CT, USA
| | - Aaron M 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
| | - Saad B Omer
- 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.
- Yale Institute for Global Health, Yale University, New Haven, CT, USA.
- Yale School of Nursing, Yale University, Orange, 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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33
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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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34
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Wang EY, Mao T, Klein J, Dai Y, Huck JD, Jaycox JR, Liu F, Zhou T, Israelow B, Wong P, Coppi A, Lucas C, Silva J, Oh JE, Song E, Perotti ES, Zheng NS, Fischer S, Campbell M, Fournier JB, Wyllie AL, Vogels CBF, Ott IM, Kalinich CC, Petrone ME, Watkins AE, Dela Cruz C, Farhadian SF, Schulz WL, Ma S, Grubaugh ND, Ko AI, Iwasaki A, Ring AM. Diverse functional autoantibodies in patients with COVID-19. Nature 2021; 595:283-288. [PMID: 34010947 DOI: 10.1038/s41586-021-03631-y] [Citation(s) in RCA: 491] [Impact Index Per Article: 163.7] [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: 12/04/2020] [Accepted: 05/11/2021] [Indexed: 12/15/2022]
Abstract
COVID-19 manifests with a wide spectrum of clinical phenotypes that are characterized by exaggerated and misdirected host immune responses1-6. Although pathological innate immune activation is well-documented in severe disease1, the effect of autoantibodies on disease progression is less well-defined. Here we use a high-throughput autoantibody discovery technique known as rapid extracellular antigen profiling7 to screen a cohort of 194 individuals infected with SARS-CoV-2, comprising 172 patients with COVID-19 and 22 healthcare workers with mild disease or asymptomatic infection, for autoantibodies against 2,770 extracellular and secreted proteins (members of the exoproteome). We found that patients with COVID-19 exhibit marked increases in autoantibody reactivities as compared to uninfected individuals, and show a high prevalence of autoantibodies against immunomodulatory proteins (including cytokines, chemokines, complement components and cell-surface proteins). We established that these autoantibodies perturb immune function and impair virological control by inhibiting immunoreceptor signalling and by altering peripheral immune cell composition, and found that mouse surrogates of these autoantibodies increase disease severity in a mouse model of SARS-CoV-2 infection. Our analysis of autoantibodies against tissue-associated antigens revealed associations with specific clinical characteristics. Our findings suggest a pathological role for exoproteome-directed autoantibodies in COVID-19, with diverse effects on immune functionality and associations with clinical outcomes.
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Affiliation(s)
- Eric Y Wang
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Tianyang Mao
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Jon Klein
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Yile Dai
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - John D Huck
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Jillian R Jaycox
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Feimei Liu
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Ting Zhou
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Benjamin Israelow
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Patrick Wong
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Andreas Coppi
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, CT, USA
| | - Carolina Lucas
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Julio Silva
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Ji Eun Oh
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Eric Song
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Emily S Perotti
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Neil S Zheng
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Suzanne Fischer
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Melissa Campbell
- Department of Internal Medicine (Infectious Diseases), Yale School of Medicine, New Haven, CT, USA
| | - John B Fournier
- Department of Internal Medicine (Infectious Diseases), Yale 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
| | - Chantal B F Vogels
- 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
| | - 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
| | - Anne E Watkins
- 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 School of Medicine, New Haven, CT, USA
| | - Shelli F Farhadian
- Department of Internal Medicine (Infectious Diseases), Yale School of Medicine, New Haven, CT, USA
| | - Wade L 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
| | - Shuangge Ma
- Department of Biostatistics, 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
| | - Albert I Ko
- Department of Internal Medicine (Infectious Diseases), Yale School of Medicine, New Haven, CT, USA
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Aaron M Ring
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.
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35
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Lucas C, Klein J, Sundaram ME, Liu F, Wong P, Silva J, Mao T, Oh JE, Mohanty S, Huang J, Tokuyama M, Lu P, Venkataraman A, Park A, Israelow B, Vogels CBF, Muenker MC, Chang CH, Casanovas-Massana A, Moore AJ, Zell J, Fournier JB, Wyllie AL, Campbell M, Lee AI, Chun HJ, Grubaugh ND, Schulz WL, Farhadian S, Dela Cruz C, Ring AM, Shaw AC, Wisnewski AV, Yildirim I, Ko AI, Omer SB, Iwasaki A. Author Correction: Delayed production of neutralizing antibodies correlates with fatal COVID-19. Nat Med 2021; 27:1309. [PMID: 34145437 PMCID: PMC8212078 DOI: 10.1038/s41591-021-01416-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Carolina Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Jon Klein
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Maria E Sundaram
- ICES, Toronto, ON, Canada.,Centre for Vaccine Preventable Diseases, University of Toronto Dalla Lana School of Public Health, Toronto, ON, Canada
| | - Feimei Liu
- 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
| | - Julio Silva
- 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
| | - Ji Eun Oh
- Department of Immunobiology, Yale University School of Medicine, 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
| | - Maria Tokuyama
- 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
| | - Arvind Venkataraman
- 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
| | - 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
| | - Chantal B F Vogels
- 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
| | - C-Hong Chang
- Department of Medicine, Section of Cardiovascular Medicine, Yale University School of Medicine, 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
| | - Joseph Zell
- Department of Internal Medicine/Section General Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - John B Fournier
- Department of Medicine, Section of Infectious Diseases, 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
| | - Melissa Campbell
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Alfred I Lee
- Department of Hematology, Yale University School of Medicine, New Haven, CT, USA
| | - Hyung J Chun
- Department of Medicine, Section of Cardiovascular 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
| | - Wade L Schulz
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA.,Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, CT, USA
| | - Shelli Farhadian
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, 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
| | - Aaron M Ring
- Department of Immunobiology, 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
| | - Adam V Wisnewski
- Department of Internal Medicine/Section General Medicine, Yale University School of Medicine, 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
| | - Albert I Ko
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA.,Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Saad B Omer
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA.,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
| | - 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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36
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Mao T, Israelow B, Lucas C, Vogels CBF, Fedorova O, Breban MI, Menasche BL, Dong H, Linehan M, Wilen CB, Landry ML, Grubaugh ND, Pyle AM, Iwasaki A. A stem-loop RNA RIG-I agonist confers prophylactic and therapeutic protection against acute and chronic SARS-CoV-2 infection in mice. bioRxiv 2021:2021.06.16.448754. [PMID: 34159330 PMCID: PMC8219094 DOI: 10.1101/2021.06.16.448754] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 12/15/2022]
Abstract
As SARS-CoV-2 continues to cause morbidity and mortality around the world, there is an urgent need for the development of effective medical countermeasures. Here, we assessed the antiviral capacity of a minimal RIG-I agonist, stem-loop RNA 14 (SLR14), in viral control, disease prevention, post-infection therapy, and cross-variant protection in mouse models of SARS-CoV-2 infection. A single dose of SLR14 prevented viral replication in the lower respiratory tract and development of severe disease in a type I interferon (IFN-I) dependent manner. SLR14 demonstrated remarkable protective capacity against lethal SARS-CoV-2 infection when used prophylactically and retained considerable efficacy as a therapeutic agent. In immunodeficient mice carrying chronic SARS-CoV-2 infection, SLR14 elicited near-sterilizing innate immunity by inducing IFN-I responses in the absence of the adaptive immune system. In the context of infection with variants of concern (VOC), SLR14 conferred broad protection and uncovered an IFN-I resistance gradient across emerging VOC. These findings demonstrate the therapeutic potential of SLR14 as a host-directed, broad-spectrum antiviral for early post-exposure treatment and for treatment of chronically infected immunosuppressed patients.
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Affiliation(s)
- Tianyang Mao
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Benjamin Israelow
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Carolina Lucas
- Department of Immunobiology, 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
| | - Olga Fedorova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Bridget L. Menasche
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Huiping Dong
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Melissa Linehan
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | | | - Craig B. Wilen
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Marie L. Landry
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
- 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
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Anna M. Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Department of Chemistry, Yale University, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Akiko Iwasaki
- Department of Immunobiology, 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 Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
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37
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Lu-Culligan A, Chavan AR, Vijayakumar P, Irshaid L, Courchaine EM, Milano KM, Tang Z, Pope SD, Song E, Vogels CBF, Lu-Culligan WJ, Campbell KH, Casanovas-Massana A, Bermejo S, Toothaker JM, Lee HJ, Liu F, Schulz W, Fournier J, Muenker MC, Moore AJ, Konnikova L, Neugebauer KM, Ring A, Grubaugh ND, Ko AI, Morotti R, Guller S, Kliman HJ, Iwasaki A, Farhadian SF. Maternal respiratory SARS-CoV-2 infection in pregnancy is associated with a robust inflammatory response at the maternal-fetal interface. Med 2021; 2:591-610.e10. [PMID: 33969332 PMCID: PMC8084634 DOI: 10.1016/j.medj.2021.04.016] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [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: 12/08/2020] [Revised: 02/01/2021] [Accepted: 04/16/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND Pregnant women are at increased risk for severe outcomes from coronavirus disease 2019 (COVID-19), but the pathophysiology underlying this increased morbidity and its potential effect on the developing fetus is not well understood. METHODS We assessed placental histology, ACE2 expression, and viral and immune dynamics at the term placenta in pregnant women with and without respiratory severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. FINDINGS The majority (13 of 15) of placentas analyzed had no detectable viral RNA. ACE2 was detected by immunohistochemistry in syncytiotrophoblast cells of the normal placenta during early pregnancy but was rarely seen in healthy placentas at full term, suggesting that low ACE2 expression may protect the term placenta from viral infection. Using immortalized cell lines and primary isolated placental cells, we found that cytotrophoblasts, the trophoblast stem cells and precursors to syncytiotrophoblasts, rather than syncytiotrophoblasts or Hofbauer cells, are most vulnerable to SARS-CoV-2 infection in vitro. To better understand potential immune mechanisms shielding placental cells from infection in vivo, we performed bulk and single-cell transcriptomics analyses and found that the maternal-fetal interface of SARS-CoV-2-infected women exhibited robust immune responses, including increased activation of natural killer (NK) and T cells, increased expression of interferon-related genes, as well as markers associated with pregnancy complications such as preeclampsia. CONCLUSIONS SARS-CoV-2 infection in late pregnancy is associated with immune activation at the maternal-fetal interface even in the absence of detectable local viral invasion. FUNDING NIH (T32GM007205, F30HD093350, K23MH118999, R01AI157488, U01DA040588) and Fast Grant funding support from Emergent Ventures at the Mercatus Center.
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Affiliation(s)
- Alice Lu-Culligan
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Arun R Chavan
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Pavithra Vijayakumar
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Lina Irshaid
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Edward M Courchaine
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Kristin M Milano
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Zhonghua Tang
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Scott D Pope
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Eric Song
- Department of Immunobiology, 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
| | - William J Lu-Culligan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Katherine H Campbell
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Santos Bermejo
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jessica M Toothaker
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hannah J Lee
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Feimei Liu
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Wade Schulz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - John Fournier
- Section of Infectious Diseases, Department of Medicine, Yale 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
| | - Adam J Moore
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Liza Konnikova
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Aaron Ring
- Department of Immunobiology, 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
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Raffaella Morotti
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Seth Guller
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Harvey J Kliman
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Molecular, Cellular and Developmental Biology, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Shelli F Farhadian
- Section of Infectious Diseases, Department of Medicine, Yale School of Medicine, New Haven, CT, USA
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38
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Mao T, Wang EY, Klein J, Dai Y, Huck JD, Liu F, Zheng NS, Zhou T, Goldman-Israelow B, Wong P, Lucas C, Silva J, Oh JE, Song E, Perotti ES, Fischer S, Campbell M, Fournier JB, Wyllie AL, Vogels CBF, Ott IM, Kalinich CC, Petrone ME, Watkins AE, Cruz CD, Farhadian SF, Schulz WL, Grubaugh ND, Ko AI, Iwasaki A, Ring AM. Diverse Functional Autoantibodies that Underlie Immune Perturbations in COVID-19. The Journal of Immunology 2021. [DOI: 10.4049/jimmunol.206.supp.114.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Abstract
Infection with SARS-CoV-2 results in a broad spectrum of immunological and clinical outcomes for patients with COVID-19. While dysregulated innate immunity has been extensively explored in severe disease, autoantibody responses and their impact on disease trajectories remain uncharted. Here, we enrolled a cohort of 194 SARS-CoV-2 infected patients and uninfected individuals, and employed a high-throughput autoantibody discovery platform, Rapid Extracellular Antigen Profiling (REAP), to assess the prevalence of autoantibodies against 2,770 extracellular and secreted proteins in COVID-19 disease. We found that COVID-19 patients harbor dramatically expanded autoantibody repertoires compared to uninfected controls. We further established that immunomodulatory proteins including cytokines, chemokines, complements, and cell surface receptors, are frequent targets of autoantibodies. Longitudinal analysis revealed the existence of both pre-existing autoantibodies, as well as a broad subset of autoantibodies induced upon SARS-CoV-2 infection. We uncovered distinct mechanisms by which immune-targeting autoantibodies perturb immunological functions, including interference of immunoreceptor signaling, depletion of circulating leukocytes, and modulation of antiviral antibody responses. Concordantly, murine surrogates of these autoantibodies hinder immune activation and exacerbate disease severity in a mouse model of SARS-CoV-2 infection. In summary, through the lens of an unbiased proteome-scale survey for autoantibody targets, these findings implicate humoral immunopathology as an integral aspect of COVID-19 pathogenesis with diverse impacts on immune functionality and clinical outcomes.
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Affiliation(s)
| | | | - Jon Klein
- 1Immunobiology, Yale Univ. Sch. of Med
| | - Yile Dai
- 1Immunobiology, Yale Univ. Sch. of Med
| | | | | | | | - Ting Zhou
- 1Immunobiology, Yale Univ. Sch. of Med
| | | | | | | | | | - Ji Eun Oh
- 1Immunobiology, Yale Univ. Sch. of Med
| | - Eric Song
- 1Immunobiology, Yale Univ. Sch. of Med
| | | | | | | | | | - Anne L. Wyllie
- 3Epidemiology of Microbial Dis., Yale Univ. Sch. of Publ. Hlth
| | | | - Isabel M. Ott
- 3Epidemiology of Microbial Dis., Yale Univ. Sch. of Publ. Hlth
| | | | - Mary E. Petrone
- 3Epidemiology of Microbial Dis., Yale Univ. Sch. of Publ. Hlth
| | - Anne E. Watkins
- 3Epidemiology of Microbial Dis., Yale Univ. Sch. of Publ. Hlth
| | | | | | | | | | - Albert I. Ko
- 3Epidemiology of Microbial Dis., Yale Univ. Sch. of Publ. Hlth
| | - Akiko Iwasaki
- 3Epidemiology of Microbial Dis., Yale Univ. Sch. of Publ. Hlth
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39
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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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40
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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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41
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Ott IM, Strine MS, Watkins AE, Boot M, Kalinich CC, Harden CA, Vogels CBF, Casanovas-Massana A, Moore AJ, Muenker MC, Nakahata M, Tokuyama M, Nelson A, Fournier J, Bermejo S, Campbell M, Datta R, Dela Cruz CS, Farhadian SF, Ko AI, Iwasaki A, Grubaugh ND, Wilen CB, Wyllie AL. Stability of SARS-CoV-2 RNA in Nonsupplemented Saliva. Emerg Infect Dis 2021; 27:1146-1150. [PMID: 33754989 PMCID: PMC8007305 DOI: 10.3201/eid2704.204199] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [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: 12/17/2022] Open
Abstract
The expense of saliva collection devices designed to stabilize severe acute respiratory syndrome coronavirus 2 RNA is prohibitive to mass testing. However, virus RNA in nonsupplemented saliva is stable for extended periods and at elevated temperatures. Simple plastic tubes for saliva collection will make large-scale testing and continued surveillance easier.
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42
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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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43
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Peters J, Alhasan S, Vogels CBF, Grubaugh ND, Farhadian S, Longbrake EE. MOG-associated encephalitis following SARS-COV-2 infection. Mult Scler Relat Disord 2021; 50:102857. [PMID: 33647592 PMCID: PMC7900751 DOI: 10.1016/j.msard.2021.102857] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [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: 01/20/2021] [Revised: 02/14/2021] [Accepted: 02/20/2021] [Indexed: 12/01/2022]
Abstract
A variety of neurologic manifestations of COVID-19 infections have been reported. Here, we present a case of steroid-responsive MOG-antibody associated encephalitis, characterized by cognitive decline, headaches, fever, unilateral FLAIR-hyperintensities, and leptomeningeal enhancement, that occurred in the setting of recent COVID-19 infection.
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Affiliation(s)
- John Peters
- Department of Neurology, Yale University School of Medicine, 333 Cedar St. New Haven, CT, 06510, USA.
| | - Saleh Alhasan
- Department of Neurology, Yale University School of Medicine, 333 Cedar St. New Haven, CT, 06510, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College St, New Haven, CT, 06510, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College St, New Haven, CT, 06510, USA
| | - Shelli Farhadian
- Department of Neurology, Yale University School of Medicine, 333 Cedar St. New Haven, CT, 06510, USA; Department of Medicine, Section of Infectious Disease, Yale University School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA
| | - Erin E Longbrake
- Department of Neurology, Yale University School of Medicine, 333 Cedar St. New Haven, CT, 06510, USA
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44
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Wang EY, Mao T, Klein J, Dai Y, Huck JD, Liu F, Zheng NS, Zhou T, Israelow B, Wong P, Lucas C, Silva J, Oh JE, Song E, Perotti ES, Fischer S, Campbell M, Fournier JB, Wyllie AL, Vogels CBF, Ott IM, Kalinich CC, Petrone ME, Watkins AE, Cruz CD, Farhadian SF, Schulz WL, Grubaugh ND, Ko AI, Iwasaki A, Ring AM. Diverse Functional Autoantibodies in Patients with COVID-19. medRxiv 2021:2020.12.10.20247205. [PMID: 33330894 PMCID: PMC7743105 DOI: 10.1101/2020.12.10.20247205] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
COVID-19 manifests with a wide spectrum of clinical phenotypes that are characterized by exaggerated and misdirected host immune responses1-8. While pathological innate immune activation is well documented in severe disease1, the impact of autoantibodies on disease progression is less defined. Here, we used a high-throughput autoantibody discovery technique called Rapid Extracellular Antigen Profiling (REAP) to screen a cohort of 194 SARS-CoV-2 infected COVID-19 patients and healthcare workers for autoantibodies against 2,770 extracellular and secreted proteins (the "exoproteome"). We found that COVID-19 patients exhibit dramatic increases in autoantibody reactivities compared to uninfected controls, with a high prevalence of autoantibodies against immunomodulatory proteins including cytokines, chemokines, complement components, and cell surface proteins. We established that these autoantibodies perturb immune function and impair virological control by inhibiting immunoreceptor signaling and by altering peripheral immune cell composition, and found that murine surrogates of these autoantibodies exacerbate disease severity in a mouse model of SARS-CoV-2 infection. Analysis of autoantibodies against tissue-associated antigens revealed associations with specific clinical characteristics and disease severity. In summary, these findings implicate a pathological role for exoproteome-directed autoantibodies in COVID-19 with diverse impacts on immune functionality and associations with clinical outcomes.
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Affiliation(s)
- Eric Y. Wang
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Tianyang Mao
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Jon Klein
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Yile Dai
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - John D. Huck
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Feimei Liu
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Neil S. Zheng
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Ting Zhou
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Benjamin Israelow
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Patrick Wong
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Carolina Lucas
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Julio Silva
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Ji Eun Oh
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Eric Song
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Emily S. Perotti
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Suzanne Fischer
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Melissa Campbell
- Department of Internal Medicine (Infectious Diseases), Yale School of Medicine, New Haven, CT, USA
| | - John B. Fournier
- Department of Internal Medicine (Infectious Diseases), Yale 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
| | - Chantal B. F. Vogels
- 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
| | - 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
| | - Anne E. Watkins
- 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 School of Medicine, New Haven, CT, USA
| | - Shelli F. Farhadian
- Department of Internal Medicine (Infectious Diseases), Yale School of Medicine, New Haven, CT, USA
| | - Wade L. Schulz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, CT, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Albert I. Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Internal Medicine (Infectious Diseases), Yale School of Medicine, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Aaron M. Ring
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
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45
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Wichgers Schreur PJ, Vloet RPM, Kant J, van Keulen L, Gonzales JL, Visser TM, Koenraadt CJM, Vogels CBF, Kortekaas J. Reproducing the Rift Valley fever virus mosquito-lamb-mosquito transmission cycle. Sci Rep 2021; 11:1477. [PMID: 33446733 PMCID: PMC7809480 DOI: 10.1038/s41598-020-79267-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 08/14/2020] [Accepted: 11/30/2020] [Indexed: 01/25/2023] Open
Abstract
Rift Valley fever virus (RVFV) is a mosquito-borne bunyavirus that is pathogenic to ruminants and humans. The virus is endemic to Africa and the Arabian Peninsula where outbreaks are characterized by abortion storms and mortality of newborns, particularly in sheep herds. Vector competence experiments in laboratory settings have suggested that over 50 mosquito species are capable of transmitting RVFV. Transmission of mosquito-borne viruses in the field is however influenced by numerous factors, including population densities, blood feeding behavior, extrinsic incubation period, longevity of vectors, and viremia levels in vertebrate hosts. Animal models to study these important aspects of RVFV transmission are currently lacking. In the present work, RVFV was transmitted to European (Texel-swifter cross-breed) lambs by laboratory-reared Aedes aegypti mosquitoes that were infected either by membrane feeding on a virus-spiked blood meal or by feeding on lambs that developed viremia after intravenous inoculation of RVFV. Feeding of mosquitoes on viremic lambs resulted in strikingly higher infection rates as compared to membrane feeding. Subsequent transmission of RVFV from lamb to lamb by infected mosquitoes was highly efficient in both models. The animal models described here can be used to study mosquito-mediated transmission of RVFV among the major natural target species and to evaluate the efficacy of vaccines against mosquito-mediated RVFV infection.
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Affiliation(s)
| | | | - Jet Kant
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | | | - Jose L Gonzales
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Tessa M Visser
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Chantal B F Vogels
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands.,Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Jeroen Kortekaas
- Wageningen Bioveterinary Research, Lelystad, The Netherlands. .,Laboratory of Virology, Wageningen University & Research, Wageningen, The Netherlands.
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46
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Silva J, Lucas C, Sundaram M, Israelow B, Wong P, Klein J, Tokuyama M, Lu P, Venkataraman A, Liu F, Mao T, Oh JE, Park A, Casanovas-Massana A, Vogels CBF, Muenker MC, Zell J, Fournier JB, Campbell M, Chiorazzi M, Fuentes ER, Petrone ME, Kalinich CC, Ott IM, Watkins A, Moore AJ, Nakahata M, Farhadian S, Cruz CD, Ko AI, Schulz WL, Ring A, Ma S, Omer S, Wyllie AL, Iwasaki A. Saliva viral load is a dynamic unifying correlate of COVID-19 severity and mortality. medRxiv 2021:2021.01.04.21249236. [PMID: 33442706 PMCID: PMC7805468 DOI: 10.1101/2021.01.04.21249236] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [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: 12/21/2022]
Abstract
While several clinical and immunological parameters correlate with disease severity and mortality in SARS-CoV-2 infection, work remains in identifying unifying correlates of coronavirus disease 2019 (COVID-19) that can be used to guide clinical practice. Here, we examine saliva and nasopharyngeal (NP) viral load over time and correlate them with patient demographics, and cellular and immune profiling. We found that saliva viral load was significantly higher in those with COVID-19 risk factors; that it correlated with increasing levels of disease severity and showed a superior ability over nasopharyngeal viral load as a predictor of mortality over time (AUC=0.90). A comprehensive analysis of immune factors and cell subsets revealed strong predictors of high and low saliva viral load, which were associated with increased disease severity or better overall outcomes, respectively. Saliva viral load was positively associated with many known COVID-19 inflammatory markers such as IL-6, IL-18, IL-10, and CXCL10, as well as type 1 immune response cytokines. Higher saliva viral loads strongly correlated with the progressive depletion of platelets, lymphocytes, and effector T cell subsets including circulating follicular CD4 T cells (cTfh). Anti-spike (S) and anti-receptor binding domain (RBD) IgG levels were negatively correlated with saliva viral load showing a strong temporal association that could help distinguish severity and mortality in COVID-19. Finally, patients with fatal COVID-19 exhibited higher viral loads, which correlated with the depletion of cTfh cells, and lower production of anti-RBD and anti-S IgG levels. Together these results demonstrated that viral load - as measured by saliva but not nasopharyngeal - is a dynamic unifying correlate of disease presentation, severity, and mortality over time.
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Affiliation(s)
- Julio Silva
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Carolina Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Maria Sundaram
- ICES, Toronto, ON, Canada
- University of Toronto Dalla Lana School of Public Health, Toronto, ON, Canada
| | - 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
| | - Patrick Wong
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Jon Klein
- 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
| | - Peiwen Lu
- 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
| | - Feimei Liu
- 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
| | - 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
| | - Arnau Casanovas-Massana
- 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
| | - M. Catherine Muenker
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Joseph Zell
- Department of Medicine, Section of Pulmonary and Critical Care Medicine; Yale University School of Medicine, New Haven, CT, USA
| | - John B. Fournier
- Department of Medicine, Section of Infectious Diseases, 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
| | - Michael Chiorazzi
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Edwin Ruiz Fuentes
- Department of Immunobiology, Yale University School of Medicine, 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
| | - Isabel M. Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Annie Watkins
- 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
| | - Maura Nakahata
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | - Shelli Farhadian
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, 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
| | - Albert I. Ko
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Wade L. Schulz
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, CT, USA
| | - Aaron Ring
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Shuangge Ma
- Department of Biostatistics, Yale University, New Haven, Connecticut, USA
| | - Saad Omer
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
- 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
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
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47
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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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48
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Lucas C, Klein J, Sundaram M, Liu F, Wong P, Silva J, Mao T, Oh JE, Tokuyama M, Lu P, Venkataraman A, Park A, Israelow B, Wyllie AL, Vogels CBF, Muenker MC, Casanovas-Massana A, Schulz WL, Zell J, Campbell M, Fournier JB, Grubaugh ND, Farhadian S, Wisnewski AV, Cruz CD, Omer S, Ko AI, Ring A, Iwasaki A. Kinetics of antibody responses dictate COVID-19 outcome. medRxiv 2020:2020.12.18.20248331. [PMID: 33398304 PMCID: PMC7781347 DOI: 10.1101/2020.12.18.20248331] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [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: 02/06/2023]
Abstract
Recent studies have provided insights into innate and adaptive immune dynamics in coronavirus disease 2019 (COVID-19). Yet, the exact feature of antibody responses that governs COVID-19 disease outcomes remain unclear. Here, we analysed humoral immune responses in 209 asymptomatic, mild, moderate and severe COVID-19 patients over time to probe the nature of antibody responses in disease severity and mortality. We observed a correlation between anti-Spike (S) IgG levels, length of hospitalization and clinical parameters associated with worse clinical progression. While high anti-S IgG levels correlated with worse disease severity, such correlation was time-dependent. Deceased patients did not have higher overall humoral response than live discharged patients. However, they mounted a robust, yet delayed response, measured by anti-S, anti-RBD IgG, and neutralizing antibody (NAb) levels, compared to survivors. Delayed seroconversion kinetics correlated with impaired viral control in deceased patients. Finally, while sera from 89% of patients displayed some neutralization capacity during their disease course, NAb generation prior to 14 days of disease onset emerged as a key factor for recovery. These data indicate that COVID-19 mortality does not correlate with the cross-sectional antiviral antibody levels per se, but rather with the delayed kinetics of NAb production.
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Affiliation(s)
- Carolina Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- These authors contributed equally: Carolina Lucas, Jon Klein
| | - Jon Klein
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- These authors contributed equally: Carolina Lucas, Jon Klein
| | - Maria Sundaram
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Feimei Liu
- 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
| | - Julio Silva
- 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
| | - Ji Eun Oh
- 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
| | - Peiwen Lu
- 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
| | - Annsea Park
- Department of Immunobiology, Yale University School of Medicine, 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
| | - Anne L. Wyllie
- 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
| | - 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
| | - Wade L. Schulz
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, CT, USA
| | - Joseph Zell
- Department of Internal Medicine/Section General Medicine; 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
| | - John B. Fournier
- 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
| | - Shelli Farhadian
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Adam V. Wisnewski
- Department of Internal Medicine/Section General Medicine; Yale University School of Medicine, 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
| | - Saad Omer
- 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
- Yale Institute for Global Health, Yale University, 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
| | - Aaron Ring
- Department of Immunobiology, 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
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Lucas C, Klein J, Sundaram M, Liu F, Wong P, Silva J, Mao T, Oh JE, Tokuyama M, Lu P, Venkataraman A, Park A, Israelow B, Wyllie AL, Vogels CBF, Muenker MC, Casanovas-Massana A, Schulz WL, Zell J, Campbell M, Fournier JB, Grubaugh ND, Farhadian S, Wisnewski AV, Cruz CD, Omer S, Ko AI, Ring A, Iwasaki A. Kinetics of antibody responses dictate COVID-19 outcome. medRxiv 2020:2020.12.18.20248331. [PMID: 33398304 DOI: 10.1101/2020.06.13.20130252] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Recent studies have provided insights into innate and adaptive immune dynamics in coronavirus disease 2019 (COVID-19). Yet, the exact feature of antibody responses that governs COVID-19 disease outcomes remain unclear. Here, we analysed humoral immune responses in 209 asymptomatic, mild, moderate and severe COVID-19 patients over time to probe the nature of antibody responses in disease severity and mortality. We observed a correlation between anti-Spike (S) IgG levels, length of hospitalization and clinical parameters associated with worse clinical progression. While high anti-S IgG levels correlated with worse disease severity, such correlation was time-dependent. Deceased patients did not have higher overall humoral response than live discharged patients. However, they mounted a robust, yet delayed response, measured by anti-S, anti-RBD IgG, and neutralizing antibody (NAb) levels, compared to survivors. Delayed seroconversion kinetics correlated with impaired viral control in deceased patients. Finally, while sera from 89% of patients displayed some neutralization capacity during their disease course, NAb generation prior to 14 days of disease onset emerged as a key factor for recovery. These data indicate that COVID-19 mortality does not correlate with the cross-sectional antiviral antibody levels per se , but rather with the delayed kinetics of NAb production.
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50
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Möhlmann TWR, Vogels CBF, Göertz GP, Pijlman GP, Ter Braak CJF, Te Beest DE, Hendriks M, Nijhuis EH, Warris S, Drolet BS, van Overbeek L, Koenraadt CJM. Impact of Gut Bacteria on the Infection and Transmission of Pathogenic Arboviruses by Biting Midges and Mosquitoes. Microb Ecol 2020; 80:703-717. [PMID: 32462391 PMCID: PMC7476999 DOI: 10.1007/s00248-020-01517-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 04/23/2020] [Indexed: 05/10/2023]
Abstract
Tripartite interactions among insect vectors, midgut bacteria, and viruses may determine the ability of insects to transmit pathogenic arboviruses. Here, we investigated the impact of gut bacteria on the susceptibility of Culicoides nubeculosus and Culicoides sonorensis biting midges for Schmallenberg virus, and of Aedes aegypti mosquitoes for Zika and chikungunya viruses. Gut bacteria were manipulated by treating the adult insects with antibiotics. The gut bacterial communities were investigated using Illumina MiSeq sequencing of 16S rRNA, and susceptibility to arbovirus infection was tested by feeding insects with an infectious blood meal. Antibiotic treatment led to changes in gut bacteria for all insects. Interestingly, the gut bacterial composition of untreated Ae. aegypti and C. nubeculosus showed Asaia as the dominant genus, which was drastically reduced after antibiotic treatment. Furthermore, antibiotic treatment resulted in relatively more Delftia bacteria in both biting midge species, but not in mosquitoes. Antibiotic treatment and subsequent changes in gut bacterial communities were associated with a significant, 1.8-fold increased infection rate of C. nubeculosus with Schmallenberg virus, but not for C. sonorensis. We did not find any changes in infection rates for Ae. aegypti mosquitoes with Zika or chikungunya virus. We conclude that resident gut bacteria may dampen arbovirus transmission in biting midges, but not so in mosquitoes. Use of antimicrobial compounds at livestock farms might therefore have an unexpected contradictory effect on the health of animals, by increasing the transmission of viral pathogens by biting midges.
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Affiliation(s)
- Tim W R Möhlmann
- Laboratory of Entomology, Wageningen University & Research, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
| | - Chantal B F Vogels
- Laboratory of Entomology, Wageningen University & Research, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College Street, New Haven, CT, 06510, USA
| | - Giel P Göertz
- Laboratory of Virology, Wageningen University & Research, P.O. Box 16, 6700, AA, Wageningen, The Netherlands
| | - Gorben P Pijlman
- Laboratory of Virology, Wageningen University & Research, P.O. Box 16, 6700, AA, Wageningen, The Netherlands
| | - Cajo J F Ter Braak
- Biometris, Wageningen University & Research, P.O. Box 16, 6700, AA, Wageningen, The Netherlands
| | - Dennis E Te Beest
- Biometris, Wageningen University & Research, P.O. Box 16, 6700, AA, Wageningen, The Netherlands
| | - Marc Hendriks
- Biointeractions and Plant Health, Wageningen University & Research, P.O. Box 16, 6700, AA, Wageningen, The Netherlands
| | - Els H Nijhuis
- Biointeractions and Plant Health, Wageningen University & Research, P.O. Box 16, 6700, AA, Wageningen, The Netherlands
| | - Sven Warris
- Bioscience, Wageningen University & Research, P.O. Box 16, 6700, AA, Wageningen, The Netherlands
| | - Barbara S Drolet
- Arthropod-Borne Animal Diseases Research Unit, USDA, Agricultural Research Service, 1515 College Ave, Manhattan, KS, USA
| | - Leo van Overbeek
- Biointeractions and Plant Health, Wageningen University & Research, P.O. Box 16, 6700, AA, Wageningen, The Netherlands
| | - Constantianus J M Koenraadt
- Laboratory of Entomology, Wageningen University & Research, P.O. Box 16, 6700 AA, Wageningen, The Netherlands.
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