1
|
Kogoj R, Grašek M, Suljič A, Zakotnik S, Vlaj D, Kotnik Koman K, Fafangel M, Petrovec M, Avšič-Županc T, Korva M. Sequencing analysis of SARS-CoV-2 cases in Slovenian long-term care facilities to support outbreak control. Front Public Health 2024; 12:1406777. [PMID: 38813418 PMCID: PMC11133669 DOI: 10.3389/fpubh.2024.1406777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/02/2024] [Indexed: 05/31/2024] Open
Abstract
Introduction Residents of long-term care facilities (LTCFs) are at high risk of morbidity and mortality due to COVID-19, especially when new variants of concern (VOC) emerge. To provide intradisciplinary data in order to tailor public health interventions during future epidemics, available epidemiologic and genomic data from Slovenian LTCFs during the initial phases of the COVID-19 pandemic was analyzed. Methods The first part of the study included SARS-CoV-2 reverse-transcription Real-Time PCR (rtRT-PCR) positive LTCF residents, from 21 facilities with COVID-19 outbreaks occurring in October 2020. The second part of the study included SARS-CoV-2 rtRT-PCR positive LTCF residents and staff between January and April 2021, when VOC Alpha emerged in Slovenia. Next-generation sequencing (NGS) was used to acquire SARS-CoV-2 genomes, and lineage determination. In-depth phylogenetic and mutational profile analysis were performed and coupled with available field epidemiological data to assess the dynamics of SARS-CoV-2 introduction and transmission. Results 370/498 SARS-CoV-2 positive residents as well as 558/699 SARS-CoV-2 positive residents and 301/358 staff were successfully sequenced in the first and second part of the study, respectively. In October 2020, COVID-19 outbreaks in the 21 LTCFs were caused by intra-facility transmission as well as multiple independent SARS-CoV-2 introductions. The Alpha variant was confirmed in the first LTCF resident approximately 1.5 months after the first Alpha case was identified in Slovenia. The data also showed a slower replacement of existing variants by Alpha in residents compared to staff and the general population. Discussion Multiple SARS CoV-2 introductions as well as intra-facility spreading impacted disease transmission in Slovenian LTCFs. Timely implementation of control measures aimed at limiting new introductions while controlling in-facility transmission are of paramount importance, especially as new VOCs emerge. Sequencing, in conjunction with epidemiological data, can facilitate the determination of the need for future improvements in control measures to protect LTCF residents from COVID-19 or other respiratory infections.
Collapse
Affiliation(s)
- Rok Kogoj
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Manja Grašek
- Communicable Diseases Center, National Institute of Public Health, Ljubljana, Slovenia
| | - Alen Suljič
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Samo Zakotnik
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Doroteja Vlaj
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Kaja Kotnik Koman
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Mario Fafangel
- Communicable Diseases Center, National Institute of Public Health, Ljubljana, Slovenia
| | - Miroslav Petrovec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tatjana Avšič-Županc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Misa Korva
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
2
|
Sun YD, Yokomi R. Genotype Sequencing and Phylogenetic Analysis Revealed the Origins of Citrus Yellow Vein Clearing Virus California Isolates. Viruses 2024; 16:188. [PMID: 38399964 PMCID: PMC10891506 DOI: 10.3390/v16020188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The Citrus yellow vein clearing virus (CYVCV) causes a viral disease that has been reported in some citrus-growing regions in countries in Eurasia including Pakistan, India, Türkiye, Iran, China, and South Korea. Recently, CYVCV was detected in a localized urban area in a town in the middle of California's citrus-growing region and marks the first occurrence of the virus in North America. CYVCV has been reported to be spread by aphid and whitefly vectors and is graft and mechanically transmitted. Hence, it is an invasive pathogen that presents a significant threat to the California citrus industry, especially lemons, which are highly symptomatic to CYVCV. To elucidate the origin of the CYVCV California strain, we used long-read sequencing technology and obtained the complete genomes of three California CYVCV isolates, CA1, CA2, and CA3. The sequences of these isolates exhibited intergenomic similarities ranging from 95.4% to 97.4% to 54 publicly available CYVCV genome sequences, which indicated a relatively low level of heterogeneity. However, CYVCV CA isolates formed a distinct clade from the other isolates when aligned against other CYVCV genomes and coat protein gene sequences as shown by the neighbor network analysis. Based on the rooted Maximum Likelihood phylogenetic trees, CYVCV CA isolates shared the most recent common ancestor with isolates from India/South Asia. Bayesian evolutionary inferences resulted in a spatiotemporal reconstruction, suggesting that the CYVCV CA lineage diverged from the Indian lineage possibly around 1995. This analysis placed the origin of all CYVCV to around 1990, with South Asia and/or Middle East as the most plausible geographic source, which matches to the first discovery of CYVCV in Pakistan in 1988. Moreover, the spatiotemporal phylogenetic analysis indicated an additional virus diffusion pathway: one from South Asia to China and South Korea. Collectively, our phylogenetic inferences offer insights into the probable dynamics of global CYVCV dissemination, emphasizing the need for citrus industries and regulatory agencies to closely monitor citrus commodities crossing state and international borders.
Collapse
Affiliation(s)
- Yong-Duo Sun
- United States Department of Agriculture, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648, USA
| | - Raymond Yokomi
- United States Department of Agriculture, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648, USA
| |
Collapse
|
3
|
Chen Z, Lemey P, Yu H. Approaches and challenges to inferring the geographical source of infectious disease outbreaks using genomic data. THE LANCET. MICROBE 2024; 5:e81-e92. [PMID: 38042165 DOI: 10.1016/s2666-5247(23)00296-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/03/2023] [Accepted: 09/13/2023] [Indexed: 12/04/2023]
Abstract
Genomic data hold increasing potential in the elucidation of transmission dynamics and geographical sources of infectious disease outbreaks. Phylogeographic methods that use epidemiological and genomic data obtained from surveillance enable us to infer the history of spatial transmission that is naturally embedded in the topology of phylogenetic trees as a record of the dispersal of infectious agents between geographical locations. In this Review, we provide an overview of phylogeographic approaches widely used for reconstructing the geographical sources of outbreaks of interest. These approaches can be classified into ancestral trait or state reconstruction and structured population models, with structured population models including popular structured coalescent and birth-death models. We also describe the major challenges associated with sequencing technologies, surveillance strategies, data sharing, and analysis frameworks that became apparent during the generation of large-scale genomic data in recent years, extending beyond inference approaches. Finally, we highlight the role of genomic data in geographical source inference and clarify how this enhances understanding and molecular investigations of outbreak sources.
Collapse
Affiliation(s)
- Zhiyuan Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Evolutionary Virology, KU Leuven, Leuven, Belgium
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China.
| |
Collapse
|
4
|
Matteson NL, Hassler GW, Kurzban E, Schwab MA, Perkins SA, Gangavarapu K, Levy JI, Parker E, Pride D, Hakim A, De Hoff P, Cheung W, Castro-Martinez A, Rivera A, Veder A, Rivera A, Wauer C, Holmes J, Wilson J, Ngo SN, Plascencia A, Lawrence ES, Smoot EW, Eisner ER, Tsai R, Chacón M, Baer NA, Seaver P, Salido RA, Aigner S, Ngo TT, Barber T, Ostrander T, Fielding-Miller R, Simmons EH, Zazueta OE, Serafin-Higuera I, Sanchez-Alavez M, Moreno-Camacho JL, García-Gil A, Murphy Schafer AR, McDonald E, Corrigan J, Malone JD, Stous S, Shah S, Moshiri N, Weiss A, Anderson C, Aceves CM, Spencer EG, Hufbauer EC, Lee JJ, King AJ, Ramesh KS, Nguyen KN, Saucedo K, Robles-Sikisaka R, Fisch KM, Gonias SL, Birmingham A, McDonald D, Karthikeyan S, Martin NK, Schooley RT, Negrete AJ, Reyna HJ, Chavez JR, Garcia ML, Cornejo-Bravo JM, Becker D, Isaksson M, Washington NL, Lee W, Garfein RS, Luna-Ruiz Esparza MA, Alcántar-Fernández J, Henson B, Jepsen K, Olivares-Flores B, Barrera-Badillo G, Lopez-Martínez I, Ramírez-González JE, Flores-León R, Kingsmore SF, Sanders A, Pradenas A, White B, Matthews G, Hale M, McLawhon RW, Reed SL, Winbush T, McHardy IH, Fielding RA, Nicholson L, Quigley MM, Harding A, Mendoza A, Bakhtar O, Browne SH, Olivas Flores J, Rincon Rodríguez DG, Gonzalez Ibarra M, Robles Ibarra LC, Arellano Vera BJ, Gonzalez Garcia J, Harvey-Vera A, Knight R, Laurent LC, Yeo GW, Wertheim JO, Ji X, Worobey M, Suchard MA, Andersen KG, Campos-Romero A, Wohl S, Zeller M. Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics. Cell 2023; 186:5690-5704.e20. [PMID: 38101407 PMCID: PMC10795731 DOI: 10.1016/j.cell.2023.11.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 08/21/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023]
Abstract
The maturation of genomic surveillance in the past decade has enabled tracking of the emergence and spread of epidemics at an unprecedented level. During the COVID-19 pandemic, for example, genomic data revealed that local epidemics varied considerably in the frequency of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage importation and persistence, likely due to a combination of COVID-19 restrictions and changing connectivity. Here, we show that local COVID-19 epidemics are driven by regional transmission, including across international boundaries, but can become increasingly connected to distant locations following the relaxation of public health interventions. By integrating genomic, mobility, and epidemiological data, we find abundant transmission occurring between both adjacent and distant locations, supported by dynamic mobility patterns. We find that changing connectivity significantly influences local COVID-19 incidence. Our findings demonstrate a complex meaning of "local" when investigating connected epidemics and emphasize the importance of collaborative interventions for pandemic prevention and mitigation.
Collapse
Affiliation(s)
| | - Gabriel W Hassler
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Madison A Schwab
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Sarah A Perkins
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - David Pride
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Peter De Hoff
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Willi Cheung
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Anelizze Castro-Martinez
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium of Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Andrea Rivera
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Anthony Veder
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Ariana Rivera
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Cassandra Wauer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jacqueline Holmes
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jedediah Wilson
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Shayla N Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Emily R Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rebecca Tsai
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, USA; Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | | | - Oscar E Zazueta
- Department of Epidemiology, Secretaria de Salud de Baja California, Tijuana, Baja California, Mexico
| | | | - Manuel Sanchez-Alavez
- Centro de Diagnostico COVID-19 UABC, Tijuana, Baja California, Mexico; Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | | | - Abraham García-Gil
- Clinical Laboratory Department, Salud Digna, A.C, Tijuana, Baja California, Mexico
| | | | - Eric McDonald
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Jeremy Corrigan
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - John D Malone
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Sarah Stous
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Seema Shah
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Alana Weiss
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Catelyn Anderson
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Emily G Spencer
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Emory C Hufbauer
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Justin J Lee
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Alison J King
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Karthik S Ramesh
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Kelly N Nguyen
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Kieran Saucedo
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | | | - Kathleen M Fisch
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Steven L Gonias
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Amanda Birmingham
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Smruthi Karthikeyan
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Natasha K Martin
- Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Robert T Schooley
- Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Agustin J Negrete
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Horacio J Reyna
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Jose R Chavez
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Maria L Garcia
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Jose M Cornejo-Bravo
- Facultad de Ciencias Quimicas e Ingenieria, Universidad Autonoma de Baja California, Tijuana, Baja California, Mexico
| | | | | | | | | | - Richard S Garfein
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, USA
| | | | | | - Benjamin Henson
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Beatriz Olivares-Flores
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - Gisela Barrera-Badillo
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - Irma Lopez-Martínez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - José E Ramírez-González
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - Rita Flores-León
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | | | - Alison Sanders
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Allorah Pradenas
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Benjamin White
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Gary Matthews
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Matt Hale
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Ronald W McLawhon
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Sharon L Reed
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Terri Winbush
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | | | | | | | | | | | | | | | - Sara H Browne
- Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA; Specialist in Global Health, Encinitas, CA, USA
| | - Jocelyn Olivas Flores
- Facultad de Ciencias Quimicas e Ingenieria, Universidad Autonoma de Baja California, Tijuana, Baja California, Mexico; University of HealthMx, Tijuana, Baja California, Mexico
| | - Diana G Rincon Rodríguez
- University of HealthMx, Tijuana, Baja California, Mexico; Facultad de Medicina, Universidad Xochicalco, Tijuana, Baja California, Mexico
| | - Martin Gonzalez Ibarra
- University of HealthMx, Tijuana, Baja California, Mexico; Facultad de Medicina, Universidad Xochicalco, Tijuana, Baja California, Mexico
| | - Luis C Robles Ibarra
- University of HealthMx, Tijuana, Baja California, Mexico; Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Tijuana, Baja California, Mexico
| | - Betsy J Arellano Vera
- University of HealthMx, Tijuana, Baja California, Mexico; Instituto Mexicano del Seguro Social, Tijuana, Baja California, Mexico
| | - Jonathan Gonzalez Garcia
- University of HealthMx, Tijuana, Baja California, Mexico; SIMNSA, Tijuana, Baja California, Mexico
| | | | - Rob Knight
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Louise C Laurent
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium of Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium of Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Joel O Wertheim
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Xiang Ji
- Department of Mathematics, School of Science and Engineering, Tulane University, New Orleans, LA, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Marc A Suchard
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
| | - Abraham Campos-Romero
- Innovation and Research Department, Salud Digna, A.C, Tijuana, Baja California, Mexico
| | - Shirlee Wohl
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
| |
Collapse
|
5
|
Colombo SA, Bicalho GC, de Oliveira CSF, de Magalhães Soares DF, Salvato LA, Keller KM, Bastos CDVE, Morais MHF, Rodrigues AM, Cunha JLR, de Azevedo MI. Emergence of zoonotic sporotrichosis due to Sporothrix brasiliensis in Minas Gerais, Brazil: A molecular approach to the current animal disease. Mycoses 2023; 66:911-922. [PMID: 37452233 DOI: 10.1111/myc.13631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/24/2023] [Accepted: 06/28/2023] [Indexed: 07/18/2023]
Abstract
Sporotrichosis is a neglected fungal zoonosis with significant impacts on human and animal health. Accurate diagnosis, treatment, and understanding of the transmission dynamics of Sporothrix species are essential for mitigating the spread of sporotrichosis. This study aimed to identify the Sporothrix species involved in the ongoing outbreaks of animal sporotrichosis in the metropolitan region of Belo Horizonte, Minas Gerais, Brazil, and analyse the phylogenetic relationships between pathogenic species to investigate the outbreak origin. Additionally, to better understand the evolution of the disease, we conducted a retrospective survey of positive feline and canine cases from November 2017 to July 2021 with proven cultures for Sporothrix. A significant increase in animal cases over the last 4 years was observed, with cats being the most affected host. Sporothrix brasiliensis was the predominant agent in 100% of the clinical isolates (n = 180) molecularly identified. Phylogenetic and haplotype analysis points towards the cases isolated from Minas Gerais sharing the haplotype originating from a long-lasting outbreak of cat-transmitted sporotrichosis in Rio de Janeiro, however, with a secondary contribution from genotypes circulating in other outbreaks in Brazil. Thus, we present clear evidence of the circulation of different S. brasiliensis genotypes associated with animal sporotrichosis in the metropolitan region of Belo Horizonte. Genetic monitoring can contribute to understanding the causal agent for zoonotic sporotrichosis in epidemiological processes and help to implement disease prevention and control measures.
Collapse
Affiliation(s)
- Salene Angelini Colombo
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Gustavo Canesso Bicalho
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Lauranne Alves Salvato
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Kelly Moura Keller
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Camila de Valgas E Bastos
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Anderson Messias Rodrigues
- Departamento de Microbiologia, Imunologia e Parasitologia, Disciplina de Biologia Celular, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - João Luis Reis Cunha
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Maria Isabel de Azevedo
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| |
Collapse
|
6
|
Taouk ML, Steinig E, Taiaroa G, Savic I, Tran T, Higgins N, Tran S, Lee A, Braddick M, Moso MA, Chow EPF, Fairley CK, Towns J, Chen MY, Caly L, Lim CK, Williamson DA. Intra- and interhost genomic diversity of monkeypox virus. J Med Virol 2023; 95:e29029. [PMID: 37565686 PMCID: PMC10952654 DOI: 10.1002/jmv.29029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/12/2023]
Abstract
The impact and frequency of infectious disease outbreaks demonstrate the need for timely genomic surveillance to inform public health responses. In the largest known outbreak of mpox, genomic surveillance efforts have primarily focused on high-incidence nations in Europe and the Americas, with a paucity of data from South-East Asia and the Western Pacific. Here we analyzed 102 monkeypox virus (MPXV) genomes sampled from 56 individuals in Melbourne, Australia. All genomes fell within the 2022 MPXV outbreak lineage (B.1), with likely onward local transmission detected. We observed within-host diversity and instances of co-infection, and highlight further examples of structural variation and apolipoprotein B editing complex-driven micro-evolution in the current MPXV outbreak. Updating our understanding of MPXV emergence and diversification will inform public health measures and enable monitoring of the virus' evolutionary trajectory throughout the mpox outbreak.
Collapse
Affiliation(s)
- Mona L. Taouk
- Department of Infectious DiseasesThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
- Victorian Infectious Diseases Reference LaboratoryThe Royal Melbourne Hospital at The Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
| | - Eike Steinig
- Department of Infectious DiseasesThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
- Victorian Infectious Diseases Reference LaboratoryThe Royal Melbourne Hospital at The Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
| | - George Taiaroa
- Department of Infectious DiseasesThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
- Victorian Infectious Diseases Reference LaboratoryThe Royal Melbourne Hospital at The Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
| | - Ivana Savic
- Victorian Infectious Diseases Reference LaboratoryThe Royal Melbourne Hospital at The Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
| | - Thomas Tran
- Victorian Infectious Diseases Reference LaboratoryThe Royal Melbourne Hospital at The Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
| | - Nasra Higgins
- Victorian Department of HealthMelbourneVictoriaAustralia
| | - Stephanie Tran
- Victorian Department of HealthMelbourneVictoriaAustralia
| | - Alvin Lee
- Victorian Department of HealthMelbourneVictoriaAustralia
| | | | - Michael A. Moso
- Department of Infectious DiseasesThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
- Victorian Infectious Diseases Reference LaboratoryThe Royal Melbourne Hospital at The Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
| | - Eric P. F. Chow
- Melbourne Sexual Health CentreAlfred HealthMelbourneVictoriaAustralia
- Central Clinical School, Faculty of Medicine, Nursing and Health SciencesMonash UniversityMelbourneVictoriaAustralia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global HealthThe University of MelbourneMelbourneVictoriaAustralia
| | - Christopher K. Fairley
- Melbourne Sexual Health CentreAlfred HealthMelbourneVictoriaAustralia
- Central Clinical School, Faculty of Medicine, Nursing and Health SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Janet Towns
- Melbourne Sexual Health CentreAlfred HealthMelbourneVictoriaAustralia
| | - Marcus Y. Chen
- Melbourne Sexual Health CentreAlfred HealthMelbourneVictoriaAustralia
| | - Leon Caly
- Department of Infectious DiseasesThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
- Victorian Infectious Diseases Reference LaboratoryThe Royal Melbourne Hospital at The Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
| | - Chuan K. Lim
- Department of Infectious DiseasesThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
- Victorian Infectious Diseases Reference LaboratoryThe Royal Melbourne Hospital at The Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
| | - Deborah A. Williamson
- Department of Infectious DiseasesThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
- Victorian Infectious Diseases Reference LaboratoryThe Royal Melbourne Hospital at The Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
| |
Collapse
|
7
|
Reichmuth ML, Hodcroft EB, Althaus CL. Importation of Alpha and Delta variants during the SARS-CoV-2 epidemic in Switzerland: Phylogenetic analysis and intervention scenarios. PLoS Pathog 2023; 19:e1011553. [PMID: 37561788 PMCID: PMC10443857 DOI: 10.1371/journal.ppat.1011553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 08/22/2023] [Accepted: 07/11/2023] [Indexed: 08/12/2023] Open
Abstract
The SARS-CoV-2 pandemic has led to the emergence of various variants of concern (VoCs) that are associated with increased transmissibility, immune evasion, or differences in disease severity. The emergence of VoCs fueled interest in understanding the potential impact of travel restrictions and surveillance strategies to prevent or delay the early spread of VoCs. We performed phylogenetic analyses and mathematical modeling to study the importation and spread of the VoCs Alpha and Delta in Switzerland in 2020 and 2021. Using a phylogenetic approach, we estimated between 383-1,038 imports of Alpha and 455-1,347 imports of Delta into Switzerland. We then used the results from the phylogenetic analysis to parameterize a dynamic transmission model that accurately described the subsequent spread of Alpha and Delta. We modeled different counterfactual intervention scenarios to quantify the potential impact of border closures and surveillance of travelers on the spread of Alpha and Delta. We found that implementing border closures after the announcement of VoCs would have been of limited impact to mitigate the spread of VoCs. In contrast, increased surveillance of travelers could prove to be an effective measure for delaying the spread of VoCs in situations where their severity remains unclear. Our study shows how phylogenetic analysis in combination with dynamic transmission models can be used to estimate the number of imported SARS-CoV-2 variants and the potential impact of different intervention scenarios to inform the public health response during the pandemic.
Collapse
Affiliation(s)
- Martina L. Reichmuth
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Emma B. Hodcroft
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Christian L. Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
| |
Collapse
|
8
|
de Moraes L, Portilho MM, Vrancken B, Van den Broeck F, Santos LA, Cucco M, Tauro LB, Kikuti M, Silva MMO, Campos GS, Reis MG, Barral A, Barral-Netto M, Boaventura VS, Vandamme AM, Theys K, Lemey P, Ribeiro GS, Khouri R. Analyses of Early ZIKV Genomes Are Consistent with Viral Spread from Northeast Brazil to the Americas. Viruses 2023; 15:1236. [PMID: 37376536 DOI: 10.3390/v15061236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
The Americas, particularly Brazil, were greatly impacted by the widespread Zika virus (ZIKV) outbreak in 2015 and 2016. Efforts were made to implement genomic surveillance of ZIKV as part of the public health responses. The accuracy of spatiotemporal reconstructions of the epidemic spread relies on the unbiased sampling of the transmission process. In the early stages of the outbreak, we recruited patients exhibiting clinical symptoms of arbovirus-like infection from Salvador and Campo Formoso, Bahia, in Northeast Brazil. Between May 2015 and June 2016, we identified 21 cases of acute ZIKV infection and subsequently recovered 14 near full-length sequences using the amplicon tiling multiplex approach with nanopore sequencing. We performed a time-calibrated discrete phylogeographic analysis to trace the spread and migration history of the ZIKV. Our phylogenetic analysis supports a consistent relationship between ZIKV migration from Northeast to Southeast Brazil and its subsequent dissemination beyond Brazil. Additionally, our analysis provides insights into the migration of ZIKV from Brazil to Haiti and the role Brazil played in the spread of ZIKV to other countries, such as Singapore, the USA, and the Dominican Republic. The data generated by this study enhances our understanding of ZIKV dynamics and supports the existing knowledge, which can aid in future surveillance efforts against the virus.
Collapse
Affiliation(s)
- Laise de Moraes
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40026-010, Brazil
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Moyra M Portilho
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Frederik Van den Broeck
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium
- Department of Biomedical Sciences, Antwerp Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Luciane Amorim Santos
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40026-010, Brazil
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Escola Bahiana de Medicina e Saúde Pública, Salvador 41150-100, Brazil
| | - Marina Cucco
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40026-010, Brazil
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Laura B Tauro
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Instituto de Biología Subtropical, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Misiones, Puerto Iguazú N3370, Argentina
| | - Mariana Kikuti
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Monaise M O Silva
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Gúbio S Campos
- Laboratório de Virologia, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador 40231-300, Brazil
| | - Mitermayer G Reis
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Departamento de Patologia e Medicina Legal, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40110-100, Brazil
| | - Aldina Barral
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Manoel Barral-Netto
- Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Viviane Sampaio Boaventura
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Hospital Santa Izabel, Salvador 40050-410, Brazil
| | - Anne-Mieke Vandamme
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisbon, Portugal
| | - Kristof Theys
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium
| | - Guilherme S Ribeiro
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Departamento de Medicina Preventiva e Social, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40110-100, Brazil
| | - Ricardo Khouri
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40026-010, Brazil
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium
| |
Collapse
|
9
|
Campigotto A, Chris A, Orkin J, Lau L, Marshall C, Bitnun A, Buchan SA, MacDonald L, Thampi N, McCready J, Juni P, Parekh RS, Science M. Utility of SARS-CoV-2 Genomic Sequencing for Understanding Transmission and School Outbreaks. Pediatr Infect Dis J 2023; 42:324-331. [PMID: 36795555 PMCID: PMC9990487 DOI: 10.1097/inf.0000000000003834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/17/2022] [Indexed: 02/17/2023]
Abstract
OBJECTIVE An understanding of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) transmission in schools is important. It is often difficult, using epidemiological information alone, to determine whether cases associated with schools represent multiple introductions from the community or transmission within the school. We describe the use of whole genome sequencing (WGS) in multiple schools to investigate outbreaks of SARS-CoV-2 in the pre-Omicron period. STUDY DESIGN School outbreaks were identified for sequencing by local public health units based on multiple cases without known epidemiological links. Cases of SARS-CoV-2 from students and staff from 4 school outbreaks in Ontario underwent WGS and phylogenetic analysis. The epidemiological clinical cohort data and genomic cluster data are described to help further characterize these outbreaks. RESULTS A total of 132 positive SARS-CoV-2 cases among students and staff from 4 school outbreaks were identified with 65 (49%) of cases able to be sequenced with high-quality genomic data. The 4 school outbreaks consisted of 53, 37, 21 and 21 positive cases; within each outbreak there were between 8 and 28 different clinical cohorts identified. Among the sequenced cases, between 3 and 7 genetic clusters, defined as different strains, were identified in each outbreak. We found genetically different viruses within several clinical cohorts. CONCLUSIONS WGS, together with public health investigation, is a useful tool to investigate SARS-CoV-2 transmission within schools. Its early use has the potential to better understand when transmission may have occurred, can aid in evaluating how well mitigation interventions are working and has the potential to reduce unnecessary school closures when multiple genetic clusters are identified.
Collapse
Affiliation(s)
- Aaron Campigotto
- From the Division of Microbiology, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children
- Department of Laboratory Medicine and Pathobiology, University of Toronto
| | | | | | - Lynette Lau
- Division of Genome Diagnostics, Department of Paediatric Laboratory Medicine
| | - Christian Marshall
- Department of Laboratory Medicine and Pathobiology, University of Toronto
- Division of Genome Diagnostics, Department of Paediatric Laboratory Medicine
| | - Ari Bitnun
- Department of Paediatrics
- Division of Infectious Diseases, The Hospital for Sick Children
| | - Sarah A Buchan
- Public Health Ontario
- Dalla Lana School of Public Health, University of Toronto
| | | | - Nisha Thampi
- Department of Paediatrics, Children’s Hospital of Eastern Ontario
| | - Janine McCready
- Division of Infectious Diseases, Department of Medicine, Michael Garron Hospital
| | - Peter Juni
- St. Michael’s Hospital, Applied Health Research Centre, Li Ka Shing Knowledge Institute, University of Toronto
| | - Rulan S Parekh
- Department of Medicine, Women’s College Hospital, Toronto, ON, Canada
| | - Michelle Science
- Division of Infectious Diseases, The Hospital for Sick Children
- Public Health Ontario
| |
Collapse
|
10
|
Senchyna F, Singh R. Dynamic Epidemiological Networks: A Data Representation Framework for Modeling and Tracking of SARS-CoV-2 Variants. J Comput Biol 2023; 30:446-468. [PMID: 37098217 DOI: 10.1089/cmb.2022.0469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023] Open
Abstract
The large-scale real-time sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes has allowed for rapid identification of concerning variants through phylogenetic analysis. However, the nature of phylogenetic reconstruction is typically static, in that the relationships between taxonomic units, once defined, are not subject to alterations. Furthermore, most phylogenetic methods are intrinsically batch mode in nature, requiring the presence of the entire data set. Finally, the emphasis of phylogenetics is on relating taxonomical units. These characteristics complicate the application of classical phylogenetics methods to represent relationships in molecular data collected from rapidly evolving strains of an etiological agent, such as SARS-CoV-2, since the molecular landscape is updated continuously as samples are collected. In such settings, variant definitions are subject to epistemological constraints and may change as data accumulate. Furthermore, representing within-variant molecular relationships may be as important as representing between variant relationships. This article describes a novel data representation framework called dynamic epidemiological networks (DENs) along with algorithms that underpin its construction to address these issues. The proposed representation is applied to study the molecular development underlying the spread of the COVID-19 (coronavirus disease 2019) pandemic in two countries: Israel and Portugal spanning a 2-year period from February 2020 to April 2022. The results demonstrate how this framework could be used to provide a multiscale representation of the data by capturing molecular relationships between samples as well as those between variants, automatically identifying the emergence of high frequency variants (lineages), including variants of concern such as Alpha and Delta, and tracking their growth. Additionally, we show how analyzing the evolution of the DEN can help identify changes in the viral population that could not be readily inferred from phylogenetic analysis.
Collapse
Affiliation(s)
- Fiona Senchyna
- Department of Computer Science, San Francisco State University, San Francisco, California, USA
| | - Rahul Singh
- Department of Computer Science, San Francisco State University, San Francisco, California, USA
- Center for Discovery and Innovation in Parasitic Diseases, University of California, San Diego, California, USA
| |
Collapse
|
11
|
Cotton S, McHugh MP, Dewar R, Haas JG, Templeton K. Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes. J Hosp Infect 2023; 135:28-36. [PMID: 36906180 PMCID: PMC9997060 DOI: 10.1016/j.jhin.2023.02.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/09/2023] [Accepted: 02/12/2023] [Indexed: 03/13/2023]
Abstract
BACKGROUND The first epidemic wave of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Scotland resulted in high case numbers and mortality in care homes. In Lothian, over a third of care homes reported an outbreak while there was limited testing of hospital patients discharged to care homes. AIM Investigate hospital discharges as a source of SARS-CoV-2 introduction into care homes during the first epidemic wave. METHODS A clinical review was performed for all discharges from hospitals to care homes starting 1st March 2020 to 31st May 2020. Episodes were ruled out based on coronavirus disease (COVID-19) test history, clinical assessment at discharge, whole genome sequencing (WGS) data and an infectious period of 14 days. Clinical samples were processed for WGS, and consensus genomes generated were used for analysis by cluster investigation and virus epidemiological tool (CIVET). Patient timelines were obtained using electronic hospital records. FINDINGS In total 787 hospital discharges to care homes were identified. Out of these 776 (99%) were ruled out for hospital discharge introduction. However, for 10 episodes the results were inconclusive as there was low genomic diversity in consensus genomes or no sequencing data. Only one discharge episode had a genomic, time and location link to positive cases during hospital admission leading to 10 further positive cases in the care home. CONCLUSION Majority of hospital discharges were ruled out for introduction into Lothian care homes highlighting the importance of screening all new admissions when faced with a novel emerging virus and no vaccine available.
Collapse
Affiliation(s)
- S Cotton
- Specialist Virology Centre, Royal Infirmary Edinburgh, NHS Lothian, UK; Infection Medicine, Edinburgh Medical School, University of Edinburgh, UK.
| | - M P McHugh
- Specialist Virology Centre, Royal Infirmary Edinburgh, NHS Lothian, UK; School of Medicine, University of St Andrews, UK
| | - R Dewar
- Specialist Virology Centre, Royal Infirmary Edinburgh, NHS Lothian, UK
| | - J G Haas
- Specialist Virology Centre, Royal Infirmary Edinburgh, NHS Lothian, UK; Infection Medicine, Edinburgh Medical School, University of Edinburgh, UK
| | - K Templeton
- Specialist Virology Centre, Royal Infirmary Edinburgh, NHS Lothian, UK; Infection Medicine, Edinburgh Medical School, University of Edinburgh, UK
| | | |
Collapse
|
12
|
Sawadogo Y, Galal L, Belarbi E, Zongo A, Schubert G, Leendertz F, Kanteh A, Sesay AK, Erhart A, Bañuls AL, Tarnagda Z, Godreuil S, Tinto H, Ouedraogo AS. Genomic Epidemiology of SARS-CoV-2 in Western Burkina Faso, West Africa. Viruses 2022; 14:v14122788. [PMID: 36560792 PMCID: PMC9782145 DOI: 10.3390/v14122788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND After its initial detection in Wuhan, China, in December 2019, SARS-CoV-2 has spread rapidly, causing successive epidemic waves worldwide. This study aims to provide a genomic epidemiology of SARS-CoV-2 in Burkina Faso. METHODS Three hundred and seventy-seven SARS-CoV-2 genomes obtained from PCR-positive nasopharyngeal samples (PCR cycle threshold score < 35) collected between 5 May 2020, and 31 January 2022 were analyzed. Genomic sequences were assigned to phylogenetic clades using NextClade and to Pango lineages using pangolin. Phylogenetic and phylogeographic analyses were performed to determine the geographical sources and time of virus introduction in Burkina Faso. RESULTS The analyzed SARS-CoV-2 genomes can be assigned to 10 phylogenetic clades and 27 Pango lineages already described worldwide. Our analyses revealed the important role of cross-border human mobility in the successive SARS-CoV-2 introductions in Burkina Faso from neighboring countries. CONCLUSIONS This study provides additional insights into the genomic epidemiology of SARS-CoV-2 in West Africa. It highlights the importance of land travel in the spread of the virus and the need to rapidly implement preventive policies. Regional cross-border collaborations and the adherence of the general population to government policies are key to prevent new epidemic waves.
Collapse
Affiliation(s)
- Yacouba Sawadogo
- Departement of Bacteriology and Virology, Souro Sanou University Hospital, Bobo Dioulasso 01 BP 676, Burkina Faso
- Laboratory of Emerging and Re-emerging Pathogens, School of Health Sciences Nazi Boni University, Bobo Dioulasso 01 BP 1091, Burkina Faso
| | - Lokman Galal
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, 34295 Montpellier, France
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), Université de Montpellier—Institut de Recherche pour le Développement (IRD)—Centre National de la Recherche Scientifique (CNRS), 34394 Montpellier, France
| | | | - Arsène Zongo
- Muraz Center, Bobo Dioulasso 01 BP 390, Burkina Faso
| | | | | | - Abdoulie Kanteh
- Genomics Core Facility, Medical Research Council Unit the Gambia (MRCG), London School of Hygiene and Tropical Medicine, Fajara P.O. Box 273, The Gambia
| | - Abdul Karim Sesay
- Genomics Core Facility, Medical Research Council Unit the Gambia (MRCG), London School of Hygiene and Tropical Medicine, Fajara P.O. Box 273, The Gambia
| | - Annette Erhart
- Disease Control and Elimination Theme, Medical Research Council Unit the Gambia (MRCG), London School of Hygiene and Tropical Medicine, Fajara P.O. Box 273, The Gambia
| | - Anne-Laure Bañuls
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), Université de Montpellier—Institut de Recherche pour le Développement (IRD)—Centre National de la Recherche Scientifique (CNRS), 34394 Montpellier, France
- Jeune Equipe Associée (JEAI), Institut de Recherche pour le Développement (IRD), Résistances Antimicrobiennes au Burkina Faso (FASORAM), 34394 Montpellier, France
| | - Zékiba Tarnagda
- Laboratoire National de Référence-Grippe (LNR-G), Institut de Recherche en Sciences de la Santé, Ouagadougou 03 BP 7192, Burkina Faso
| | - Sylvain Godreuil
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, 34295 Montpellier, France
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), Université de Montpellier—Institut de Recherche pour le Développement (IRD)—Centre National de la Recherche Scientifique (CNRS), 34394 Montpellier, France
- Jeune Equipe Associée (JEAI), Institut de Recherche pour le Développement (IRD), Résistances Antimicrobiennes au Burkina Faso (FASORAM), 34394 Montpellier, France
| | - Halidou Tinto
- Centre National de la Recherche Scientifique et Technologique/Institut de Recherche en Sciences de la Santé (CNRST/IRSS), Nanoro BP 18, Burkina Faso
| | - Abdoul-Salam Ouedraogo
- Departement of Bacteriology and Virology, Souro Sanou University Hospital, Bobo Dioulasso 01 BP 676, Burkina Faso
- Laboratory of Emerging and Re-emerging Pathogens, School of Health Sciences Nazi Boni University, Bobo Dioulasso 01 BP 1091, Burkina Faso
- Muraz Center, Bobo Dioulasso 01 BP 390, Burkina Faso
- Jeune Equipe Associée (JEAI), Institut de Recherche pour le Développement (IRD), Résistances Antimicrobiennes au Burkina Faso (FASORAM), 34394 Montpellier, France
- Correspondence: or
| |
Collapse
|
13
|
Botz J, Wang D, Lambert N, Wagner N, Génin M, Thommes E, Madan S, Coudeville L, Fröhlich H. Modeling approaches for early warning and monitoring of pandemic situations as well as decision support. Front Public Health 2022; 10:994949. [PMID: 36452960 PMCID: PMC9702983 DOI: 10.3389/fpubh.2022.994949] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/21/2022] [Indexed: 11/15/2022] Open
Abstract
The COVID-19 pandemic has highlighted the lack of preparedness of many healthcare systems against pandemic situations. In response, many population-level computational modeling approaches have been proposed for predicting outbreaks, spatiotemporally forecasting disease spread, and assessing as well as predicting the effectiveness of (non-) pharmaceutical interventions. However, in several countries, these modeling efforts have only limited impact on governmental decision-making so far. In light of this situation, the review aims to provide a critical review of existing modeling approaches and to discuss the potential for future developments.
Collapse
Affiliation(s)
- Jonas Botz
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany
| | - Danqi Wang
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany
- Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn, Bonn, Germany
| | | | | | | | | | - Sumit Madan
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany
- Department of Computer Science, University of Bonn, Bonn, Germany
| | | | - Holger Fröhlich
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany
- Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn, Bonn, Germany
| |
Collapse
|
14
|
Attwood SW, Hill SC, Aanensen DM, Connor TR, Pybus OG. Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic. Nat Rev Genet 2022; 23:547-562. [PMID: 35459859 PMCID: PMC9028907 DOI: 10.1038/s41576-022-00483-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2022] [Indexed: 01/05/2023]
Abstract
Determining the transmissibility, prevalence and patterns of movement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is central to our understanding of the impact of the pandemic and to the design of effective control strategies. Phylogenies (evolutionary trees) have provided key insights into the international spread of SARS-CoV-2 and enabled investigation of individual outbreaks and transmission chains in specific settings. Phylodynamic approaches combine evolutionary, demographic and epidemiological concepts and have helped track virus genetic changes, identify emerging variants and inform public health strategy. Here, we review and synthesize studies that illustrate how phylogenetic and phylodynamic techniques were applied during the first year of the pandemic, and summarize their contributions to our understanding of SARS-CoV-2 transmission and control.
Collapse
Affiliation(s)
- Stephen W Attwood
- Department of Zoology, University of Oxford, Oxford, UK.
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK.
| | - Sarah C Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, London, UK
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas R Connor
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, London, UK.
| |
Collapse
|
15
|
Turcinovic J, Schaeffer B, Taylor BP, Bouton TC, Odom-Mabey AR, Weber SE, Lodi S, Ragan EJ, Connor JH, Jacobson KR, Hanage WP. Understanding early pandemic SARS-CoV-2 transmission in a medical center by incorporating public sequencing databases to mitigate bias. J Infect Dis 2022; 226:1704-1711. [PMID: 35993116 PMCID: PMC9452097 DOI: 10.1093/infdis/jiac348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/19/2022] [Indexed: 11/28/2022] Open
Abstract
Background Throughout the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, healthcare workers (HCWs) have faced risk of infection from within the workplace via patients and staff as well as from the outside community, complicating our ability to resolve transmission chains in order to inform hospital infection control policy. Here we show how the incorporation of sequences from public genomic databases aided genomic surveillance early in the pandemic when circulating viral diversity was limited. Methods We sequenced a subset of discarded, diagnostic SARS-CoV-2 isolates between March and May 2020 from Boston Medical Center HCWs and combined this data set with publicly available sequences from the surrounding community deposited in GISAID with the goal of inferring specific transmission routes. Results Contextualizing our data with publicly available sequences reveals that 73% (95% confidence interval, 63%–84%) of coronavirus disease 2019 cases in HCWs are likely novel introductions rather than nosocomial spread. Conclusions We argue that introductions of SARS-CoV-2 into the hospital environment are frequent and that expanding public genomic surveillance can better aid infection control when determining routes of transmission.
Collapse
Affiliation(s)
- Jacquelyn Turcinovic
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA.,Bioinformatics Program, Boston University, Boston, MA, USA
| | - Beau Schaeffer
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Bradford P Taylor
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Tara C Bouton
- Section of Infectious Diseases, Boston University School of Medicine and Boston Medical Center, Boston, Massachusetts, USA
| | - Aubrey R Odom-Mabey
- Bioinformatics Program, Boston University, Boston, MA, USA.,Division of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Sarah E Weber
- Section of Infectious Diseases, Boston University School of Medicine and Boston Medical Center, Boston, Massachusetts, USA
| | - Sara Lodi
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Elizabeth J Ragan
- Section of Infectious Diseases, Boston University School of Medicine and Boston Medical Center, Boston, Massachusetts, USA
| | - John H Connor
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA.,Bioinformatics Program, Boston University, Boston, MA, USA.,Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Karen R Jacobson
- Section of Infectious Diseases, Boston University School of Medicine and Boston Medical Center, Boston, Massachusetts, USA
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| |
Collapse
|
16
|
Strong R, McCleary S, Grierson S, Choudhury B, Steinbach F, Crooke HR. Molecular Epidemiology Questions Transmission Pathways Identified During the Year 2000 Outbreak of Classical Swine Fever in the UK. Front Microbiol 2022; 13:909396. [PMID: 35836425 PMCID: PMC9274199 DOI: 10.3389/fmicb.2022.909396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/06/2022] [Indexed: 11/18/2022] Open
Abstract
The last outbreak of classical swine fever (CSF) in the UK occurred in 2000. A total of 16 domestic pig holdings in the East Anglia region were confirmed as infected over a 3-month period. Obtaining viral genome sequences has since become easier and more cost-effective and has accordingly been applied to trace viral transmission events for a variety of viruses. The rate of genetic evolution varies for different viruses and is influenced by different transmission events, which will vary according to the epidemiology of an outbreak. To examine if genetic changes over the course of any future CSF outbreak would occur to supplement epidemiological investigations and help to track virus movements, the E2 gene and full genome of the virus present in archived tonsil samples from 14 of these infected premises were sequenced. Insufficient changes occurred in the full E2 gene to discriminate between the viruses from the different premises. In contrast, between 5 and 14 nucleotide changes were detected between the genome sequence of the virus from the presumed index case and the sequences from the other 13 infected premises. Phylogenetic analysis of these full CSFV genome sequences identified clusters of closely related viruses that allowed to corroborate some of the transmission pathways inferred by epidemiological investigations at the time. However, other sequences were more distinct and raised questions about the virus transmission routes previously implicated. We are thus confident that in future outbreaks, real-time monitoring of the outbreak via full genome sequencing will be beneficial.
Collapse
|
17
|
Romano CM, de Oliveira CM, da Silva LS, Levi JE. Early Emergence and Dispersal of Delta SARS-CoV-2 Lineage AY.99.2 in Brazil. Front Med (Lausanne) 2022; 9:930380. [PMID: 35783651 PMCID: PMC9249134 DOI: 10.3389/fmed.2022.930380] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
The year of 2021 was marked by the emergence and dispersal of a number of SARS-CoV-2 lineages, resulting in the “third wave” of COVID-19 in several countries despite the level of vaccine coverage. Soon after the first confirmed cases of COVID-19 by the Delta variant in Brazil, at least seven Delta sub-lineages emerged, including the globally spread AY.101 and AY.99.2. In this study we performed a detailed analysis of the COVID-19 scenario in Brazil from April to December 2021 by using data collected by the largest private medical diagnostic company in Latin America (Dasa), and SARS-CoV-2 genomic sequences generated by its SARS-CoV-2 genomic surveillance project (GENOV). For phylogenetic and Bayesian analysis, SARS-CoV-2 genomes available at GISAID public database were also retrieved. We confirmed that the Brazilian AY.99.2 and AY.101 were the most prevalent lineages during this period, overpassing the Gamma variant in July/August. We also estimated that AY.99.2 likely emerged a few weeks after the entry of the B.1.617.2 in the country, at some point between late April and May and rapidly spread to other countries. Despite no increased fitness described for the AY.99.2 lineage, a rapid shift in the composition of Delta SARS-CoV-2 lineages prevalence in Brazil took place. Understanding the reasons leading the AY.99.2 to become the dominant lineage in the country is important to understand the process of lineage competitions that may inform future control measures.
Collapse
Affiliation(s)
- Camila Malta Romano
- Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP), São Paulo, Brazil
- Instituto de Medicina Tropical de São Paulo, Moléstias Infecciosas, Universidade de São Paulo, São Paulo, Brazil
- *Correspondence: Camila Malta Romano
| | | | | | - José Eduardo Levi
- Instituto de Medicina Tropical de São Paulo, Moléstias Infecciosas, Universidade de São Paulo, São Paulo, Brazil
- Research & Development, Dasa Laboratories, Dasa, Brazil
| |
Collapse
|
18
|
Sá R, Isidro J, Borges V, Duarte S, Vieira L, Gomes JP, Tedim S, Matias J, Leite A. Unravelling the hurdles of a large COVID-19 epidemiological investigation by viral genomics. J Infect 2022; 85:64-74. [PMID: 35609706 PMCID: PMC9123803 DOI: 10.1016/j.jinf.2022.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/16/2022] [Accepted: 05/17/2022] [Indexed: 11/25/2022]
|
19
|
Lee K, Pusterla N, Barnum SM, Lee DH, Martínez-López B. Investigation of cross-regional spread and evolution of equine influenza H3N8 at US and global scales using Bayesian phylogeography based on balanced subsampling. Transbound Emerg Dis 2022; 69:e1734-e1748. [PMID: 35263501 DOI: 10.1111/tbed.14509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/03/2022] [Accepted: 03/05/2022] [Indexed: 11/28/2022]
Abstract
Equine influenza virus (EIV) is a highly contagious pathogen of equids, and a well-known burden in global equine health. EIV H3N8 variants seasonally emerged and resulted in EIV outbreaks in the United States (US) and worldwide. The present study evaluated the pattern of cross-regional EIV H3N8 spread and evolutionary characteristics at US and global scales using Bayesian phylogeography with balanced subsampling based on regional horse population size. A total of 297 Haemagglutinin (HA) sequences of global EIV H3N8 were collected from 1963 to 2019 and subsampled to global subset (n = 67), raw US sequences (n = 100) and US subset (n = 44) datasets. Discrete trait phylogeography analysis was used to estimate the transmission history of EIV using four global and US genome datasets. The North American lineage was the major source of globally dominant EIV variants and spread to other global regions. The US EIV strains generally spread from the southern and midwestern regions to other regions. The EIV H3N8 accumulated approximately three nucleotide substitutions per year in the HA gene under heterogenous local positive selection. Our findings will guide better decision making of target intervention strategies of EIV H3N8 infection and provide the better scheme of genomic surveillance in the US and global equine health. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Kyuyoung Lee
- Center for Animal Disease Modeling and Surveillance (CADMS), Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, USA
| | - Nicola Pusterla
- Department of Medicine & Epidemiology, School Veterinary Medicine, University of California, Davis, USA
| | - Samantha M Barnum
- Department of Medicine & Epidemiology, School Veterinary Medicine, University of California, Davis, USA
| | - Dong-Hun Lee
- College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Beatriz Martínez-López
- Center for Animal Disease Modeling and Surveillance (CADMS), Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, USA
| |
Collapse
|
20
|
Aggarwal D, Myers R, Hamilton WL, Bharucha T, Tumelty NM, Brown CS, Meader EJ, Connor T, Smith DL, Bradley DT, Robson S, Bashton M, Shallcross L, Zambon M, Goodfellow I, Chand M, O'Grady J, Török ME, Peacock SJ, Page AJ. The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities. THE LANCET. MICROBE 2022; 3:e151-e158. [PMID: 34608459 PMCID: PMC8480962 DOI: 10.1016/s2666-5247(21)00208-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We reviewed all genomic epidemiology studies on COVID-19 in long-term care facilities (LTCFs) that had been published to date. We found that staff and residents were usually infected with identical, or near identical, SARS-CoV-2 genomes. Outbreaks usually involved one predominant cluster, and the same lineages persisted in LTCFs despite infection control measures. Outbreaks were most commonly due to single or few introductions followed by a spread rather than a series of seeding events from the community into LTCFs. The sequencing of samples taken consecutively from the same individuals at the same facilities showed the persistence of the same genome sequence, indicating that the sequencing technique was robust over time. When combined with local epidemiology, genomics allowed probable transmission sources to be better characterised. The transmission between LTCFs was detected in multiple studies. The mortality rate among residents was high in all facilities, regardless of the lineage. Bioinformatics methods were inadequate in a third of the studies reviewed, and reproducing the analyses was difficult because sequencing data were not available in many facilities.
Collapse
Affiliation(s)
- Dinesh Aggarwal
- Department of Medicine, University of Cambridge, Cambridge, UK
- Public Health England, London, UK
- Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | - William L Hamilton
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Tehmina Bharucha
- Public Health England, London, UK
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, UK
- Lao-Oxford-Mahosot Hospital, Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Niamh M Tumelty
- Cambridge University Libraries, University of Cambridge, Cambridge, UK
| | - Colin S Brown
- Public Health England, London, UK
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, UK
- Lao-Oxford-Mahosot Hospital, Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Emma J Meader
- Norfolk and Norwich University Hospital, Norwich, UK
| | - Tom Connor
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, Wales, UK
- Public Health Wales, University Hospital of Wales, Cardiff, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Darren L Smith
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Declan T Bradley
- Public Health Agency, Belfast, UK
- Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Samuel Robson
- University of Portsmouth, Centre for Enzyme Innovation, Portsmouth, UK
| | - Matthew Bashton
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Laura Shallcross
- Institute of Health Informatics, University College London, London, UK
| | | | - Ian Goodfellow
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Meera Chand
- Public Health England, London, UK
- Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Justin O'Grady
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - M Estée Török
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Andrew J Page
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| |
Collapse
|
21
|
Muenchhoff M, Graf A, Krebs S, Quartucci C, Hasmann S, Hellmuth JC, Scherer C, Osterman A, Boehm S, Mandel C, Becker-Pennrich AS, Zoller M, Stubbe HC, Munker S, Munker D, Milger K, Gapp M, Schneider S, Ruhle A, Jocham L, Nicolai L, Pekayvaz K, Weinberger T, Mairhofer H, Khatamzas E, Hofmann K, Spaeth PM, Bender S, Kääb S, Zwissler B, Mayerle J, Behr J, von Bergwelt-Baildon M, Reincke M, Grabein B, Hinske CL, Blum H, Keppler OT. Genomic epidemiology reveals multiple introductions of SARS-CoV-2 followed by community and nosocomial spread, Germany, February to May 2020. ACTA ACUST UNITED AC 2021; 26. [PMID: 34713795 PMCID: PMC8555370 DOI: 10.2807/1560-7917.es.2021.26.43.2002066] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background In the SARS-CoV-2 pandemic, viral genomes are available at unprecedented speed, but spatio-temporal bias in genome sequence sampling precludes phylogeographical inference without additional contextual data. Aim We applied genomic epidemiology to trace SARS-CoV-2 spread on an international, national and local level, to illustrate how transmission chains can be resolved to the level of a single event and single person using integrated sequence data and spatio-temporal metadata. Methods We investigated 289 COVID-19 cases at a university hospital in Munich, Germany, between 29 February and 27 May 2020. Using the ARTIC protocol, we obtained near full-length viral genomes from 174 SARS-CoV-2-positive respiratory samples. Phylogenetic analyses using the Auspice software were employed in combination with anamnestic reporting of travel history, interpersonal interactions and perceived high-risk exposures among patients and healthcare workers to characterise cluster outbreaks and establish likely scenarios and timelines of transmission. Results We identified multiple independent introductions in the Munich Metropolitan Region during the first weeks of the first pandemic wave, mainly by travellers returning from popular skiing areas in the Alps. In these early weeks, the rate of presumable hospital-acquired infections among patients and in particular healthcare workers was high (9.6% and 54%, respectively) and we illustrated how transmission chains can be dissected at high resolution combining virus sequences and spatio-temporal networks of human interactions. Conclusions Early spread of SARS-CoV-2 in Europe was catalysed by superspreading events and regional hotspots during the winter holiday season. Genomic epidemiology can be employed to trace viral spread and inform effective containment strategies.
Collapse
Affiliation(s)
- Maximilian Muenchhoff
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Caroline Quartucci
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Munich, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Sandra Hasmann
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Department of Medicine IV, University Hospital, LMU Munich, Munich, Germany
| | - Johannes C Hellmuth
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Department of Medicine III, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany
| | - Clemens Scherer
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Andreas Osterman
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Stephan Boehm
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Christopher Mandel
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Department of Medicine IV, University Hospital, LMU Munich, Munich, Germany
| | - Andrea Sabine Becker-Pennrich
- Department of Anesthesiology, University Hospital, LMU Munich, Munich, Germany.,Department of Medical Information Processing, Biometry and Epidemiology (IBE), LMU Munich, Munich, Germany
| | - Michael Zoller
- Department of Anesthesiology, University Hospital, LMU Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Hans Christian Stubbe
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Stefan Munker
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Dieter Munker
- Department of Medicine V, University Hospital, LMU Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Katrin Milger
- Department of Medicine V, University Hospital, LMU Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Madeleine Gapp
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Stephanie Schneider
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Adrian Ruhle
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Linda Jocham
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Leo Nicolai
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Kami Pekayvaz
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Tobias Weinberger
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Helga Mairhofer
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Elham Khatamzas
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Department of Medicine III, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany
| | - Katharina Hofmann
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Patricia M Spaeth
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Sabine Bender
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Stefan Kääb
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Bernhard Zwissler
- Department of Anesthesiology, University Hospital, LMU Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Julia Mayerle
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Juergen Behr
- Department of Medicine V, University Hospital, LMU Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Michael von Bergwelt-Baildon
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Department of Medicine III, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany
| | - Martin Reincke
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Department of Medicine IV, University Hospital, LMU Munich, Munich, Germany
| | - Beatrice Grabein
- Department of Clinical Microbiology and Hospital Hygiene, University Hospital, LMU Munich, Munich, Germany
| | - Christian Ludwig Hinske
- Department of Anesthesiology, University Hospital, LMU Munich, Munich, Germany.,Department of Medical Information Processing, Biometry and Epidemiology (IBE), LMU Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Oliver T Keppler
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| |
Collapse
|
22
|
Zeller M, Gangavarapu K, Anderson C, Smither AR, Vanchiere JA, Rose R, Snyder DJ, Dudas G, Watts A, Matteson NL, Robles-Sikisaka R, Marshall M, Feehan AK, Sabino-Santos G, Bell-Kareem AR, Hughes LD, Alkuzweny M, Snarski P, Garcia-Diaz J, Scott RS, Melnik LI, Klitting R, McGraw M, Belda-Ferre P, DeHoff P, Sathe S, Marotz C, Grubaugh ND, Nolan DJ, Drouin AC, Genemaras KJ, Chao K, Topol S, Spencer E, Nicholson L, Aigner S, Yeo GW, Farnaes L, Hobbs CA, Laurent LC, Knight R, Hodcroft EB, Khan K, Fusco DN, Cooper VS, Lemey P, Gardner L, Lamers SL, Kamil JP, Garry RF, Suchard MA, Andersen KG. Emergence of an early SARS-CoV-2 epidemic in the United States. Cell 2021; 184:4939-4952.e15. [PMID: 34508652 PMCID: PMC8313480 DOI: 10.1016/j.cell.2021.07.030] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/07/2021] [Accepted: 07/22/2021] [Indexed: 12/12/2022]
Abstract
The emergence of the COVID-19 epidemic in the United States (U.S.) went largely undetected due to inadequate testing. New Orleans experienced one of the earliest and fastest accelerating outbreaks, coinciding with Mardi Gras. To gain insight into the emergence of SARS-CoV-2 in the U.S. and how large-scale events accelerate transmission, we sequenced SARS-CoV-2 genomes during the first wave of the COVID-19 epidemic in Louisiana. We show that SARS-CoV-2 in Louisiana had limited diversity compared to other U.S. states and that one introduction of SARS-CoV-2 led to almost all of the early transmission in Louisiana. By analyzing mobility and genomic data, we show that SARS-CoV-2 was already present in New Orleans before Mardi Gras, and the festival dramatically accelerated transmission. Our study provides an understanding of how superspreading during large-scale events played a key role during the early outbreak in the U.S. and can greatly accelerate epidemics.
Collapse
Affiliation(s)
- Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Catelyn Anderson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Allison R Smither
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - John A Vanchiere
- Department of Pediatrics, Louisiana State University Health Sciences Center - Shreveport, Shreveport, LA 71130, USA
| | | | - Daniel J Snyder
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15219, USA; Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Gytis Dudas
- Gothenburg Global Biodiversity Centre (GGBC), Gothenburg, Sweden
| | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada; Bluedot, Toronto, Canada
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Maximilian Marshall
- Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Amy K Feehan
- Ochsner Clinic Foundation, New Orleans, Louisiana, USA
| | - Gilberto Sabino-Santos
- Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA; Centre for Virology Research, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP 14049900, Brazil
| | - Antoinette R Bell-Kareem
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Laura D Hughes
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Manar Alkuzweny
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Patricia Snarski
- Heart and Vascular Institute, John W. Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Department of Physiology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | | | - Rona S Scott
- Department of Microbiology and Immunology, Louisiana State University Health Science Center Shreveport, Shreveport, LA 71103, USA
| | - Lilia I Melnik
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Raphaëlle Klitting
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michelle McGraw
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Peter DeHoff
- Department of Obstetrics, Gynecology, and Reproductive Science, University of California, San Diego, La Jolla, CA 92037, USA
| | - Shashank Sathe
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Clarisse Marotz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA; Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | | | - Arnaud C Drouin
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Department of Physiology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Kaylynn J Genemaras
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Bioinnovation Program, Tulane University, New Orleans, LA 70118, USA
| | - Karissa Chao
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Bioinnovation Program, Tulane University, New Orleans, LA 70118, USA
| | - Sarah Topol
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Emily Spencer
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Laura Nicholson
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, USA
| | - Lauge Farnaes
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Charlotte A Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Science, University of California, San Diego, La Jolla, CA 92037, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA; Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA; Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | | | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada; Bluedot, Toronto, Canada; Department of Medicine, University of Toronto, Toronto, Canada
| | - Dahlene N Fusco
- Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA; Department of Medicine, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA 70114, USA
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15219, USA; Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Phillipe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Belgium; Global Virology Network
| | - Lauren Gardner
- Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD, USA
| | | | - Jeremy P Kamil
- Department of Microbiology and Immunology, Louisiana State University Health Science Center Shreveport, Shreveport, LA 71103, USA
| | - Robert F Garry
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Zalgen Labs LLC, Germantown, MD, USA
| | - Marc A Suchard
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Scripps Research Translational Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
23
|
Kahn R, Wang R, Leavitt SV, Hanage WP, Lipsitch M. Leveraging Pathogen Sequence and Contact Tracing Data to Enhance Vaccine Trials in Emerging Epidemics. Epidemiology 2021; 32:698-704. [PMID: 34039898 PMCID: PMC8338748 DOI: 10.1097/ede.0000000000001367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
INTRODUCTION Advance planning of vaccine trials conducted during outbreaks increases our ability to rapidly define the efficacy and potential impact of a vaccine. Vaccine efficacy against infectiousness (VEI) is an important measure for understanding a vaccine's full impact, yet it is currently not identifiable in many trial designs because it requires knowledge of infectors' vaccination status. Recent advances in genomics have improved our ability to reconstruct transmission networks. We aim to assess if augmenting trials with pathogen sequence and contact tracing data can permit them to estimate VEI. METHODS We develop a transmission model with a vaccine trial in an outbreak setting, incorporate pathogen sequence data and contact tracing data, and assign probabilities to likely infectors. We then propose and evaluate the performance of an estimator of VEI. RESULTS We find that under perfect knowledge of infector-infectee pairs, we are able to accurately estimate VEI. Use of sequence data results in imperfect reconstruction of transmission networks, biasing estimates of VEI towards the null, with approaches using deep sequence data performing better than approaches using consensus sequence data. Inclusion of contact tracing data reduces the bias. CONCLUSION Pathogen genomics enhance identifiability of VEI, but imperfect transmission network reconstruction biases estimate toward the null and limits our ability to detect VEI. Given the consistent direction of the bias, estimates obtained from trials using these methods will provide lower bounds on the true VEI. A combination of sequence and epidemiologic data results in the most accurate estimates, underscoring the importance of contact tracing.
Collapse
Affiliation(s)
- Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
| | - Rui Wang
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, Massachusetts, USA
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
| | - Sarah V. Leavitt
- Department of Biostatistics, School of Public Health, Boston University, Boston, Massachusetts, USA
| | - William P. Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
| |
Collapse
|
24
|
Abstract
Assembly and publication of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome in January 2020 enabled the immediate development of tests to detect the new virus. This began the largest global testing programme in history, in which hundreds of millions of individuals have been tested to date. The unprecedented scale of testing has driven innovation in the strategies, technologies and concepts that govern testing in public health. This Review describes the changing role of testing during the COVID-19 pandemic, including the use of genomic surveillance to track SARS-CoV-2 transmission around the world, the use of contact tracing to contain disease outbreaks and testing for the presence of the virus circulating in the environment. Despite these efforts, widespread community transmission has become entrenched in many countries and has required the testing of populations to identify and isolate infected individuals, many of whom are asymptomatic. The diagnostic and epidemiological principles that underpin such population-scale testing are also considered, as are the high-throughput and point-of-care technologies that make testing feasible on a massive scale.
Collapse
Affiliation(s)
- Tim R Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia.
- Garvan Institute of Medical Research, Sydney, NSW, Australia.
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia.
| | - Marc Salit
- Departments of Pathology and Bioengineering, Stanford University, Stanford, CA, USA
- Joint Initiative for Metrology in Biology, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| |
Collapse
|
25
|
Stirrup O, Hughes J, Parker M, Partridge DG, Shepherd JG, Blackstone J, Coll F, Keeley A, Lindsey BB, Marek A, Peters C, Singer JB, Tamuri A, de Silva TI, Thomson EC, Breuer J. Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data. eLife 2021; 10:e65828. [PMID: 34184637 PMCID: PMC8285103 DOI: 10.7554/elife.65828] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 06/25/2021] [Indexed: 12/29/2022] Open
Abstract
Background Rapid identification and investigation of healthcare-associated infections (HCAIs) is important for suppression of SARS-CoV-2, but the infection source for hospital onset COVID-19 infections (HOCIs) cannot always be readily identified based only on epidemiological data. Viral sequencing data provides additional information regarding potential transmission clusters, but the low mutation rate of SARS-CoV-2 can make interpretation using standard phylogenetic methods difficult. Methods We developed a novel statistical method and sequence reporting tool (SRT) that combines epidemiological and sequence data in order to provide a rapid assessment of the probability of HCAI among HOCI cases (defined as first positive test >48 hr following admission) and to identify infections that could plausibly constitute outbreak events. The method is designed for prospective use, but was validated using retrospective datasets from hospitals in Glasgow and Sheffield collected February-May 2020. Results We analysed data from 326 HOCIs. Among HOCIs with time from admission ≥8 days, the SRT algorithm identified close sequence matches from the same ward for 160/244 (65.6%) and in the remainder 68/84 (81.0%) had at least one similar sequence elsewhere in the hospital, resulting in high estimated probabilities of within-ward and within-hospital transmission. For HOCIs with time from admission 3-7 days, the SRT probability of healthcare acquisition was >0.5 in 33/82 (40.2%). Conclusions The methodology developed can provide rapid feedback on HOCIs that could be useful for infection prevention and control teams, and warrants further prospective evaluation. The integration of epidemiological and sequence data is important given the low mutation rate of SARS-CoV-2 and its variable incubation period. Funding COG-UK HOCI funded by COG-UK consortium, supported by funding from UK Research and Innovation, National Institute of Health Research and Wellcome Sanger Institute.
Collapse
Affiliation(s)
- Oliver Stirrup
- Institute for Global Health, University College LondonLondonUnited Kingdom
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
| | - Matthew Parker
- Sheffield Bioinformatics Core, The University of SheffieldSheffieldUnited Kingdom
- Sheffield Institute for Translational Neuroscience, The University of SheffieldSheffieldUnited Kingdom
- Sheffield Biomedical Research Centre, The University of SheffieldSheffieldUnited Kingdom
| | - David G Partridge
- Sheffield Teaching Hospitals NHS Foundation TrustSheffieldUnited Kingdom
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of SheffieldSheffieldUnited Kingdom
| | - James G Shepherd
- MRC-University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
| | - James Blackstone
- The Comprehensive Clinical Trials Unit at UCL , University College LondonLondonUnited Kingdom
| | - Francesc Coll
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
| | - Alexander Keeley
- Sheffield Teaching Hospitals NHS Foundation TrustSheffieldUnited Kingdom
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of SheffieldSheffieldUnited Kingdom
| | - Benjamin B Lindsey
- Sheffield Teaching Hospitals NHS Foundation TrustSheffieldUnited Kingdom
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of SheffieldSheffieldUnited Kingdom
| | - Aleksandra Marek
- Clinical Microbiology, NHS Greater Glasgow and ClydeGlasgowUnited Kingdom
| | - Christine Peters
- Clinical Microbiology, NHS Greater Glasgow and ClydeGlasgowUnited Kingdom
| | - Joshua B Singer
- MRC-University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
| | | | - Asif Tamuri
- Research Computing, University College LondonLondonUnited Kingdom
| | - Thushan I de Silva
- Sheffield Teaching Hospitals NHS Foundation TrustSheffieldUnited Kingdom
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of SheffieldSheffieldUnited Kingdom
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of GlasgowGlasgowUnited Kingdom
- Department of Infectious Diseases, Queen Elizabeth University HospitalGlasgowUnited Kingdom
| | - Judith Breuer
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| |
Collapse
|
26
|
Hochstatter KR, Tully DC, Power KA, Koepke R, Akhtar WZ, Prieve AF, Whyte T, Bean DJ, Seal DW, Allen TM, Westergaard RP. Hepatitis C Virus Transmission Clusters in Public Health and Correctional Settings, Wisconsin, USA, 2016-2017 1. Emerg Infect Dis 2021; 27:480-489. [PMID: 33496239 PMCID: PMC7853590 DOI: 10.3201/eid2702.202957] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
Abstract
Ending the hepatitis C virus (HCV) epidemic requires stopping transmission among networks of persons who inject drugs. Identifying transmission networks by using genomic epidemiology may inform community responses that can quickly interrupt transmission. We retrospectively identified HCV RNA–positive specimens corresponding to 459 persons in settings that use the state laboratory, including correctional facilities and syringe services programs, in Wisconsin, USA, during 2016–2017. We conducted next-generation sequencing of HCV and analyzed it for phylogenetic linkage by using the Centers for Disease Control and Prevention Global Hepatitis Outbreak Surveillance Technology platform. Analysis showed that 126 persons were linked across 42 clusters. Phylogenetic clustering was higher in rural communities and associated with female sex and younger age among rural residents. These data highlight that HCV transmission could be reduced by expanding molecular-based surveillance strategies to rural communities affected by the opioid crisis.
Collapse
|
27
|
Retchless AC, Chen A, Chang HY, Blain AE, McNamara LA, Mustapha MM, Harrison LH, Wang X. Using Neisseria meningitidis genomic diversity to inform outbreak strain identification. PLoS Pathog 2021; 17:e1009586. [PMID: 34003852 PMCID: PMC8177650 DOI: 10.1371/journal.ppat.1009586] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 06/04/2021] [Accepted: 04/26/2021] [Indexed: 11/18/2022] Open
Abstract
Meningococcal disease is a life-threatening illness caused by the human-restricted bacterium Neisseria meningitidis. Outbreaks in the USA involve at least two cases in an organization or community caused by the same serogroup within three months. Genome comparisons, including phylogenetic analysis and quantification of genome distances can provide confirmatory evidence of pathogen transmission during an outbreak. Interpreting genome distances depends on understanding their distribution both among isolates from outbreaks and among those not from outbreaks. Here, we identify outbreak strains based on phylogenetic relationships among 141 N. meningitidis isolates collected from 28 outbreaks in the USA during 2010-2017 and 1516 non-outbreak isolates collected through contemporaneous meningococcal surveillance. We show that genome distance thresholds based on the maximum SNPs and allele distances among isolates in the phylogenetically defined outbreak strains are sufficient to separate most pairs of non-outbreak isolates into separate strains. Non-outbreak isolate pairs that could not be distinguished from each other based on genetic distances were concentrated in the clonal complexes CC11, CC103, and CC32. Within each of these clonal complexes, phylodynamic analysis identified a group of isolates with extremely low diversity, collected over several years and multiple states. Clusters of isolates with low genetic diversity could indicate increased pathogen transmission, potentially resulting in local outbreaks or nationwide clonal expansions.
Collapse
Affiliation(s)
- Adam C. Retchless
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Alex Chen
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - How-Yi Chang
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Amy E. Blain
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Lucy A. McNamara
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Mustapha M. Mustapha
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Lee H. Harrison
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Xin Wang
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
| |
Collapse
|
28
|
Morel B, Barbera P, Czech L, Bettisworth B, Hübner L, Lutteropp S, Serdari D, Kostaki EG, Mamais I, Kozlov AM, Pavlidis P, Paraskevis D, Stamatakis A. Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult. Mol Biol Evol 2021; 38:1777-1791. [PMID: 33316067 PMCID: PMC7798910 DOI: 10.1093/molbev/msaa314] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by example of a data snapshot comprising a quality-filtered subset of 8,736 out of all 16,453 virus sequences available on May 5, 2020 from gisaid.org. We find that it is difficult to infer a reliable phylogeny on these data due to the large number of sequences in conjunction with the low number of mutations. We further find that rooting the inferred phylogeny with some degree of confidence either via the bat and pangolin outgroups or by applying novel computational methods on the ingroup phylogeny does not appear to be credible. Finally, an automatic classification of the current sequences into subclasses using the mPTP tool for molecular species delimitation is also, as might be expected, not possible, as the sequences are too closely related. We conclude that, although the application of phylogenetic methods to disentangle the evolution and spread of COVID-19 provides some insight, results of phylogenetic analyses, in particular those conducted under the default settings of current phylogenetic inference tools, as well as downstream analyses on the inferred phylogenies, should be considered and interpreted with extreme caution.
Collapse
Affiliation(s)
- Benoit Morel
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Pierre Barbera
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Lucas Czech
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Ben Bettisworth
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Lukas Hübner
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Sarah Lutteropp
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Dora Serdari
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Evangelia-Georgia Kostaki
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Ioannis Mamais
- Department of Health Sciences, European University Cyprus, Nicosia, Cyprus
| | - Alexey M Kozlov
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Crete, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| |
Collapse
|
29
|
Gutierrez B, Márquez S, Prado-Vivar B, Becerra-Wong M, Guadalupe JJ, da Silva Candido D, Fernandez-Cadena JC, Morey-Leon G, Armas-Gonzalez R, Andrade-Molina DM, Bruno A, de Mora D, Olmedo M, Portugal D, Gonzalez M, Orlando A, Drexler JF, Moreira-Soto A, Sander AL, Brünink S, Kühne A, Patiño L, Carrazco-Montalvo A, Mestanza O, Zurita J, Sevillano G, du Plessis L, McCrone JT, Coloma J, Trueba G, Barragán V, Rojas-Silva P, Grunauer M, Kraemer MU, Faria NR, Escalera-Zamudio M, Pybus OG, Cárdenas P. Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.03.31.21254685. [PMID: 33851177 PMCID: PMC8043474 DOI: 10.1101/2021.03.31.21254685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Characterisation of SARS-CoV-2 genetic diversity through space and time can reveal trends in virus importation and domestic circulation, and permit the exploration of questions regarding the early transmission dynamics. Here we present a detailed description of SARS-CoV-2 genomic epidemiology in Ecuador, one of the hardest hit countries during the early stages of the COVID-19 pandemic. We generate and analyse 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylgeographic analysis of these sequences in the context of global SARS-CoV-2 diversity enable us to identify and characterise individual transmission lineages within Ecuador, explore their spatiotemporal distributions, and consider their introduction and domestic circulation. Our results reveal a pattern of multiple international importations across the country, with apparent differences between key provinces. Transmission lineages were mostly introduced before the implementation of non-pharmaceutical interventions (NPIs), with differential degrees of persistence and national dissemination.
Collapse
Affiliation(s)
- Bernardo Gutierrez
- Department of Zoology, University of Oxford, Oxford, UK
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Sully Márquez
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Belén Prado-Vivar
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Mónica Becerra-Wong
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Juan José Guadalupe
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Juan Carlos Fernandez-Cadena
- Omics Sciences Laboratory, Faculty of Medical Sciences, Universidad de Especialidades Espíritu Santo, Samborondón, Ecuador
| | - Gabriel Morey-Leon
- Faculty of Medical Sciences, Universidad de Guayaquil, Guayaquil, Ecuador
| | - Rubén Armas-Gonzalez
- Faculty of Sciences, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - Derly Madeleiny Andrade-Molina
- Omics Sciences Laboratory, Faculty of Medical Sciences, Universidad de Especialidades Espíritu Santo, Samborondón, Ecuador
| | - Alfredo Bruno
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
- Universidad Agraria del Ecuador
| | - Domenica de Mora
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Maritza Olmedo
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Denisse Portugal
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Manuel Gonzalez
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Alberto Orlando
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Andres Moreira-Soto
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Anna-Lena Sander
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Sebastian Brünink
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Arne Kühne
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Leandro Patiño
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | | | - Orson Mestanza
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Jeannete Zurita
- Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador
| | - Gabriela Sevillano
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador
| | | | - John T. McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Josefina Coloma
- School of Public Health, University of California, Berkeley, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Verónica Barragán
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Michelle Grunauer
- Escuela de Medicina, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Nuno R. Faria
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
| | | | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK
| | - Paúl Cárdenas
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| |
Collapse
|
30
|
Valesano AL, Rumfelt KE, Dimcheff DE, Blair CN, Fitzsimmons WJ, Petrie JG, Martin ET, Lauring AS. Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts. PLoS Pathog 2021; 17:e1009499. [PMID: 33826681 PMCID: PMC8055005 DOI: 10.1371/journal.ppat.1009499] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/19/2021] [Accepted: 03/24/2021] [Indexed: 01/12/2023] Open
Abstract
Analysis of SARS-CoV-2 genetic diversity within infected hosts can provide insight into the generation and spread of new viral variants and may enable high resolution inference of transmission chains. However, little is known about temporal aspects of SARS-CoV-2 intrahost diversity and the extent to which shared diversity reflects convergent evolution as opposed to transmission linkage. Here we use high depth of coverage sequencing to identify within-host genetic variants in 325 specimens from hospitalized COVID-19 patients and infected employees at a single medical center. We validated our variant calling by sequencing defined RNA mixtures and identified viral load as a critical factor in variant identification. By leveraging clinical metadata, we found that intrahost diversity is low and does not vary by time from symptom onset. This suggests that variants will only rarely rise to appreciable frequency prior to transmission. Although there was generally little shared variation across the sequenced cohort, we identified intrahost variants shared across individuals who were unlikely to be related by transmission. These variants did not precede a rise in frequency in global consensus genomes, suggesting that intrahost variants may have limited utility for predicting future lineages. These results provide important context for sequence-based inference in SARS-CoV-2 evolution and epidemiology.
Collapse
Affiliation(s)
- Andrew L. Valesano
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kalee E. Rumfelt
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Derek E. Dimcheff
- Division of Hospital Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Christopher N. Blair
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - William J. Fitzsimmons
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Joshua G. Petrie
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Emily T. Martin
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Adam S. Lauring
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| |
Collapse
|
31
|
Ramazzotti D, Angaroni F, Maspero D, Gambacorti-Passerini C, Antoniotti M, Graudenzi A, Piazza R. VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples. PATTERNS (NEW YORK, N.Y.) 2021; 2:100212. [PMID: 33728416 PMCID: PMC7953447 DOI: 10.1016/j.patter.2021.100212] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 11/30/2020] [Accepted: 01/22/2021] [Indexed: 12/22/2022]
Abstract
We introduce VERSO, a two-step framework for the characterization of viral evolution from sequencing data of viral genomes, which is an improvement on phylogenomic approaches for consensus sequences. VERSO exploits an efficient algorithmic strategy to return robust phylogenies from clonal variant profiles, also in conditions of sampling limitations. It then leverages variant frequency patterns to characterize the intra-host genomic diversity of samples, revealing undetected infection chains and pinpointing variants likely involved in homoplasies. On simulations, VERSO outperforms state-of-the-art tools for phylogenetic inference. Notably, the application to 6,726 amplicon and RNA sequencing samples refines the estimation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution, while co-occurrence patterns of minor variants unveil undetected infection paths, which are validated with contact tracing data. Finally, the analysis of SARS-CoV-2 mutational landscape uncovers a temporal increase of overall genomic diversity and highlights variants transiting from minor to clonal state and homoplastic variants, some of which fall on the spike gene. Available at: https://github.com/BIMIB-DISCo/VERSO.
Collapse
Affiliation(s)
- Daniele Ramazzotti
- Department of Medicine and Surgery, Università degli Studi di Milano-Bicocca, Monza, Italy
| | - Fabrizio Angaroni
- Department of Informatics, Systems and Communication, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Davide Maspero
- Department of Informatics, Systems and Communication, Università degli Studi di Milano-Bicocca, Milan, Italy
- Inst. of Molecular Bioimaging and Physiology, Consiglio Nazionale delle Ricerche (IBFM-CNR), Segrate, Milan, Italy
| | | | - Marco Antoniotti
- Department of Informatics, Systems and Communication, Università degli Studi di Milano-Bicocca, Milan, Italy
- Bicocca Bioinformatics, Biostatistics and Bioimaging Centre – B4, Milan, Italy
| | - Alex Graudenzi
- Inst. of Molecular Bioimaging and Physiology, Consiglio Nazionale delle Ricerche (IBFM-CNR), Segrate, Milan, Italy
- Bicocca Bioinformatics, Biostatistics and Bioimaging Centre – B4, Milan, Italy
| | - Rocco Piazza
- Department of Medicine and Surgery, Università degli Studi di Milano-Bicocca, Monza, Italy
| |
Collapse
|
32
|
Resende PC, Delatorre E, Gräf T, Mir D, Motta FC, Appolinario LR, da Paixão ACD, Mendonça ACDF, Ogrzewalska M, Caetano B, Wallau GL, Docena C, dos Santos MC, de Almeida Ferreira J, Sousa Junior EC, da Silva SP, Fernandes SB, Vianna LA, Souza LDC, Ferro JFG, Nardy VB, Santos CA, Riediger I, do Carmo Debur M, Croda J, Oliveira WK, Abreu A, Bello G, Siqueira MM. Evolutionary Dynamics and Dissemination Pattern of the SARS-CoV-2 Lineage B.1.1.33 During the Early Pandemic Phase in Brazil. Front Microbiol 2021; 11:615280. [PMID: 33679622 PMCID: PMC7925893 DOI: 10.3389/fmicb.2020.615280] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022] Open
Abstract
A previous study demonstrates that most of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Brazilian strains fell in three local clades that were introduced from Europe around late February 2020. Here we investigated in more detail the origin of the major and most widely disseminated SARS-CoV-2 Brazilian lineage B.1.1.33. We recovered 190 whole viral genomes collected from 13 Brazilian states from February 29 to April 31, 2020 and combined them with other B.1.1 genomes collected globally. Our genomic survey confirms that lineage B.1.1.33 is responsible for a variable fraction of the community viral transmissions in Brazilian states, ranging from 2% of all SARS-CoV-2 genomes from Pernambuco to 80% of those from Rio de Janeiro. We detected a moderate prevalence (5-18%) of lineage B.1.1.33 in some South American countries and a very low prevalence (<1%) in North America, Europe, and Oceania. Our study reveals that lineage B.1.1.33 evolved from an ancestral clade, here designated B.1.1.33-like, that carries one of the two B.1.1.33 synapomorphic mutations. The B.1.1.33-like lineage may have been introduced from Europe or arose in Brazil in early February 2020 and a few weeks later gave origin to the lineage B.1.1.33. These SARS-CoV-2 lineages probably circulated during February 2020 and reached all Brazilian regions and multiple countries around the world by mid-March, before the implementation of air travel restrictions in Brazil. Our phylodynamic analysis also indicates that public health interventions were partially effective to control the expansion of lineage B.1.1.33 in Rio de Janeiro because its median effective reproductive number (R e ) was drastically reduced by about 66% during March 2020, but failed to bring it to below one. Continuous genomic surveillance of lineage B.1.1.33 might provide valuable information about epidemic dynamics and the effectiveness of public health interventions in some Brazilian states.
Collapse
Affiliation(s)
- Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Edson Delatorre
- Departamento de Biologia, Centro de Ciencias Exatas, Naturais e da Saude, Universidade Federal do Espirito Santo, Alegre, Brazil
| | - Tiago Gräf
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Daiana Mir
- Unidad de Genomica y Bioinformatica, Centro Universitario Regional del Litoral Norte, Universidad de la Republica, Salto, Uruguay
| | - Fernando Couto Motta
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Luciana Reis Appolinario
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Anna Carolina Dias da Paixão
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Ana Carolina da Fonseca Mendonça
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Maria Ogrzewalska
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Braulia Caetano
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | | | - Cássia Docena
- Instituto Aggeu Magalhaes, Fundação Oswaldo Cruz, Recife, Brazil
| | | | | | | | | | | | - Lucas Alves Vianna
- Laboratorio Central de Saude Publica do Estado Espirito Santo (LACEN-ES), Vitoria, Brazil
| | | | - Jean F. G. Ferro
- Laboratorio Central de Saude Publica de Alagoas (LACEN-AL), Maceio, Brazil
| | - Vanessa B. Nardy
- Laboratorio Central de Saude Publica da Bahia (LACEN-BA), Salvador, Brazil
| | - Cliomar A. Santos
- Laboratorio Central de Saude Publica de Sergipe (LACEN-SE), Aracaju, Brazil
| | - Irina Riediger
- Laboratorio Central de Saude Publica de Parana (LACEN-PR), Curitiba, Brazil
| | | | - Júlio Croda
- Fiocruz Mato Grosso do Sul, Campo Grande, Brazil
- Universidade Federal de Mato Grosso do Sul – UFMS, Campo Grande, Brazil
| | | | - André Abreu
- Coordenadoria Geral de Laboratorios – Ministério da Saude, Brazilia, Brazil
| | - Gonzalo Bello
- Laboratorio de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Marilda M. Siqueira
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| |
Collapse
|
33
|
du Plessis L, McCrone JT, Zarebski AE, Hill V, Ruis C, Gutierrez B, Raghwani J, Ashworth J, Colquhoun R, Connor TR, Faria NR, Jackson B, Loman NJ, O'Toole Á, Nicholls SM, Parag KV, Scher E, Vasylyeva TI, Volz EM, Watts A, Bogoch II, Khan K, Aanensen DM, Kraemer MUG, Rambaut A, Pybus OG. Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK. Science 2021; 371:708-712. [PMID: 33419936 PMCID: PMC7877493 DOI: 10.1126/science.abf2946] [Citation(s) in RCA: 247] [Impact Index Per Article: 82.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022]
Abstract
The United Kingdom's COVID-19 epidemic during early 2020 was one of world's largest and was unusually well represented by virus genomic sampling. We determined the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes, including 26,181 from the UK sampled throughout the country's first wave of infection. Using large-scale phylogenetic analyses combined with epidemiological and travel data, we quantified the size, spatiotemporal origins, and persistence of genetically distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, whereas lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.
Collapse
Affiliation(s)
| | - John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Christopher Ruis
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Bernardo Gutierrez
- Department of Zoology, University of Oxford, Oxford, UK
- School of Biological and Environmental Sciences, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Jordan Ashworth
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Rachel Colquhoun
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Thomas R Connor
- School of Biosciences, Cardiff University, Cardiff, UK
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
| | - Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Samuel M Nicholls
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Kris V Parag
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
| | - Emily Scher
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Erik M Volz
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
| | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Isaac I Bogoch
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK
| |
Collapse
|
34
|
Zeller M, Gangavarapu K, Anderson C, Smither AR, Vanchiere JA, Rose R, Dudas G, Snyder DJ, Watts A, Matteson NL, Robles-Sikisaka R, Marshall M, Feehan AK, Sabino-Santos G, Bell-Kareem A, Hughes LD, Alkuzweny M, Snarski P, Garcia-Diaz J, Scott RS, Melnik LI, Klitting R, McGraw M, Belda-Ferre P, DeHoff P, Sathe S, Marotz C, Grubaugh N, Nolan DJ, Drouin AC, Genemaras KJ, Chao K, Topol S, Spencer E, Nicholson L, Aigner S, Yeo GW, Farnaes L, Hobbs CA, Laurent LC, Knight R, Hodcroft EB, Khan K, Fusco DN, Cooper VS, Lemey P, Gardner L, Lamers SL, Kamil JP, Garry RF, Suchard MA, Andersen KG. Emergence of an early SARS-CoV-2 epidemic in the United States. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021. [PMID: 33564781 PMCID: PMC7872376 DOI: 10.1101/2021.02.05.21251235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The emergence of the early COVID-19 epidemic in the United States (U.S.) went largely undetected, due to a lack of adequate testing and mitigation efforts. The city of New Orleans, Louisiana experienced one of the earliest and fastest accelerating outbreaks, coinciding with the annual Mardi Gras festival, which went ahead without precautions. To gain insight into the emergence of SARS-CoV-2 in the U.S. and how large, crowded events may have accelerated early transmission, we sequenced SARS-CoV-2 genomes during the first wave of the COVID-19 epidemic in Louisiana. We show that SARS-CoV-2 in Louisiana initially had limited sequence diversity compared to other U.S. states, and that one successful introduction of SARS-CoV-2 led to almost all of the early SARS-CoV-2 transmission in Louisiana. By analyzing mobility and genomic data, we show that SARS-CoV-2 was already present in New Orleans before Mardi Gras and that the festival dramatically accelerated transmission, eventually leading to secondary localized COVID-19 epidemics throughout the Southern U.S.. Our study provides an understanding of how superspreading during large-scale events played a key role during the early outbreak in the U.S. and can greatly accelerate COVID-19 epidemics on a local and regional scale.
Collapse
|
35
|
Komissarov AB, Safina KR, Garushyants SK, Fadeev AV, Sergeeva MV, Ivanova AA, Danilenko DM, Lioznov D, Shneider OV, Shvyrev N, Spirin V, Glyzin D, Shchur V, Bazykin GA. Genomic epidemiology of the early stages of the SARS-CoV-2 outbreak in Russia. Nat Commun 2021; 12:649. [PMID: 33510171 PMCID: PMC7844267 DOI: 10.1038/s41467-020-20880-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/17/2020] [Indexed: 01/19/2023] Open
Abstract
The ongoing pandemic of SARS-CoV-2 presents novel challenges and opportunities for the use of phylogenetics to understand and control its spread. Here, we analyze the emergence of SARS-CoV-2 in Russia in March and April 2020. Combining phylogeographic analysis with travel history data, we estimate that the sampled viral diversity has originated from at least 67 closely timed introductions into Russia, mostly in late February to early March. All but one of these introductions were not from China, suggesting that border closure with China has helped delay establishment of SARS-CoV-2 in Russia. These introductions resulted in at least 9 distinct Russian lineages corresponding to domestic transmission. A notable transmission cluster corresponded to a nosocomial outbreak at the Vreden hospital in Saint Petersburg; phylodynamic analysis of this cluster reveals multiple (2-3) introductions each giving rise to a large number of cases, with a high initial effective reproduction number of 3.0 [1.9, 4.3].
Collapse
Affiliation(s)
| | - Ksenia R Safina
- Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia.,A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Sofya K Garushyants
- A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Artem V Fadeev
- Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia
| | - Mariia V Sergeeva
- Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia
| | - Anna A Ivanova
- Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia
| | - Daria M Danilenko
- Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia
| | - Dmitry Lioznov
- Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia.,First Pavlov State Medical University, Saint Petersburg, Russia
| | - Olga V Shneider
- Vreden Russian Research Institute of Traumatology and Orthopaedics, Saint Petersburg, Russia
| | - Nikita Shvyrev
- National Research University Higher School of Economics, Moscow, Russia
| | - Vadim Spirin
- National Research University Higher School of Economics, Moscow, Russia
| | - Dmitry Glyzin
- National Research University Higher School of Economics, Moscow, Russia
| | - Vladimir Shchur
- National Research University Higher School of Economics, Moscow, Russia
| | - Georgii A Bazykin
- Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia. .,A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.
| |
Collapse
|
36
|
Valesano AL, Rumfelt KE, Dimcheff DE, Blair CN, Fitzsimmons WJ, Petrie JG, Martin ET, Lauring AS. Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.19.427330. [PMID: 33501443 PMCID: PMC7836113 DOI: 10.1101/2021.01.19.427330] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Analysis of SARS-CoV-2 genetic diversity within infected hosts can provide insight into the generation and spread of new viral variants and may enable high resolution inference of transmission chains. However, little is known about temporal aspects of SARS-CoV-2 intrahost diversity and the extent to which shared diversity reflects convergent evolution as opposed to transmission linkage. Here we use high depth of coverage sequencing to identify within-host genetic variants in 325 specimens from hospitalized COVID-19 patients and infected employees at a single medical center. We validated our variant calling by sequencing defined RNA mixtures and identified a viral load threshold that minimizes false positives. By leveraging clinical metadata, we found that intrahost diversity is low and does not vary by time from symptom onset. This suggests that variants will only rarely rise to appreciable frequency prior to transmission. Although there was generally little shared variation across the sequenced cohort, we identified intrahost variants shared across individuals who were unlikely to be related by transmission. These variants did not precede a rise in frequency in global consensus genomes, suggesting that intrahost variants may have limited utility for predicting future lineages. These results provide important context for sequence-based inference in SARS-CoV-2 evolution and epidemiology.
Collapse
Affiliation(s)
- Andrew L. Valesano
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Kalee E. Rumfelt
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Derek E. Dimcheff
- Division of Hospital Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Christopher N. Blair
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - William J. Fitzsimmons
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Joshua G. Petrie
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Emily T. Martin
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Adam S. Lauring
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
37
|
Alteri C, Cento V, Piralla A, Costabile V, Tallarita M, Colagrossi L, Renica S, Giardina F, Novazzi F, Gaiarsa S, Matarazzo E, Antonello M, Vismara C, Fumagalli R, Epis OM, Puoti M, Perno CF, Baldanti F. Genomic epidemiology of SARS-CoV-2 reveals multiple lineages and early spread of SARS-CoV-2 infections in Lombardy, Italy. Nat Commun 2021; 12:434. [PMID: 33469026 PMCID: PMC7815831 DOI: 10.1038/s41467-020-20688-x] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 12/10/2020] [Indexed: 12/21/2022] Open
Abstract
From February to April 2020, Lombardy (Italy) reported the highest numbers of SARS-CoV-2 cases worldwide. By analyzing 346 whole SARS-CoV-2 genomes, we demonstrate the presence of seven viral lineages in Lombardy, frequently sustained by local transmission chains and at least two likely to have originated in Italy. Six single nucleotide polymorphisms (five of them non-synonymous) characterized the SARS-CoV-2 sequences, none of them affecting N-glycosylation sites. The seven lineages, and the presence of local transmission clusters within three of them, revealed that sustained community transmission was underway before the first COVID-19 case had been detected in Lombardy. The Lombardy region of Italy was heavily affected early in the SARS-CoV-2 pandemic. Here, the authors use whole genome sequencing and show that there were multiple introductions into the region, with transmission occurring before the first case was detected.
Collapse
Affiliation(s)
- Claudia Alteri
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Valeria Cento
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Antonio Piralla
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Valentino Costabile
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Monica Tallarita
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Luna Colagrossi
- Microbiology and Diagnostic Immunology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Silvia Renica
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Federica Giardina
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Federica Novazzi
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Stefano Gaiarsa
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Elisa Matarazzo
- Residency in Microbiology and Virology, University of Milan, Milan, Italy
| | - Maria Antonello
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Chiara Vismara
- Chemico-clinical and Microbiological Analyses, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Roberto Fumagalli
- Department of Anesthesiology, Critical Care and Pain Medicine, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | | | - Massimo Puoti
- Infectious Diseases Unit, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Carlo Federico Perno
- Microbiology and Diagnostic Immunology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.,Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy
| |
Collapse
|
38
|
Gutierrez B, Márquez S, Prado-Vivar B, Becerra-Wong M, Guadalupe JJ, Candido DDS, Fernandez-Cadena JC, Morey-Leon G, Armas-Gonzalez R, Andrade-Molina DM, Bruno A, De Mora D, Olmedo M, Portugal D, Gonzalez M, Orlando A, Drexler JF, Moreira-Soto A, Sander AL, Brünink S, Kühne A, Patiño L, Carrazco-Montalvo A, Mestanza O, Zurita J, Sevillano G, Du Plessis L, McCrone JT, Coloma J, Trueba G, Barragán V, Rojas-Silva P, Grunauer M, Kraemer MUG, Faria NR, Escalera-Zamudio M, Pybus OG, Cárdenas P. Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador. Virus Evol 2021; 7:veab051. [PMID: 34527281 PMCID: PMC8244811 DOI: 10.1093/ve/veab051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/12/2021] [Accepted: 06/03/2021] [Indexed: 12/23/2022] Open
Abstract
Characterisation of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic diversity through space and time can reveal trends in virus importation and domestic circulation and permit the exploration of questions regarding the early transmission dynamics. Here, we present a detailed description of SARS-CoV-2 genomic epidemiology in Ecuador, one of the hardest hit countries during the early stages of the coronavirus-19 pandemic. We generated and analysed 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylogeographic analysis of these sequences in the context of global SARS-CoV-2 diversity enable us to identify and characterise individual transmission lineages within Ecuador, explore their spatiotemporal distributions, and consider their introduction and domestic circulation. Our results reveal a pattern of multiple international importations across the country, with apparent differences between key provinces. Transmission lineages were mostly introduced before the implementation of non-pharmaceutical interventions, with differential degrees of persistence and national dissemination.
Collapse
Affiliation(s)
- Bernardo Gutierrez
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SY, UK
| | - Sully Márquez
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Belén Prado-Vivar
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Mónica Becerra-Wong
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Juan José Guadalupe
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | | | - Juan Carlos Fernandez-Cadena
- Omics Sciences Laboratory, Faculty of Medical Sciences, Universidad de Especialidades Espíritu Santo, Samborondón 092301, Ecuador
| | - Gabriel Morey-Leon
- Faculty of Medical Sciences, Universidad de Guayaquil, Guayaquil 090613, Ecuador
| | - Rubén Armas-Gonzalez
- Faculty of Sciences, Escuela Superior Politécnica del Litoral, Guayaquil 090112, Ecuador
| | - Derly Madeleiny Andrade-Molina
- Omics Sciences Laboratory, Faculty of Medical Sciences, Universidad de Especialidades Espíritu Santo, Samborondón 092301, Ecuador
| | - Alfredo Bruno
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Domenica De Mora
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Maritza Olmedo
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Denisse Portugal
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Manuel Gonzalez
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Alberto Orlando
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Jan Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Andres Moreira-Soto
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Anna-Lena Sander
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Sebastian Brünink
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Arne Kühne
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Leandro Patiño
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | | | - Orson Mestanza
- Servicio de Genética, Instituto Nacional de Salud del Niño San Borja, Lima 15037, Perú
| | - Jeannete Zurita
- Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito 170143, Ecuador
| | - Gabriela Sevillano
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito 170104, Ecuador
| | - Louis Du Plessis
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SY, UK
| | - John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JW, UK
| | - Josefina Coloma
- School of Public Health, University of California, Berkeley CA 94704, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Verónica Barragán
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Patricio Rojas-Silva
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Michelle Grunauer
- Escuela de Medicina, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SY, UK
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SY, UK
| | | | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SY, UK
| | - Paúl Cárdenas
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| |
Collapse
|
39
|
Miller D, Martin MA, Harel N, Tirosh O, Kustin T, Meir M, Sorek N, Gefen-Halevi S, Amit S, Vorontsov O, Shaag A, Wolf D, Peretz A, Shemer-Avni Y, Roif-Kaminsky D, Kopelman NM, Huppert A, Koelle K, Stern A. Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel. Nat Commun 2020; 11:5518. [PMID: 33139704 DOI: 10.1101/2020.05.21.20104521] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/02/2020] [Indexed: 05/22/2023] Open
Abstract
Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequence 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. We find that travelers returning from the United States of America significantly contributed to viral spread in Israel, more than their proportion in incoming infected travelers. Using phylodynamic analysis, we estimate that the basic reproduction number of the virus was initially around 2.5, dropping by more than two-thirds following the implementation of social distancing measures. We further report high levels of transmission heterogeneity in SARS-CoV-2 spread, with between 2-10% of infected individuals resulting in 80% of secondary infections. Overall, our findings demonstrate the effectiveness of social distancing measures for reducing viral spread.
Collapse
MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Base Sequence
- Basic Reproduction Number/statistics & numerical data
- Betacoronavirus/genetics
- COVID-19
- Child
- Child, Preschool
- Communicable Diseases, Imported/epidemiology
- Communicable Diseases, Imported/virology
- Coronavirus Infections/epidemiology
- Coronavirus Infections/prevention & control
- Coronavirus Infections/transmission
- Female
- Genome, Viral/genetics
- Humans
- Infant
- Infant, Newborn
- Israel/epidemiology
- Male
- Middle Aged
- Pandemics/prevention & control
- Phylogeny
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/prevention & control
- Pneumonia, Viral/transmission
- Psychological Distance
- RNA, Viral/genetics
- SARS-CoV-2
- Sequence Analysis, RNA
- United States
- Young Adult
Collapse
Affiliation(s)
- Danielle Miller
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Michael A Martin
- Department of Biology, Emory University, Atlanta, GA, USA
- Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA, USA
| | - Noam Harel
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Omer Tirosh
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Talia Kustin
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Moran Meir
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Nadav Sorek
- Microbiology Laboratory, Assuta Ashdod University-Affiliated Hospital, Ashdod, Israel
| | | | - Sharon Amit
- Clinical Microbiology Laboratory, Sheba Medical Center, Ramat-Gan, Israel
| | - Olesya Vorontsov
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Avraham Shaag
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Dana Wolf
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Avi Peretz
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Clinical Microbiology Laboratory, The Baruch Padeh Medical Center, Poriya, Tiberias, Israel
| | - Yonat Shemer-Avni
- Clinical Virology Laboratory, Soroka Medical Center and the Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | - Naama M Kopelman
- Department of Computer Science, Holon Institute of Technology, Holon, Israel
| | - Amit Huppert
- Bio-statistical and Bio-mathematical Unit, The Gertner Institute for Epidemiology and Health Policy Research, Chaim Sheba Medical Center, 52621, Tel Hashomer, Israel
- School of Public Health, The Sackler Faculty of Medicine, Tel-Aviv University, 69978, Tel Aviv, Israel
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, GA, USA
- Emory-UGA Center of Excellence of Influenza Research and Surveillance (CEIRS), Atlanta, GA, USA
| | - Adi Stern
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel.
| |
Collapse
|
40
|
Miller D, Martin MA, Harel N, Tirosh O, Kustin T, Meir M, Sorek N, Gefen-Halevi S, Amit S, Vorontsov O, Shaag A, Wolf D, Peretz A, Shemer-Avni Y, Roif-Kaminsky D, Kopelman NM, Huppert A, Koelle K, Stern A. Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel. Nat Commun 2020; 11:5518. [PMID: 33139704 PMCID: PMC7606475 DOI: 10.1038/s41467-020-19248-0] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/02/2020] [Indexed: 12/18/2022] Open
Abstract
Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequence 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. We find that travelers returning from the United States of America significantly contributed to viral spread in Israel, more than their proportion in incoming infected travelers. Using phylodynamic analysis, we estimate that the basic reproduction number of the virus was initially around 2.5, dropping by more than two-thirds following the implementation of social distancing measures. We further report high levels of transmission heterogeneity in SARS-CoV-2 spread, with between 2-10% of infected individuals resulting in 80% of secondary infections. Overall, our findings demonstrate the effectiveness of social distancing measures for reducing viral spread.
Collapse
MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Base Sequence
- Basic Reproduction Number/statistics & numerical data
- Betacoronavirus/genetics
- COVID-19
- Child
- Child, Preschool
- Communicable Diseases, Imported/epidemiology
- Communicable Diseases, Imported/virology
- Coronavirus Infections/epidemiology
- Coronavirus Infections/prevention & control
- Coronavirus Infections/transmission
- Female
- Genome, Viral/genetics
- Humans
- Infant
- Infant, Newborn
- Israel/epidemiology
- Male
- Middle Aged
- Pandemics/prevention & control
- Phylogeny
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/prevention & control
- Pneumonia, Viral/transmission
- Psychological Distance
- RNA, Viral/genetics
- SARS-CoV-2
- Sequence Analysis, RNA
- United States
- Young Adult
Collapse
Affiliation(s)
- Danielle Miller
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Michael A Martin
- Department of Biology, Emory University, Atlanta, GA, USA
- Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA, USA
| | - Noam Harel
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Omer Tirosh
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Talia Kustin
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Moran Meir
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Nadav Sorek
- Microbiology Laboratory, Assuta Ashdod University-Affiliated Hospital, Ashdod, Israel
| | | | - Sharon Amit
- Clinical Microbiology Laboratory, Sheba Medical Center, Ramat-Gan, Israel
| | - Olesya Vorontsov
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Avraham Shaag
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Dana Wolf
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Avi Peretz
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Clinical Microbiology Laboratory, The Baruch Padeh Medical Center, Poriya, Tiberias, Israel
| | - Yonat Shemer-Avni
- Clinical Virology Laboratory, Soroka Medical Center and the Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | - Naama M Kopelman
- Department of Computer Science, Holon Institute of Technology, Holon, Israel
| | - Amit Huppert
- Bio-statistical and Bio-mathematical Unit, The Gertner Institute for Epidemiology and Health Policy Research, Chaim Sheba Medical Center, 52621, Tel Hashomer, Israel
- School of Public Health, The Sackler Faculty of Medicine, Tel-Aviv University, 69978, Tel Aviv, Israel
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, GA, USA
- Emory-UGA Center of Excellence of Influenza Research and Surveillance (CEIRS), Atlanta, GA, USA
| | - Adi Stern
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel.
| |
Collapse
|
41
|
Franco-Muñoz C, Álvarez-Díaz DA, Laiton-Donato K, Wiesner M, Escandón P, Usme-Ciro JA, Franco-Sierra ND, Flórez-Sánchez AC, Gómez-Rangel S, Rodríguez-Calderon LD, Barbosa-Ramirez J, Ospitia-Baez E, Walteros DM, Ospina-Martinez ML, Mercado-Reyes M. Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104557. [PMID: 32950697 PMCID: PMC7497549 DOI: 10.1016/j.meegid.2020.104557] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/31/2020] [Accepted: 09/11/2020] [Indexed: 12/15/2022]
Abstract
SARS-CoV-2 is a new member of the genus Betacoronavirus, responsible for the COVID-19 pandemic. The virus crossed the species barrier and established in the human population taking advantage of the spike protein high affinity for the ACE receptor to infect the lower respiratory tract. The Nucleocapsid (N) and Spike (S) are highly immunogenic structural proteins and most commercial COVID-19 diagnostic assays target these proteins. In an unpredictable epidemic, it is essential to know about their genetic variability. The objective of this study was to describe the substitution frequency of the S and N proteins of SARS-CoV-2 in South America. A total of 504 amino acid and nucleotide sequences of the S and N proteins of SARS-CoV-2 from seven South American countries (Argentina, Brazil, Chile, Ecuador, Peru, Uruguay, and Colombia), reported as of June 3, and corresponding to samples collected between March and April 2020, were compared through substitution matrices using the Muscle algorithm. Forty-three sequences from 13 Colombian departments were obtained in this study using the Oxford Nanopore and Illumina MiSeq technologies, following the amplicon-based ARTIC network protocol. The substitutions D614G in S and R203K/G204R in N were the most frequent in South America, observed in 83% and 34% of the sequences respectively. Strikingly, genomes with the conserved position D614 were almost completely replaced by genomes with the G614 substitution between March to April 2020. A similar replacement pattern was observed with R203K/G204R although more marked in Chile, Argentina and Brazil, suggesting similar introduction history and/or control strategies of SARS-CoV-2 in these countries. It is necessary to continue with the genomic surveillance of S and N proteins during the SARS-CoV-2 pandemic as this information can be useful for developing vaccines, therapeutics and diagnostic tests.
Collapse
Affiliation(s)
- Carlos Franco-Muñoz
- Unidad de Secuenciación y Genómica, Grupo de Investigación Básica y Aplicada en Enfermedades Emergentes, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia; Grupo de Parasitología, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.
| | - Diego A Álvarez-Díaz
- Unidad de Secuenciación y Genómica, Grupo de Investigación Básica y Aplicada en Enfermedades Emergentes, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Katherine Laiton-Donato
- Unidad de Secuenciación y Genómica, Grupo de Investigación Básica y Aplicada en Enfermedades Emergentes, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Magdalena Wiesner
- Grupo de Microbiología, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Patricia Escandón
- Grupo de Microbiología, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - José A Usme-Ciro
- Unidad de Secuenciación y Genómica, Grupo de Investigación Básica y Aplicada en Enfermedades Emergentes, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia; Centro de Investigación en Salud para el Trópico-CIST, Universidad Cooperativa de Colombia, Santa Marta, 470003, Colombia
| | - Nicolás D Franco-Sierra
- Programa Ciencias de la Biodiversidad, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogotá 111311, Colombia
| | | | - Sergio Gómez-Rangel
- Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Luz D Rodríguez-Calderon
- Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Juliana Barbosa-Ramirez
- Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Erika Ospitia-Baez
- Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Diana M Walteros
- Dirección de Vigilancia en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | | | - Marcela Mercado-Reyes
- Unidad de Secuenciación y Genómica, Grupo de Investigación Básica y Aplicada en Enfermedades Emergentes, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia; Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| |
Collapse
|
42
|
Maurano MT, Ramaswami S, Zappile P, Dimartino D, Boytard L, Ribeiro-Dos-Santos AM, Vulpescu NA, Westby G, Shen G, Feng X, Hogan MS, Ragonnet-Cronin M, Geidelberg L, Marier C, Meyn P, Zhang Y, Cadley J, Ordoñez R, Luther R, Huang E, Guzman E, Arguelles-Grande C, Argyropoulos KV, Black M, Serrano A, Call ME, Kim MJ, Belovarac B, Gindin T, Lytle A, Pinnell J, Vougiouklakis T, Chen J, Lin LH, Rapkiewicz A, Raabe V, Samanovic MI, Jour G, Osman I, Aguero-Rosenfeld M, Mulligan MJ, Volz EM, Cotzia P, Snuderl M, Heguy A. Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City region. Genome Res 2020; 30:1781-1788. [PMID: 33093069 PMCID: PMC7706732 DOI: 10.1101/gr.266676.120] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/20/2020] [Indexed: 11/30/2022]
Abstract
Effective public response to a pandemic relies upon accurate measurement of the extent and dynamics of an outbreak. Viral genome sequencing has emerged as a powerful approach to link seemingly unrelated cases, and large-scale sequencing surveillance can inform on critical epidemiological parameters. Here, we report the analysis of 864 SARS-CoV-2 sequences from cases in the New York City metropolitan area during the COVID-19 outbreak in spring 2020. The majority of cases had no recent travel history or known exposure, and genetically linked cases were spread throughout the region. Comparison to global viral sequences showed that early transmission was most linked to cases from Europe. Our data are consistent with numerous seeds from multiple sources and a prolonged period of unrecognized community spreading. This work highlights the complementary role of genomic surveillance in addition to traditional epidemiological indicators.
Collapse
Affiliation(s)
- Matthew T Maurano
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.,Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Sitharam Ramaswami
- Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA
| | - Paul Zappile
- Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA
| | - Dacia Dimartino
- Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA
| | - Ludovic Boytard
- Center for Biospecimen Research and Development, NYU Langone Health, New York, New York 10016, USA
| | - André M Ribeiro-Dos-Santos
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.,Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Nicholas A Vulpescu
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.,Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Gael Westby
- Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA
| | - Guomiao Shen
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Xiaojun Feng
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Megan S Hogan
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.,Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Manon Ragonnet-Cronin
- MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, United Kingdom
| | - Lily Geidelberg
- MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, United Kingdom
| | - Christian Marier
- Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA
| | - Peter Meyn
- Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA
| | - Yutong Zhang
- Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA
| | - John Cadley
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.,Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Raquel Ordoñez
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.,Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Raven Luther
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.,Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Emily Huang
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.,Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Emily Guzman
- Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA
| | | | - Kimon V Argyropoulos
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Margaret Black
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Antonio Serrano
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Melissa E Call
- Department of Dermatology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Min Jae Kim
- Department of Dermatology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Brendan Belovarac
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Tatyana Gindin
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Andrew Lytle
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Jared Pinnell
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | | | - John Chen
- Medical Center IT, NYU Langone Health, New York, New York 10016, USA
| | - Lawrence H Lin
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Amy Rapkiewicz
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Vanessa Raabe
- Division of Infectious Diseases and Immunology, Department of Medicine and NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Marie I Samanovic
- Division of Infectious Diseases and Immunology, Department of Medicine and NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - George Jour
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.,Department of Dermatology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Iman Osman
- Center for Biospecimen Research and Development, NYU Langone Health, New York, New York 10016, USA.,Department of Dermatology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | | | - Mark J Mulligan
- Division of Infectious Diseases and Immunology, Department of Medicine and NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Erik M Volz
- MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, United Kingdom
| | - Paolo Cotzia
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.,Center for Biospecimen Research and Development, NYU Langone Health, New York, New York 10016, USA
| | - Matija Snuderl
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA
| | - Adriana Heguy
- Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.,Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA
| |
Collapse
|
43
|
Zhang W, Govindavari JP, Davis BD, Chen SS, Kim JT, Song J, Lopategui J, Plummer JT, Vail E. Analysis of Genomic Characteristics and Transmission Routes of Patients With Confirmed SARS-CoV-2 in Southern California During the Early Stage of the US COVID-19 Pandemic. JAMA Netw Open 2020; 3:e2024191. [PMID: 33026453 PMCID: PMC7542329 DOI: 10.1001/jamanetworkopen.2020.24191] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/23/2020] [Indexed: 12/15/2022] Open
Abstract
Importance In late December 2019, an outbreak of a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China. Data on the routes of transmission to Los Angeles, California, the US West Coast epicenter for coronavirus disease 2019 (COVID-19), and subsequent community spread are limited. Objective To determine the transmission routes of SARS-CoV-2 to Southern California and elucidate local community spread within the Los Angeles metropolitan area. Design, Setting, and Participants This case series included 192 consecutive patients with reverse transcription-polymerase chain reaction (RT-PCR) test results positive for SARS-CoV-2 who were evaluated at Cedars-Sinai Medical Center in Los Angeles, California, from March 22 to April 15, 2020. Data analysis was performed from April to May 2020. Main Outcomes and Measures SARS-CoV-2 viral genomes were sequenced. Los Angeles isolates were compared with genomes from global subsampling and from New York, New York; Washington state; and China to determine potential sources of viral dissemination. Demographic data and outcomes were collected. Results The cohort included 192 patients (median [interquartile range] age, 59.5 [43-75] years; 110 [57.3%] men). The genetic characterization of SARS-CoV-2 isolates in the Los Angeles population pinpointed community transmission of 13 patients within a 3.81 km2 radius. Variation landscapes of this case series also revealed a cluster of 10 patients that contained 5 residents at a skilled nursing facility, 1 resident of a nearby skilled nursing facility, 3 health care workers, and a family member of a resident of one of the skilled nursing facilities. Person-to-person transmission was detected in a cluster of 5 patients who shared the same single-nucleotide variation in their SARS-CoV-2 genomes. High viral genomic diversity was identified: 20 Los Angeles isolates (15.0%) resembled SARS-CoV-2 genomes from Asia, while 109 Los Angeles isolates (82.0%) were similar to isolates originating from Europe. Analysis of other common respiratory viral pathogens did not reveal coinfection in the cohort. Conclusions and Relevance These findings highlight the precision of detecting person-to-person transmission and accurate contact tracing directly through SARS-CoV-2 genome isolation and sequencing. Development and application of phylogenetic analyses from the Los Angeles population established connections between COVID-19 clusters locally and throughout the US.
Collapse
Affiliation(s)
- Wenjuan Zhang
- Molecular Pathology Laboratory, Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - John Paul Govindavari
- Molecular Pathology Laboratory, Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Brian D. Davis
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
- Applied Genomics, Computation and Translational Core, Cedars-Sinai Cancer Center, Los Angeles, California
| | - Stephanie S. Chen
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
- Applied Genomics, Computation and Translational Core, Cedars-Sinai Cancer Center, Los Angeles, California
| | - Jong Taek Kim
- Molecular Pathology Laboratory, Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jianbo Song
- Molecular Pathology Laboratory, Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jean Lopategui
- Molecular Pathology Laboratory, Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jasmine T. Plummer
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
- Applied Genomics, Computation and Translational Core, Cedars-Sinai Cancer Center, Los Angeles, California
| | - Eric Vail
- Molecular Pathology Laboratory, Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| |
Collapse
|
44
|
Sironi M, Hasnain SE, Rosenthal B, Phan T, Luciani F, Shaw MA, Sallum MA, Mirhashemi ME, Morand S, González-Candelas F. SARS-CoV-2 and COVID-19: A genetic, epidemiological, and evolutionary perspective. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 84:104384. [PMID: 32473976 PMCID: PMC7256558 DOI: 10.1016/j.meegid.2020.104384] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 12/15/2022]
Abstract
In less than five months, COVID-19 has spread from a small focus in Wuhan, China, to more than 5 million people in almost every country in the world, dominating the concern of most governments and public health systems. The social and political distresses caused by this epidemic will certainly impact our world for a long time to come. Here, we synthesize lessons from a range of scientific perspectives rooted in epidemiology, virology, genetics, ecology and evolutionary biology so as to provide perspective on how this pandemic started, how it is developing, and how best we can stop it.
Collapse
Affiliation(s)
- Manuela Sironi
- Bioinformatics Unit, Scientific Institute IRCCS E. MEDEA, Bosisio Parini (LC), Italy.
| | - Seyed E Hasnain
- JH Institute of Molecular Medicine, Jamia Hamdard, Tughlakabad, New Delhi, India.
| | - Benjamin Rosenthal
- Animal Parasitic Disease Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA.
| | - Tung Phan
- Division of Clinical Microbiology, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
| | - Fabio Luciani
- University of New South Wales, Sydney, 2052, New South Wales, Australia.
| | - Marie-Anne Shaw
- Leeds Institute of Medical Research at St James's, School of Medicine, University of Leeds, Leeds, United Kingdom.
| | - M Anice Sallum
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, Brazil.
| | | | - Serge Morand
- Institute of Evolution Science of Montpellier, Case Courier 064, F-34095 Montpellier, France.
| | - Fernando González-Candelas
- Joint Research Unit Infection and Public Health FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio) and CIBER in Epidemiology and Public Health, Valencia, Spain.
| |
Collapse
|
45
|
Gómez-Carballa A, Bello X, Pardo-Seco J, Martinón-Torres F, Salas A. Mapping genome variation of SARS-CoV-2 worldwide highlights the impact of COVID-19 super-spreaders. Genome Res 2020; 30:1434-1448. [PMID: 32878977 PMCID: PMC7605265 DOI: 10.1101/gr.266221.120] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/31/2020] [Indexed: 01/08/2023]
Abstract
The human pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the major pandemic of the twenty-first century. We analyzed more than 4700 SARS-CoV-2 genomes and associated metadata retrieved from public repositories. SARS-CoV-2 sequences have a high sequence identity (>99.9%), which drops to >96% when compared to bat coronavirus genome. We built a mutation-annotated reference SARS-CoV-2 phylogeny with two main macro-haplogroups, A and B, both of Asian origin, and more than 160 sub-branches representing virus strains of variable geographical origins worldwide, revealing a rather uniform mutation occurrence along branches that could have implications for diagnostics and the design of future vaccines. Identification of the root of SARS-CoV-2 genomes is not without problems, owing to conflicting interpretations derived from either using the bat coronavirus genomes as an outgroup or relying on the sampling chronology of the SARS-CoV-2 genomes and TMRCA estimates; however, the overall scenario favors haplogroup A as the ancestral node. Phylogenetic analysis indicates a TMRCA for SARS-CoV-2 genomes dating to November 12, 2019, thus matching epidemiological records. Sub-haplogroup A2 most likely originated in Europe from an Asian ancestor and gave rise to subclade A2a, which represents the major non-Asian outbreak, especially in Africa and Europe. Multiple founder effect episodes, most likely associated with super-spreader hosts, might explain COVID-19 pandemic to a large extent.
Collapse
Affiliation(s)
- Alberto Gómez-Carballa
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Galicia, Spain
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), 15706, Galicia, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela (SERGAS), 15706, Galicia, Spain
| | - Xabier Bello
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Galicia, Spain
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), 15706, Galicia, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela (SERGAS), 15706, Galicia, Spain
| | - Jacobo Pardo-Seco
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Galicia, Spain
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), 15706, Galicia, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela (SERGAS), 15706, Galicia, Spain
| | - Federico Martinón-Torres
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), 15706, Galicia, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela (SERGAS), 15706, Galicia, Spain
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Galicia, Spain
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), 15706, Galicia, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela (SERGAS), 15706, Galicia, Spain
| |
Collapse
|
46
|
Delatorre E, Mir D, Gräf T, Bello G. Tracking the onset date of the community spread of SARS-CoV-2 in western countries. Mem Inst Oswaldo Cruz 2020; 115:e200183. [PMID: 32901696 PMCID: PMC7472723 DOI: 10.1590/0074-02760200183] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/12/2020] [Indexed: 01/21/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rapidly spread around the world during 2020, but the precise time in which the virus began to spread locally is difficult to trace for most countries. Here, we estimate the probable onset date of the community spread of SARS-CoV-2 for heavily affected countries from Western Europe and the Americas on the basis of the cumulative number of deaths reported during the early stage of the epidemic. Our results support that SARS-CoV-2 probably started to spread locally in all western countries analysed between mid-January and mid-February 2020, thus long before community transmission was officially recognised and control measures were implemented.
Collapse
Affiliation(s)
- Edson Delatorre
- Universidade Federal do Espírito Santo, Centro de Ciências Exatas, Naturais e da Saúde, Departamento de Biologia, Alegre, ES, Brasil
| | - Daiana Mir
- Universidad de la República, Centro Universitario Regional del Litoral Norte, Unidad de Genómica y Bioinformática, Salto, Uruguay
| | - Tiago Gräf
- Fundação Oswaldo Cruz-Fiocruz, Instituto Gonçalo Moniz, Salvador, BA, Brasil
| | - Gonzalo Bello
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de AIDS e Imunologia Molecular, Rio de Janeiro, RJ, Brasil
| |
Collapse
|
47
|
Zhao Z, Sokhansanj BA, Malhotra C, Zheng K, Rosen GL. Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization. PLoS Comput Biol 2020; 16:e1008269. [PMID: 32941419 PMCID: PMC7523987 DOI: 10.1371/journal.pcbi.1008269] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/29/2020] [Accepted: 08/17/2020] [Indexed: 12/19/2022] Open
Abstract
We propose an efficient framework for genetic subtyping of SARS-CoV-2, the novel coronavirus that causes the COVID-19 pandemic. Efficient viral subtyping enables visualization and modeling of the geographic distribution and temporal dynamics of disease spread. Subtyping thereby advances the development of effective containment strategies and, potentially, therapeutic and vaccine strategies. However, identifying viral subtypes in real-time is challenging: SARS-CoV-2 is a novel virus, and the pandemic is rapidly expanding. Viral subtypes may be difficult to detect due to rapid evolution; founder effects are more significant than selection pressure; and the clustering threshold for subtyping is not standardized. We propose to identify mutational signatures of available SARS-CoV-2 sequences using a population-based approach: an entropy measure followed by frequency analysis. These signatures, Informative Subtype Markers (ISMs), define a compact set of nucleotide sites that characterize the most variable (and thus most informative) positions in the viral genomes sequenced from different individuals. Through ISM compression, we find that certain distant nucleotide variants covary, including non-coding and ORF1ab sites covarying with the D614G spike protein mutation which has become increasingly prevalent as the pandemic has spread. ISMs are also useful for downstream analyses, such as spatiotemporal visualization of viral dynamics. By analyzing sequence data available in the GISAID database, we validate the utility of ISM-based subtyping by comparing spatiotemporal analyses using ISMs to epidemiological studies of viral transmission in Asia, Europe, and the United States. In addition, we show the relationship of ISMs to phylogenetic reconstructions of SARS-CoV-2 evolution, and therefore, ISMs can play an important complementary role to phylogenetic tree-based analysis, such as is done in the Nextstrain project. The developed pipeline dynamically generates ISMs for newly added SARS-CoV-2 sequences and updates the visualization of pandemic spatiotemporal dynamics, and is available on Github at https://github.com/EESI/ISM (Jupyter notebook), https://github.com/EESI/ncov_ism (command line tool) and via an interactive website at https://covid19-ism.coe.drexel.edu/.
Collapse
Affiliation(s)
- Zhengqiao Zhao
- Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Department of Electrical and Computer Engineering, College of Engineering, Drexel University, Philadelphia, PA, USA
| | - Bahrad A. Sokhansanj
- Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Department of Electrical and Computer Engineering, College of Engineering, Drexel University, Philadelphia, PA, USA
| | - Charvi Malhotra
- College of Medicine, Drexel University, Philadelphia, PA, USA
| | - Kitty Zheng
- College of Medicine, Drexel University, Philadelphia, PA, USA
| | - Gail L. Rosen
- Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Department of Electrical and Computer Engineering, College of Engineering, Drexel University, Philadelphia, PA, USA
| |
Collapse
|
48
|
Maurano MT, Ramaswami S, Zappile P, Dimartino D, Boytard L, Ribeiro-dos-Santos AM, Vulpescu NA, Westby G, Shen G, Feng X, Hogan MS, Ragonnet-Cronin M, Geidelberg L, Marier C, Meyn P, Zhang Y, Cadley J, Ordoñez R, Luther R, Huang E, Guzman E, Arguelles-Grande C, Argyropoulos KV, Black M, Serrano A, Call ME, Kim MJ, Belovarac B, Gindin T, Lytle A, Pinnell J, Vougiouklakis T, Chen J, Lin LH, Rapkiewicz A, Raabe V, Samanovic MI, Jour G, Osman I, Aguero-Rosenfeld M, Mulligan MJ, Volz EM, Cotzia P, Snuderl M, Heguy A. Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City Region. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.04.15.20064931. [PMID: 32511587 PMCID: PMC7276014 DOI: 10.1101/2020.04.15.20064931] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Effective public response to a pandemic relies upon accurate measurement of the extent and dynamics of an outbreak. Viral genome sequencing has emerged as a powerful approach to link seemingly unrelated cases, and large-scale sequencing surveillance can inform on critical epidemiological parameters. Here, we report the analysis of 864 SARS-CoV-2 sequences from cases in the New York City metropolitan area during the COVID-19 outbreak in Spring 2020. The majority of cases had no recent travel history or known exposure, and genetically linked cases were spread throughout the region. Comparison to global viral sequences showed that early transmission was most linked to cases from Europe. Our data are consistent with numerous seeds from multiple sources and a prolonged period of unrecognized community spreading. This work highlights the complementary role of genomic surveillance in addition to traditional epidemiological indicators.
Collapse
Affiliation(s)
- Matthew T. Maurano
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
| | - Sitharam Ramaswami
- Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, USA
| | - Paul Zappile
- Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, USA
| | - Dacia Dimartino
- Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, USA
| | - Ludovic Boytard
- Center for Biospecimen Research and Development, NYU Langone Health, New York, USA
| | - André M. Ribeiro-dos-Santos
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
| | - Nicholas A. Vulpescu
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
| | - Gael Westby
- Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, USA
| | - Guomiao Shen
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
| | - Xiaojun Feng
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
| | - Megan S. Hogan
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
| | - Manon Ragonnet-Cronin
- MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Imperial College London
| | - Lily Geidelberg
- MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Imperial College London
| | - Christian Marier
- Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, USA
| | - Peter Meyn
- Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, USA
| | - Yutong Zhang
- Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, USA
| | - John Cadley
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
| | - Raquel Ordoñez
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
| | - Raven Luther
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
| | - Emily Huang
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
| | - Emily Guzman
- Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, USA
| | | | | | - Margaret Black
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
| | - Antonio Serrano
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
| | - Melissa E. Call
- Department of Dermatology, NYU Grossman School of Medicine, New York, USA
| | - Min Jae Kim
- Department of Dermatology, NYU Grossman School of Medicine, New York, USA
| | - Brendan Belovarac
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
| | - Tatyana Gindin
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
| | - Andrew Lytle
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
| | - Jared Pinnell
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
| | | | - John Chen
- Medical Center IT, NYU Langone Health, New York, USA
| | - Lawrence H. Lin
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
| | - Amy Rapkiewicz
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
| | - Vanessa Raabe
- Division of Infectious Diseases and Immunology, Department of Medicine and NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, USA
| | | | - George Jour
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
- Department of Dermatology, NYU Grossman School of Medicine, New York, USA
| | - Iman Osman
- Center for Biospecimen Research and Development, NYU Langone Health, New York, USA
- Department of Dermatology, NYU Grossman School of Medicine, New York, USA
| | | | - Mark J. Mulligan
- Division of Infectious Diseases and Immunology, Department of Medicine and NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, USA
| | - Erik M. Volz
- MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Imperial College London
| | - Paolo Cotzia
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
- Center for Biospecimen Research and Development, NYU Langone Health, New York, USA
| | - Matija Snuderl
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
| | - Adriana Heguy
- Department of Pathology, NYU Grossman School of Medicine, New York, USA
- Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, USA
| |
Collapse
|
49
|
Poterico JA, Mestanza O. Response to comment on "genetic variants and source of introduction of SARS-CoV-2 in South America". J Med Virol 2020; 93:25-27. [PMID: 32716059 DOI: 10.1002/jmv.26359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/24/2020] [Indexed: 12/31/2022]
Abstract
During a pandemic, science needs data to generate helpful evidence, and researchers assume this responsibility despite the risk of potential bias. This is the response to the comment made by Pedro Romero, who argued that our manuscript did not use reassembling and mapping strategies for corroborating mutations, and lacked bootstrap support in the phylogenetic analysis.
Collapse
Affiliation(s)
- Julio A Poterico
- Genetics Service, Instituto Nacional de Salud del Niño-San Borja (INSN-SB), Lima, Peru
| | - Orson Mestanza
- Genetics Service, Instituto Nacional de Salud del Niño-San Borja (INSN-SB), Lima, Peru
| |
Collapse
|
50
|
Kalinich CC, Jensen CG, Neugebauer P, Petrone ME, Peña-Hernández M, Ott IM, Wyllie AL, Alpert T, Vogels CBF, Fauver JR, Grubaugh ND, Brito AF. Real-time public health communication of local SARS-CoV-2 genomic epidemiology. PLoS Biol 2020; 18:e3000869. [PMID: 32822393 PMCID: PMC7467297 DOI: 10.1371/journal.pbio.3000869] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/02/2020] [Indexed: 01/20/2023] Open
Abstract
Genomic epidemiology can provide a unique, real-time understanding of SARS-CoV-2 transmission patterns. Yet the potential for genomic analyses to guide local policy and community-based behavioral decisions is limited because they are often oriented towards specially trained scientists and conducted on a national or global scale. Here, we propose a new paradigm: Phylogenetic analyses performed on a local level (municipal, county, or state), with results communicated in a clear, timely, and actionable manner to strengthen public health responses. We believe that presenting results rapidly, and tailored to a non-expert audience, can serve as a template for effective public health response to COVID-19 and other emerging viral diseases.
Collapse
Affiliation(s)
- Chaney C. Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Cole G. Jensen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Peter Neugebauer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Mario Peña-Hernández
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Isabel M. Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Anne L. Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Chantal B. F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Joseph R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Anderson F. Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| |
Collapse
|