1
|
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.
Collapse
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.
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
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.
Collapse
|
4
|
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 CB, Morrison A, Michael SF, Grubaugh ND. Travel surveillance uncovers dengue virus dynamics and introductions in the Caribbean. medRxiv 2023:2023.11.11.23298412. [PMID: 37986857 PMCID: PMC10659465 DOI: 10.1101/2023.11.11.23298412] [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: 11/22/2023]
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.
Collapse
Affiliation(s)
- Emma Taylor-Salmon
- Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Lauren M. Paul
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, United States of America
| | - Robert T. Koch
- 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
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Afeez Sodeinde
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Joshua L. Warren
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
- Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Sylvia Bunch
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, United States of America
| | - Natalia Cano
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, United States of America
| | - Marshall Cone
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, United States of America
| | - Sarah Eysoldt
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, United States of America
| | - Alezaundra Garcia
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, United States of America
| | - Nicadia Gilles
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, United States of America
| | - Andrew Hagy
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, United States of America
| | - Lea Heberlein
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, United States of America
| | - Rayah Jaber
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, United States of America
| | - Elizabeth Kassens
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, United States of America
| | - Pamela Colarusso
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, Florida, United States of America
| | - Amanda Davis
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, Florida, United States of America
| | - Samantha Baudin
- Florida Department of Health in Miami-Dade County, Miami, Florida, United States of America
| | - Edhelene Rico
- Florida Department of Health in Miami-Dade County, Miami, Florida, United States of America
| | - Álvaro Mejía-Echeverri
- Florida Department of Health in Miami-Dade County, Miami, Florida, United States of America
| | - Blake Scott
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, Florida, United States of America
| | - Danielle Stanek
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, Florida, United States of America
| | - Rebecca Zimler
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, Florida, United States of America
| | - 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, Georgia, United States of America
- Bureau for Global Health, United States Agency for International Development, Arlington, Virginia, United States of America
| | - Volha Katebi
- Office of Data, Analytics, and Technology, Division of Global Migration Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - 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, Massachusetts, 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
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, United States of America
| | - Andrea Morrison
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, Florida, United States of America
| | - Scott F. Michael
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, 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
- Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, United States of America
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, United States of America
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| |
Collapse
|
5
|
Vogels CB, Hill V, Breban MI, Chaguza C, Paul LM, Sodeinde A, Taylor-Salmon E, Ott IM, Petrone ME, Dijk D, Jonges M, Welkers MR, 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, Morrison AM, Michael SF, Grubaugh ND. DengueSeq: A pan-serotype whole genome amplicon sequencing protocol for dengue virus. medRxiv 2023:2023.10.13.23296997. [PMID: 37873191 PMCID: PMC10592998 DOI: 10.1101/2023.10.13.23296997] [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] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
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 101-102 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.
Collapse
Affiliation(s)
- Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, United States of America
| | - Verity Hill
- 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
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, United States of America
| | - Lauren M. Paul
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, United States of America
| | - Afeez Sodeinde
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Emma Taylor-Salmon
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Isabel M. Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of 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, United States of America
| | - Yibo Dong
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, United States of America
| | - Namratha Tarigopula
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, United States of America
| | - Omer Tekin
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, United States of America
| | - Sarah Schmedes
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, United States of America
| | - Sylvia Bunch
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, United States of America
| | - Natalia Cano
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, United States of America
| | - Rayah Jaber
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, United States of America
| | - Charles Panzera
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, United States of America
| | - Ian Stryker
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, United States of America
| | - Julieta Vergara
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, United States of America
| | - Rebecca Zimler
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, United States of America
| | - Edgar Kopp
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, United States of America
| | - Lea Heberlein
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, United States of America
| | - Andrea M. Morrison
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, United States of America
| | - Scott F. Michael
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, 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
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, United States of America
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, United States of America
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Allicock OM, Yolda-Carr D, Earnest R, Breban MI, Vega N, Ott IM, Kalinich C, Alpert T, Petrone ME, Wyllie AL. Method versatility in RNA extraction-free PCR detection of SARS-CoV-2 in saliva samples. Prog Biophys Mol Biol 2023; 182:103-108. [PMID: 37369293 PMCID: PMC10290768 DOI: 10.1016/j.pbiomolbio.2023.06.004] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 05/18/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023]
Abstract
Early in the pandemic, a simple, open-source, RNA extraction-free RT-qPCR protocol for SARS-CoV-2 detection in saliva was developed and made widely available. This simplified approach (SalivaDirect) requires only sample treatment with proteinase K prior to PCR testing. However, feedback from clinical laboratories highlighted a need for a flexible workflow that can be seamlessly integrated into their current health and safety requirements for the receiving and handling of potentially infectious samples. To address these varying needs, we explored additional pre-PCR workflows. We built upon the original SalivaDirect workflow to include an initial incubation step (95 °C for 30 min, 95 °C for 5 min or 65 °C for 15 min) with or without addition of proteinase K. The limit of detection for the workflows tested did not significantly differ from that of the original SalivaDirect workflow. When tested on de-identified saliva samples from confirmed COVID-19 individuals, these workflows also produced comparable virus detection and assay sensitivities, as determined by RT-qPCR analysis. Exclusion of proteinase K did not negatively affect the sensitivity of the assay. The addition of multiple heat pretreatment options to the SalivaDirect protocol increases the accessibility of this cost-effective SARS-CoV-2 test as it gives diagnostic laboratories the flexibility to implement the workflow which best suits their safety protocols.
Collapse
Affiliation(s)
- Orchid M Allicock
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA.
| | - Devyn Yolda-Carr
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Noel Vega
- 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
| | - Chaney Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - 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
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Chaguza C, Hahn AM, Petrone ME, Zhou S, Ferguson D, Breban MI, Pham K, Peña-Hernández MA, Castaldi C, Hill V, Schulz W, Swanstrom RI, Roberts SC, Grubaugh ND. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. Cell Rep Med 2023; 4:100943. [PMID: 36791724 PMCID: PMC9906997 DOI: 10.1016/j.xcrm.2023.100943] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [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: 07/01/2022] [Revised: 10/12/2022] [Accepted: 01/20/2023] [Indexed: 01/28/2023]
Abstract
The chronic infection hypothesis for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant emergence is increasingly gaining credence following the appearance of Omicron. Here, we investigate intrahost evolution and genetic diversity of lineage B.1.517 during a SARS-CoV-2 chronic infection lasting for 471 days (and still ongoing) with consistently recovered infectious virus and high viral genome copies. During the infection, we find an accelerated virus evolutionary rate translating to 35 nucleotide substitutions per year, approximately 2-fold higher than the global SARS-CoV-2 evolutionary rate. This intrahost evolution results in the emergence and persistence of at least three genetically distinct genotypes, suggesting the establishment of spatially structured viral populations continually reseeding different genotypes into the nasopharynx. Finally, we track the temporal dynamics of genetic diversity to identify advantageous mutations and highlight hallmark changes for chronic infection. Our findings demonstrate that untreated chronic infections accelerate SARS-CoV-2 evolution, providing an opportunity for the emergence of genetically divergent variants.
Collapse
Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
| | - Anne M Hahn
- 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; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Shuntai Zhou
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David Ferguson
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mallery I Breban
- 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
| | - Mario A Peña-Hernández
- Department of Biological and Biomedical Sciences, Yale School of Medicine, New Haven, CT, USA
| | | | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Wade 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
| | - Ronald I Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott C Roberts
- Infectious Disease, 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.
| |
Collapse
|
11
|
Paulino-Ramírez R, Pham K, Breban MI, Peguero A, Jabier M, Sánchez N, Eustate I, Ruiz I, Grubaugh ND, Hahn AM. Genome Sequence of a Recombinant SARS-CoV-2 Lineage XAM (BA.1.1/BA.2.9) Strain from a Clinical Sample in Santo Domingo, Dominican Republic. Microbiol Resour Announc 2023; 12:e0111322. [PMID: 36448812 PMCID: PMC9872639 DOI: 10.1128/mra.01113-22] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/16/2022] [Indexed: 12/05/2022] Open
Abstract
Here, we report a recombinant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage XAM (Omicron BA.1.1/BA.2.9) strain that was collected in Santo Domingo, Dominican Republic. This demonstrates how SARS-CoV-2 variants can vary greatly between regions and thus underlines the great importance of regional genomic surveillance efforts.
Collapse
Affiliation(s)
- Robert Paulino-Ramírez
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
| | - Kien Pham
- 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
| | - Armando Peguero
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
| | - Maridania Jabier
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
- Servicio Nacional de Salud, Ministry of Health, Santo Domingo, Dominican Republic
| | - Nelissa Sánchez
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
| | - Iscania Eustate
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
- Servicio Nacional de Salud, Ministry of Health, Santo Domingo, Dominican Republic
| | - Ingrid Ruiz
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Anne M. Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| |
Collapse
|
12
|
Chen NF, 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 FM, Salvato RS, Ceniseros A, Breban MI, Grubaugh ND, Gallagher GR, Vogels CB. Development of an amplicon-based sequencing approach in response to the global emergence of human monkeypox virus. medRxiv 2023:2022.10.14.22280783. [PMID: 36299420 PMCID: PMC9603838 DOI: 10.1101/2022.10.14.22280783] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The 2022 multi-country monkeypox (mpox) outbreak concurrent with the ongoing COVID-19 pandemic has 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 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 samples that tested presumptive 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 (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 cycle threshold 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.
Collapse
Affiliation(s)
- Nicholas F.G. Chen
- 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
| | - Luc Gagne
- Massachusetts Department of Public Health, Boston, MA, USA
| | | | - Sandra Smole
- Massachusetts Department of Public Health, Boston, MA, USA
| | - Erika Buzby
- Massachusetts Department of Public Health, Boston, MA, USA
| | - Joshua Hall
- Massachusetts Department of Public Health, Boston, MA, USA
| | - Stephanie Ash
- Massachusetts Department of Public Health, Boston, MA, USA
| | | | - Seana Cofsky
- Massachusetts Department of Public Health, Boston, MA, USA
| | - Selina Clancy
- Massachusetts Department of Public Health, Boston, MA, USA
| | | | | | | | | | | | | | - Nicole M. Green
- Los Angeles County Public Health Laboratories, Downey, CA, USA
| | - Sean Sierra-Patev
- Rhode Island Department of Health, Rhode Island State Health Laboratory, Providence, RI, USA
| | | | - Richard C. Huard
- Rhode Island Department of Health, Rhode Island State Health Laboratory, Providence, RI, USA
| | - Claire Pearson
- Connecticut Department of Public Health, Rocky Hill, CT, USA
| | | | | | - Jian Ping Huang
- Connecticut Department of Public Health, Rocky Hill, CT, USA
| | - Emily Gagnon
- Connecticut Department of Public Health, Rocky Hill, CT, USA
| | - Ethan Reever
- Connecticut Department of Public Health, Rocky Hill, CT, USA
| | - Jafar Razeq
- Connecticut Department of Public Health, Rocky Hill, CT, USA
| | | | - 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, DE, USA
| | | | | | - Moneeb Bajwa
- Delaware Public Health Laboratory, Smyrna, DE, USA
| | | | - Holly Miller
- Delaware Public Health Laboratory, Smyrna, DE, USA
| | | | - Ria Allman
- Delaware Public Health Laboratory, Smyrna, DE, USA
| | - Neel Greer
- Delaware Public Health Laboratory, Smyrna, DE, USA
| | - Amary Fall
- Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Martin P. McHugh
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK,School of Medicine, University of St Andrews, St Andrews, UK
| | - Daniel M. Maloney
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK,Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Rebecca Dewar
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Juliet Kenicer
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Abby Parker
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Katharine Mathers
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Jonathan Wild
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Seb Cotton
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Kate E. Templeton
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - George Churchwell
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, FL, USA
| | - Philip A. Lee
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, FL, USA
| | - Maria Pedrosa
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, FL, USA
| | - Brenna McGruder
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, FL, USA
| | - Sarah Schmedes
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, FL, USA
| | - Matthew R. Plumb
- Minnesota Department of Health, Public Health Laboratory, St. Paul, MN, USA
| | - Xiong Wang
- Minnesota Department of Health, Public Health Laboratory, St. Paul, MN, USA
| | - 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
| | | | - Mallery I. Breban
- 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
| | - Glen R. Gallagher
- Massachusetts Department of Public Health, Boston, MA, USA,Rhode Island Department of Health, Rhode Island State Health Laboratory, Providence, RI, USA
| | - Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Chaguza C, Hahn AM, Petrone ME, Zhou S, Ferguson D, Breban MI, Pham K, Peña-Hernández MA, Castaldi C, Hill V, Schulz W, Swanstrom RI, Roberts SC, Grubaugh ND. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. medRxiv 2022:2022.06.29.22276868. [PMID: 35794895 PMCID: PMC9258298 DOI: 10.1101/2022.06.29.22276868] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The chronic infection hypothesis for novel SARS-CoV-2 variant emergence is increasingly gaining credence following the appearance of Omicron. Here we investigate intrahost evolution and genetic diversity of lineage B.1.517 during a SARS-CoV-2 chronic infection lasting for 471 days (and still ongoing) with consistently recovered infectious virus and high viral loads. During the infection, we found an accelerated virus evolutionary rate translating to 35 nucleotide substitutions per year, approximately two-fold higher than the global SARS-CoV-2 evolutionary rate. This intrahost evolution led to the emergence and persistence of at least three genetically distinct genotypes suggesting the establishment of spatially structured viral populations continually reseeding different genotypes into the nasopharynx. Finally, using unique molecular indexes for accurate intrahost viral sequencing, we tracked the temporal dynamics of genetic diversity to identify advantageous mutations and highlight hallmark changes for chronic infection. Our findings demonstrate that untreated chronic infections accelerate SARS-CoV-2 evolution, ultimately providing opportunity for the emergence of genetically divergent and potentially highly transmissible variants as seen with Delta and Omicron.
Collapse
Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Correspondence: (C.C.) and (N.D.G.)
| | - Anne M. Hahn
- 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
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Shuntai Zhou
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David Ferguson
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mallery I. Breban
- 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
| | - Mario A. Peña-Hernández
- Department of Biological and Biomedical Sciences, Yale School of Medicine, New Haven, Connecticut, USA
| | | | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | - Wade 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
| | - Ronald I. Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 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
- Correspondence: (C.C.) and (N.D.G.)
| |
Collapse
|
15
|
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).
Collapse
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
| |
Collapse
|
16
|
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).
Collapse
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
| |
Collapse
|
17
|
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.
Collapse
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.
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
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.
Collapse
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.
| |
Collapse
|
20
|
Mao T, Israelow B, Lucas C, Vogels CB, Gomez-Calvo ML, 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 protects against acute and chronic SARS-CoV-2 infection in mice. J Exp Med 2022; 219:e20211818. [PMID: 34757384 PMCID: PMC8590200 DOI: 10.1084/jem.20211818] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [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: 08/26/2021] [Revised: 10/19/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022] Open
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 infection in the lower respiratory tract and development of severe disease in a type I interferon (IFN-I)-dependent manner. SLR14 demonstrated remarkable prophylactic protective capacity against lethal SARS-CoV-2 infection and retained considerable efficacy as a therapeutic agent. In immunodeficient mice carrying chronic SARS-CoV-2 infection, SLR14 elicited near-sterilizing innate immunity in the absence of the adaptive immune system. In the context of infection with variants of concern (VOCs), SLR14 conferred broad protection against emerging VOCs. These findings demonstrate the therapeutic potential of SLR14 as a host-directed, broad-spectrum antiviral for early post-exposure treatment and treatment of chronically infected immunosuppressed patients.
Collapse
Affiliation(s)
- Tianyang Mao
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Benjamin Israelow
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT
| | - Carolina Lucas
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT
| | | | - Olga Fedorova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT
- Howard Hughes Medical Institute, Chevy Chase, MD
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT
| | | | - Huiping Dong
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Melissa Linehan
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | | | - Craig B. Wilen
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
| | - Marie L. Landry
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
| | - Anna M. Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT
- Department of Chemistry, Yale University, New Haven, CT
- Howard Hughes Medical Institute, Chevy Chase, MD
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT
- Howard Hughes Medical Institute, Chevy Chase, MD
| |
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Roberts SC, Palacios CF, Grubaugh ND, Alpert T, Ott IM, Breban MI, Martinello RA, Smith C, Davis MW, Mcmanus D, Tirmizi S, Topal JE, Azar MM, Malinis M. An outbreak of SARS-CoV-2 on a transplant unit in the early vaccination era. Transpl Infect Dis 2021; 24:e13782. [PMID: 34969164 DOI: 10.1111/tid.13782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/30/2021] [Accepted: 12/07/2021] [Indexed: 11/29/2022]
Abstract
Solid organ transplant recipients are at increased risk of COVID-19 associated morbidity and mortality. We describe the first nosocomial outbreak investigation on an immunocompromised inpatient unit aided by SARS-CoV-2 whole genome sequencing. Two patients were identified as potential index cases; one presented with diarrhea and the other tested positive on hospital day 18 after developing hypoxemia and subsequently testing positive for SARS-CoV-2. Following identification of the SARS-CoV-2 cluster, the unit was closed to new admissions, and the remaining patients and staff members underwent surveillance SARS-CoV-2 testing. Four additional patients and four staff members tested positive for SARS-CoV-2. Asymptomatic patients with COVID-19 were treated with bamlanivimab and all were alive at discharge. The unit was then re-opened with no additional positives reported since the initial outbreak. Preventing SARS-CoV-2 outbreaks in transplant units poses unique challenges as patients may have atypical presentations of COVID-19. Immunocompromised patients who test positive for SARS-CoV-2 while asymptomatic may benefit from monoclonal antibody therapy to prevent disease progression. All hospital staff members working with immunocompromised patients should be promptly encouraged to receive SARS-CoV-2 vaccination. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Scott C Roberts
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine.,Department of Infection Prevention, Yale New Haven Health
| | - Carlo Foppiano Palacios
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health
| | - Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health
| | - Isabel M Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health
| | -
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine
| | - Richard A Martinello
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine.,Department of Infection Prevention, Yale New Haven Health.,Department of Pediatrics, Yale School of Medicine
| | - Cindy Smith
- Department of Infection Prevention, Yale New Haven Health
| | | | - Dayna Mcmanus
- Department of Pharmacy Services, Yale New Haven Hospital
| | - Samad Tirmizi
- Department of Pharmacy Services, Yale New Haven Hospital
| | - Jeffrey E Topal
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine.,Department of Epidemiology of Microbial Diseases, Yale School of Public Health
| | - Marwan M Azar
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine
| | - Maricar Malinis
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine
| |
Collapse
|
23
|
Kissler SM, Fauver JR, Mack C, Tai CG, Breban MI, Watkins AE, Samant RM, Anderson DJ, Metti J, Khullar G, Baits R, MacKay M, Salgado D, Baker T, Dudley JT, Mason CE, Ho DD, Grubaugh ND, Grad YH. Viral Dynamics of SARS-CoV-2 Variants in Vaccinated and Unvaccinated Persons. N Engl J Med 2021; 385:2489-2491. [PMID: 34941024 PMCID: PMC8693673 DOI: 10.1056/nejmc2102507] [Citation(s) in RCA: 150] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Deverick J Anderson
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Durham, NC
| | | | | | | | | | | | | | | | | | - David D Ho
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | | | | |
Collapse
|
24
|
Wyllie A, Vogels CB, Allicock OM, Watkins A, Petrone M, Yolda-Carr D, Harden C, Brackney D, Kalinich CC, Breban MI, Ott IM, Sikka R, Kadiri L, Grubaugh ND. 362. Saliva as a Reliable Sample Type for Mass SARS-CoV-2 Testing Strategies. Open Forum Infect Dis 2021. [PMCID: PMC8644416 DOI: 10.1093/ofid/ofab466.563] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Background Quickly detecting and isolating individuals positive for SARS-CoV-2 is essential for limiting virus spread. Policy makers rely on the number of active cases to make decisions, and individuals use this information to evaluate risk should they return to public spaces. Robust testing strategies have been plagued with limited authorized diagnostic assays and high test prices, with large-scale implementation hampered by worldwide supply chain issues. Methods Having identified its potential early in the pandemic, we simplified saliva-based COVID-19 diagnostic testing by (1) not requiring collection tubes with preservatives, (2) replacing nucleic acid extraction with a simple enzymatic and heating step, and (3) testing specimens for SARS-CoV-2 in dualplex RT-qPCR. Moreover, we validated this approach (“SalivaDirect”) with reagents and instruments from multiple vendors to circumvent supply chain disruptions. Results SalivaDirect’s simplified protocol does not compromise on sensitivity. In our hospital cohort, we found a high positive agreement (94%) between saliva tested with SalivaDirect and nasopharyngeal swabs tested with a commercial RT-qPCR kit. With the National Basketball Association we tested 3,779 saliva specimens from healthy individuals and detected low rates of invalid (0.3%) and false-positive (< 0.05%) results. Using comparative assays and sample types, we also demonstrated SalivaDirect to efficiently detect SARS-CoV-2 in asymptomatic individuals. SalivaDirect is a simplified method for SARS-CoV-2 detection ![]()
(A) Schematic overview of SalivaDirect workflow depicting the main steps of mixing saliva with proteinase K, heat inactivation, and dualplex qRT-PCR testing. Figure created with Biorender.com. (B) SARS-CoV-2 is stable in saliva for at least 7 days at 4C, room temperature (RT; 19C), and 30C without addition of stabilizing buffers. Spiked-in saliva samples of low virus concentrations (12, 25, and 50 SARS-CoV-2 copies/mL) were kept at the indicated temperature for 7 days and then tested with SalivaDirect. N1 cycle threshold (Ct) values were lower when kept for 7 days at 30C as compared to fresh specimens (Kruskal-Wallis; p = 0.03). Horizontal bars indicate the median. (C) Comparing Ct values for saliva treated with proteinase K and heat as compared to nucleic extraction yields higher N1 Ct values without extraction (Wilcoxon; p < 0.01). (D) Testing extracted nucleic acid from saliva with the N1 primer-probe set (singleplex) as compared to a multiplex assay showed stronger N1 detection in multiplex (Wilcoxon; p < 0.01). The dotted line in (B)–(D) indicates the limit of detection. Conclusion Saliva is a valid alternative to swabs for SARS-CoV-2 screening. Importantly, SalivaDirect enables labs to utilize existing infrastructure, improving test implementation time and requiring limited investment to scale-up to meet mass testing needs. With the safe and reliable self-collection of saliva, our vision is to help provide accessible and equitable testing solutions, especially in low-resource and remote settings. Disclosures Anne Wyllie, PhD, Global Diagnostic Systems (Consultant)Pfizer (Advisor or Review Panel member, Research Grant or Support)PPS Health (Consultant)Tempus Labs, Inc (Research Grant or Support) Nathan D. Grubaugh, PhD, Tempus Labs (Consultant)
Collapse
Affiliation(s)
- Anne Wyllie
- Yale School of Medicine, New Haven, Connecticut
| | | | | | - Anne Watkins
- Yale School of Public Health, New Haven, Connecticut
| | - Mary Petrone
- Yale School of Public Health, New Haven, Connecticut
| | | | | | - Doug Brackney
- Yale School of Public Health, New Haven, Connecticut
| | | | | | - Isabel M Ott
- Yale School of Public Health, New Haven, Connecticut
| | - Robby Sikka
- Minnesota Timberwolves, Minneapolis, Minnesota
| | | | | |
Collapse
|
25
|
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.
Collapse
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.
| |
Collapse
|
26
|
McMillan JR, Harden CA, Burtis JC, Breban MI, Shepard JJ, Petruff TA, Misencik MJ, Bransfield AB, Poggi JD, Harrington LC, Andreadis TG, Armstrong PM. The community-wide effectiveness of municipal larval control programs for West Nile virus risk reduction in Connecticut, USA. Pest Manag Sci 2021; 77:5186-5201. [PMID: 34272800 PMCID: PMC9291174 DOI: 10.1002/ps.6559] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/02/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Mosquito larval control through the use of insecticides is the most common strategy for suppressing West Nile virus (WNV) vector populations in Connecticut (CT), USA. To evaluate the ability of larval control to reduce entomological risk metrics associated with WNV, we performed WNV surveillance and assessments of municipal larvicide application programs in Milford and Stratford, CT in 2019 and 2020. Each town treated catch basins and nonbasin habitats (Milford only) with biopesticide products during both WNV transmission seasons. Adult mosquitoes were collected weekly with gravid and CO2 -baited light traps and tested for WNV; larvae and pupae were sampled weekly from basins within 500 m of trapping sites, and Culex pipiens larval mortality was determined with laboratory bioassays of catch basin water samples. RESULTS Declines in 4th instar larvae and pupae were observed in catch basins up to 2-week post-treatment, and we detected a positive relationship between adult female C. pipiens collections in gravid traps and pupal abundance in basins. We also detected a significant difference in total light trap collections between the two towns. Despite these findings, C. pipiens adult collections and WNV mosquito infection prevalence in gravid traps were similar between towns. CONCLUSION Larvicide applications reduced pupal abundance and the prevalence of host-seeking adults with no detectable impact on entomological risk metrics for WNV. Further research is needed to better determine the level of mosquito larval control required to reduce WNV transmission risk.
Collapse
Affiliation(s)
- Joseph R McMillan
- The Connecticut Agricultural Experiment StationNew HavenCTUSA
- The Northeast Regional Center of Excellence in Vector‐borne DiseasesCornell UniversityIthacaNew YorkUSA
| | | | - James C Burtis
- The Northeast Regional Center of Excellence in Vector‐borne DiseasesCornell UniversityIthacaNew YorkUSA
- Division of Vector‐borne DiseasesCenters for Disease Control and PreventionFort CollinsCOUSA
| | | | - John J Shepard
- The Connecticut Agricultural Experiment StationNew HavenCTUSA
| | - Tanya A Petruff
- The Connecticut Agricultural Experiment StationNew HavenCTUSA
| | | | | | - Joseph D Poggi
- The Northeast Regional Center of Excellence in Vector‐borne DiseasesCornell UniversityIthacaNew YorkUSA
- Cornell UniversityIthacaNYUSA
| | - Laura C Harrington
- The Northeast Regional Center of Excellence in Vector‐borne DiseasesCornell UniversityIthacaNew YorkUSA
- Cornell UniversityIthacaNYUSA
| | - Theodore G Andreadis
- The Connecticut Agricultural Experiment StationNew HavenCTUSA
- The Northeast Regional Center of Excellence in Vector‐borne DiseasesCornell UniversityIthacaNew YorkUSA
| | - Philip M Armstrong
- The Connecticut Agricultural Experiment StationNew HavenCTUSA
- The Northeast Regional Center of Excellence in Vector‐borne DiseasesCornell UniversityIthacaNew YorkUSA
| |
Collapse
|
27
|
Earnest R, Uddin R, Matluk N, Renzette N, Siddle KJ, Loreth C, Adams G, Tomkins-Tinch CH, Petrone ME, Rothman JE, Breban MI, Koch RT, Billig K, Fauver JR, Vogels CB, Turbett S, Bilguvar K, De Kumar B, Landry ML, Peaper DR, Kelly K, Omerza G, Grieser H, Meak S, Martha J, Dewey HH, Kales S, Berenzy D, Carpenter-Azevedo K, King E, Huard RC, Smole SC, Brown CM, Fink T, Lang AS, Gallagher GR, Sabeti PC, Gabriel S, MacInnis BL, Tewhey R, Adams MD, Park DJ, Lemieux JE, Grubaugh ND. Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA. medRxiv 2021:2021.10.06.21264641. [PMID: 34642698 PMCID: PMC8509091 DOI: 10.1101/2021.10.06.21264641] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant quickly rose to dominance in mid-2021, displacing other variants, including Alpha. Studies using data from the United Kingdom and India estimated that Delta was 40-80% more transmissible than Alpha, allowing Delta to become the globally dominant variant. However, it was unclear if the ostensible difference in relative transmissibility was due mostly to innate properties of Delta's infectiousness or differences in the study populations. To investigate, we formed a partnership with SARS-CoV-2 genomic surveillance programs from all six New England US states. By comparing logistic growth rates, we found that Delta emerged 37-163% faster than Alpha in early 2021 (37% Massachusetts, 75% New Hampshire, 95% Maine, 98% Rhode Island, 151% Connecticut, and 163% Vermont). We next computed variant-specific effective reproductive numbers and estimated that Delta was 58-120% more transmissible than Alpha across New England (58% New Hampshire, 68% Massachusetts, 76% Connecticut, 85% Rhode Island, 98% Maine, and 120% Vermont). Finally, using RT-PCR data, we estimated that Delta infections generate on average ∼6 times more viral RNA copies per mL than Alpha infections. Overall, our evidence indicates that Delta's enhanced transmissibility could be attributed to its innate ability to increase infectiousness, but its epidemiological dynamics may vary depending on the underlying immunity and behavior of distinct populations.
Collapse
Affiliation(s)
- Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Rockib Uddin
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nicholas Matluk
- Maine Center for Disease Control and Prevention, Augusta, ME 04333
- Health and Environmental Testing Laboratory, Augusta, ME 04333
| | - Nicholas Renzette
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | | | | | - Gordon Adams
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Jessica E. Rothman
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Robert Tobias Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Kendall Billig
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Joseph R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Sarah Turbett
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kaya Bilguvar
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
- Departments of Neurosurgery and Genetics, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Medical Genetics, Acibadem University School of Medicine, Istanbul, Turkey
| | - Bony De Kumar
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
| | - Marie L. Landry
- Departments of Laboratory Medicine and Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - David R. Peaper
- Departments of Laboratory Medicine and Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Kevin Kelly
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Greg Omerza
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Heather Grieser
- Maine Center for Disease Control and Prevention, Augusta, ME 04333
- Health and Environmental Testing Laboratory, Augusta, ME 04333
| | - Sim Meak
- Maine Center for Disease Control and Prevention, Augusta, ME 04333
- Health and Environmental Testing Laboratory, Augusta, ME 04333
| | - John Martha
- Maine Center for Disease Control and Prevention, Augusta, ME 04333
- Health and Environmental Testing Laboratory, Augusta, ME 04333
| | | | - Susan Kales
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | | | | | - Ewa King
- Rhode Island Department of Health, State Health Laboratories, Providence, RI 02904, USA
| | - Richard C. Huard
- Rhode Island Department of Health, State Health Laboratories, Providence, RI 02904, USA
| | - Sandra C. Smole
- Massachusetts Department of Public Health, Boston MA 02130, USA
| | | | - Timelia Fink
- Massachusetts Department of Public Health, Boston MA 02130, USA
| | - Andrew S. Lang
- Massachusetts Department of Public Health, Boston MA 02130, USA
| | | | | | - Stacey Gabriel
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Ryan Tewhey
- Department of Medical Genetics, Acibadem University School of Medicine, Istanbul, Turkey
- Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, USA
| | - Mark D. Adams
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Daniel J. Park
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jacob E. Lemieux
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06510, USA
| |
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
Petrone ME, Rothman JE, Breban MI, Ott IM, Russell A, Lasek-Nesselquist E, Kelly K, Omerza G, Renzette N, Watkins AE, Kalinich CC, Alpert T, Brito AF, Earnest R, Tikhonova IR, Castaldi C, Kelly JP, Shudt M, Plitnick J, Schneider E, Murphy S, Neal C, Laszlo E, Altajar A, Pearson C, Muyombwe A, Downing R, Razeq J, Niccolai L, Wilson MS, Anderson ML, Wang J, Liu C, Hui P, Mane S, Taylor BP, Hanage WP, Landry ML, Peaper DR, Bilguvar K, Fauver JR, Vogels CB, Gardner LM, Pitzer VE, St. George K, Adams MD, Grubaugh ND. Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 lineages. medRxiv 2021:2021.07.01.21259859. [PMID: 34230938 PMCID: PMC8259915 DOI: 10.1101/2021.07.01.21259859] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Emerging SARS-CoV-2 variants have shaped the second year of the COVID-19 pandemic and the public health discourse around effective control measures. Evaluating the public health threat posed by a new variant is essential for appropriately adapting response efforts when community transmission is detected. However, this assessment requires that a true comparison can be made between the new variant and its predecessors because factors other than the virus genotype may influence spread and transmission. In this study, we develop a framework that integrates genomic surveillance data to estimate the relative effective reproduction number (R t ) of co-circulating lineages. We use Connecticut, a state in the northeastern United States in which the SARS-CoV-2 variants B.1.1.7 and B.1.526 co-circulated in early 2021, as a case study for implementing this framework. We find that the R t of B.1.1.7 was 6-10% larger than that of B.1.526 in Connecticut in the midst of a COVID-19 vaccination campaign. To assess the generalizability of this framework, we apply it to genomic surveillance data from New York City and observe the same trend. Finally, we use discrete phylogeography to demonstrate that while both variants were introduced into Connecticut at comparable frequencies, clades that resulted from introductions of B.1.1.7 were larger than those resulting from B.1.526 introductions. Our framework, which uses open-source methods requiring minimal computational resources, may be used to monitor near real-time variant dynamics in a myriad of settings.
Collapse
Affiliation(s)
- Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Jessica E. Rothman
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Isabel M. Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Alexis Russell
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Erica Lasek-Nesselquist
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | - Kevin Kelly
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Greg Omerza
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Nicholas Renzette
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Anne E. Watkins
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Chaney C. Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Anderson F. Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Irina R. Tikhonova
- Yale Center for Genome Analysis, Yale University, New Haven, CT, 06510, USA
| | | | - John P. Kelly
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Matthew Shudt
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Jonathan Plitnick
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | - Erasmus Schneider
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | | | - Caleb Neal
- Murphy Medical Associates, Greenwich, CT 06830, USA
| | - Eva Laszlo
- Murphy Medical Associates, Greenwich, CT 06830, USA
| | | | - Claire Pearson
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Anthony Muyombwe
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Randy Downing
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Jafar Razeq
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Linda Niccolai
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | | | - Margaret L. Anderson
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Jianhui Wang
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Chen Liu
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Pei Hui
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Shrikant Mane
- Yale Center for Genome Analysis, Yale University, New Haven, CT, 06510, USA
| | - Bradford P. Taylor
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - William P. Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Marie L. Landry
- Departments of Laboratory Medicine and Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - David R. Peaper
- Departments of Laboratory Medicine and Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Kaya Bilguvar
- Yale Center for Genome Analysis, Yale University, New Haven, CT, 06510, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Joseph R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Lauren M. Gardner
- Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore 21218, MD, USA
| | - Virginia E. Pitzer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Kirsten St. George
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | - Mark D. Adams
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06510, USA
| |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
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.
Collapse
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
| |
Collapse
|
32
|
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.
Collapse
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
| |
Collapse
|
33
|
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.
Collapse
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.
| |
Collapse
|
34
|
Vogels CB, Breban MI, Alpert T, Petrone ME, Watkins AE, Ott IM, de Jesus JG, Claro IM, Ferreira GM, Crispim MA, Singh L, Tegally H, Anyaneji UJ, Hodcroft EB, Mason CE, Khullar G, Metti J, Dudley JT, MacKay MJ, Nash M, Wang J, Liu C, Hui P, Murphy S, Neal C, Laszlo E, Landry ML, Muyombwe A, Downing R, Razeq J, de Oliveira T, Faria NR, Sabino EC, Neher RA, Fauver JR, Grubaugh ND. PCR assay to enhance global surveillance for SARS-CoV-2 variants of concern. medRxiv 2021:2021.01.28.21250486. [PMID: 33758901 PMCID: PMC7987060 DOI: 10.1101/2021.01.28.21250486] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
With the emergence of SARS-CoV-2 variants that may increase transmissibility and/or cause escape from immune responses 1-3 , there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) variant first detected in the UK 4,5 could be serendipitously detected by the ThermoFisher TaqPath COVID-19 PCR assay because a key deletion in these viruses, spike Δ69-70, would cause a "spike gene target failure" (SGTF) result. However, a SGTF result is not definitive for B.1.1.7, and this assay cannot detect other variants of concern that lack spike Δ69-70, such as B.1.351 (also 501Y.V2) detected in South Africa 6 and P.1 (also 501Y.V3) recently detected in Brazil 7 . We identified a deletion in the ORF1a gene (ORF1a Δ3675-3677) in all three variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Δ3675-3677 as the primary target and spike Δ69-70 to differentiate, we designed and validated an open source PCR assay to detect SARS-CoV-2 variants of concern 8 . Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence spread of B.1.1.7, B.1.351, and P.1.
Collapse
Affiliation(s)
- Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Anne E. Watkins
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Isabel M. Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Jaqueline Goes de Jesus
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP 05403–000, Brazil
| | - Ingra Morales Claro
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP 05403–000, Brazil
| | - Giulia Magalhães Ferreira
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP 05403–000, Brazil
- Laboratório de Virologia, Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Myuki A.E. Crispim
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | | | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ugochukwu J. Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | - Emma B. Hodcroft
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | | | | | | | | | | | | | - Jianhui Wang
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Chen Liu
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Pei Hui
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | | | - Caleb Neal
- Murphy Medical Associates, Greenwich, CT 06614, USA
| | - Eva Laszlo
- Murphy Medical Associates, Greenwich, CT 06614, USA
| | - Marie L. Landry
- Departments of Laboratory Medicine and Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Anthony Muyombwe
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Randy Downing
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Jafar Razeq
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nuno R. Faria
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP 05403–000, Brazil
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
- Department of Zoology, University of Oxford, Oxford, UK
| | - Ester C. Sabino
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP 05403–000, Brazil
| | - Richard A. Neher
- Biozentrum, University of Basel, 4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Joseph R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06510, USA
| |
Collapse
|
35
|
Alpert T, Brito AF, Lasek-Nesselquist E, Rothman J, Valesano AL, MacKay MJ, Petrone ME, Breban MI, Watkins AE, Vogels CB, Kalinich CC, Dellicour S, Russell A, Kelly JP, Shudt M, Plitnick J, Schneider E, Fitzsimmons WJ, Khullar G, Metti J, Dudley JT, Nash M, Beaubier N, Wang J, Liu C, Hui P, Muyombwe A, Downing R, Razeq J, Bart SM, Grills A, Morrison SM, Murphy S, Neal C, Laszlo E, Rennert H, Cushing M, Westblade L, Velu P, Craney A, Fauntleroy KA, Peaper DR, Landry ML, Cook PW, Fauver JR, Mason CE, Lauring AS, George KS, MacCannell DR, Grubaugh ND. Early introductions and community transmission of SARS-CoV-2 variant B.1.1.7 in the United States. medRxiv 2021:2021.02.10.21251540. [PMID: 33594373 PMCID: PMC7885932 DOI: 10.1101/2021.02.10.21251540] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The emergence and spread of SARS-CoV-2 lineage B.1.1.7, first detected in the United Kingdom, has become a global public health concern because of its increased transmissibility. Over 2500 COVID-19 cases associated with this variant have been detected in the US since December 2020, but the extent of establishment is relatively unknown. Using travel, genomic, and diagnostic data, we highlight the primary ports of entry for B.1.1.7 in the US and locations of possible underreporting of B.1.1.7 cases. Furthermore, we found evidence for many independent B.1.1.7 establishments starting in early December 2020, followed by interstate spread by the end of the month. Finally, we project that B.1.1.7 will be the dominant lineage in many states by mid to late March. Thus, genomic surveillance for B.1.1.7 and other variants urgently needs to be enhanced to better inform the public health response.
Collapse
Affiliation(s)
- Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Anderson F. Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Erica Lasek-Nesselquist
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | - Jessica Rothman
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Andrew L. Valesano
- Department of Internal Medicine, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Anne E. Watkins
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Chaney C. Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Alexis Russell
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - John P. Kelly
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Matthew Shudt
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | - Jonathan Plitnick
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | - Erasmus Schneider
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | - William J. Fitzsimmons
- Department of Internal Medicine, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | | | | | | | | | - Jianhui Wang
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Chen Liu
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Pei Hui
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Anthony Muyombwe
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Randy Downing
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Jafar Razeq
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Stephen M. Bart
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Ardath Grills
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | | | | | - Caleb Neal
- Murphy Medical Associates, Greenwich, CT 06830, USA
| | - Eva Laszlo
- Murphy Medical Associates, Greenwich, CT 06830, USA
| | - Hanna Rennert
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA
| | - Melissa Cushing
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA
| | - Lars Westblade
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA
| | - Priya Velu
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA
| | - Arryn Craney
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA
| | - Kathy A. Fauntleroy
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA
| | - David R. Peaper
- Departments of Laboratory Medicine and Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Marie L. Landry
- Departments of Laboratory Medicine and Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Peter W. Cook
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Joseph R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Christopher E. Mason
- Tempus Labs, Chicago, IL 60654, USA
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA
| | - Adam S. Lauring
- Department of Internal Medicine, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kirsten St. George
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | | | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06510, USA
| |
Collapse
|