Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection Clusters Based on Integrated Genomic Surveillance, Outbreak Analysis and Contact Tracing in an Urban Setting

被引：23

作者：

Walker, Andreas ^{[1
]}

Houwaart, Torsten ^{[2
]}

Finzer, Patrick ^{[2
,3
]}

Ehlkes, Lutz ^{[4
]}

Tyshaieva, Alona ^{[2
]}

Damagnez, Maximilian ^{[1
]}

Strelow, Daniel ^{[2
]}

Duplessis, Ashley ^{[1
]}

Nicolai, Jessica ^{[2
]}

Wienemann, Tobias ^{[2
]}

Tamayo, Teresa ^{[2
]}

Vasconcelos, Malte Kohns ^{[2
]}

Huelse, Lisanna ^{[2
]}

Hoffmann, Katrin ^{[3
]}

Luebke, Nadine ^{[1
]}

Hauka, Sandra ^{[1
]}

Andree, Marcel ^{[1
]}

Daeumer, Martin P. ^{[5
]}

Thielen, Alexander ^{[5
]}

Kolbe-Busch, Susanne ^{[2
]}

Goebels, Klaus ^{[4
]}

Zotz, Rainer ^{[3
]}

Pfeffer, Klaus ^{[2
]}

Timm, Joerg ^{[1
]}

Dilthey, Alexander T. ^{[2
,6
,7
]}

机构：

[1] Heinrich Heine Univ Dusseldorf, Univ Hosp Dusseldorf, Inst Virol, Dusseldorf, Germany

[2] Heinrich Heine Univ Dusseldorf, Inst Med Microbiol & Hosp Hyg, Univ Str 2, D-40225 Dusseldorf, Germany

[3] Zotz Klimas, Dusseldorf, Germany

[4] Dusseldorf Hlth Dept Gesundheitsamt Dusseldorf, Dusseldorf, Germany

[5] SeqIT GmbH, Pfaffpl 10, D-67655 Kaiserslautern, Germany

[6] Univ Cologne, Inst Med Stat & Computat Biol, Cologne, Germany

[7] Univ Cologne, Cologne Excellence Cluster Cellular Stress Respon, Cologne, Germany

来源：

CLINICAL INFECTIOUS DISEASES | 2022年 / 74卷 / 06期

关键词：

genomic epidemiology; infection chain; community transmission; rapid sequencing; Nanopore sequencing; REAL-TIME; VIRUS; ZIKA;

D O I：

10.1093/cid/ciab588

中图分类号：

R392 [医学免疫学]; Q939.91 [免疫学];

学科分类号：

100102 ;

摘要：

Background Tracing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission chains is still a major challenge for public health authorities, when incidental contacts are not recalled or are not perceived as potential risk contacts. Viral sequencing can address key questions about SARS-CoV-2 evolution and may support reconstruction of viral transmission networks by integration of molecular epidemiology into classical contact tracing. Methods In collaboration with local public health authorities, we set up an integrated system of genomic surveillance in an urban setting, combining a) viral surveillance sequencing, b) genetically based identification of infection clusters in the population, c) integration of public health authority contact tracing data, and d) a user-friendly dashboard application as a central data analysis platform. Results Application of the integrated system from August to December 2020 enabled a characterization of viral population structure, analysis of 4 outbreaks at a maximum care hospital, and genetically based identification of 5 putative population infection clusters, all of which were confirmed by contact tracing. The system contributed to the development of improved hospital infection control and prevention measures and enabled the identification of previously unrecognized transmission chains, involving a martial arts gym and establishing a link between the hospital to the local population. Conclusions Integrated systems of genomic surveillance could contribute to the monitoring and, potentially, improved management of SARS-CoV-2 transmission in the population. Tracing of SARS-CoV-2 population transmission chains is still a major challenge. We present an integrated system of genomic surveillance and show it to be capable of detecting infection chains in a large city during ongoing community transmission.

引用

页码：1039 / 1046

页数：8

共 31 条

[1] BEAST 2: A Software Platform for Bayesian Evolutionary Analysis [J].

Bouckaert, Remco ;

Heled, Joseph ;

Kuehnert, Denise ;

Vaughan, Tim ;

Wu, Chieh-Hsi ;

Xie, Dong ;

Suchard, Marc A. ;

Rambaut, Andrew ;

Drummond, Alexei J. .

PLOS COMPUTATIONAL BIOLOGY, 2014, 10 (04)

[2]

Drummond AJ, 2005, MOL BIOL EVOL, V22, P1185, DOI [10.1093/molbev/msi103, 10.1093/molbev/mss075]

[3]

Florian D., 2020, IFO SCHNELLDIENST, V73, P29

[4] APPLICATIONS OF NEXT-GENERATION SEQUENCING Towards a genomics-informed, real-time, global pathogen surveillance system [J].

Gardy, Jennifer L. ;

Loman, Nicholas J. .

NATURE REVIEWS GENETICS, 2018, 19 (01) :9-20

[5] Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand [J].

Geoghegan, Jemma L. ;

Ren, Xiaoyun ;

Storey, Matthew ;

Hadfield, James ;

Jelley, Lauren ;

Jefferies, Sarah ;

Sherwood, Jill ;

Paine, Shevaun ;

Huang, Sue ;

Douglas, Jordan ;

Mendes, Fabio K. ;

Sporle, Andrew ;

Baker, Michael G. ;

Murdoch, David R. ;

French, Nigel ;

Simpson, Colin R. ;

Welch, David ;

Drummond, Alexei J. ;

Holmes, Edward C. ;

Duchene, Sebastian ;

de Ligt, Joep .

NATURE COMMUNICATIONS, 2020, 11 (01)

[6] Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis [J].

Greninger, Alexander L. ;

Naccache, Samia N. ;

Federman, Scot ;

Yu, Guixia ;

Mbala, Placide ;

Bres, Vanessa ;

Stryke, Doug ;

Bouquet, Jerome ;

Somasekar, Sneha ;

Linnen, Jeffrey M. ;

Dodd, Roger ;

Mulembakani, Prime ;

Schneider, Bradley S. ;

Muyembe-Tamfum, Jean-Jacques ;

Stramer, Susan L. ;

Chiu, Charles Y. .

GENOME MEDICINE, 2015, 7

[7] Tracking virus outbreaks in the twenty-first century [J].

Grubaugh, Nathan D. ;

Ladner, Jason T. ;

Lemey, Philippe ;

Pybus, Oliver G. ;

Rambaut, Andrew ;

Holmes, Edward C. ;

Andersen, Kristian G. .

NATURE MICROBIOLOGY, 2019, 4 (01) :10-19

[8] Genomic epidemiology reveals multiple introductions of Zika virus into the United States [J].

Grubaugh, Nathan D. ;

Ladner, Jason T. ;

Kraemer, Moritz U. G. ;

Dudas, Gytis ;

Tan, Amanda L. ;

Gangavarapu, Karthik ;

Wiley, Michael R. ;

White, Stephen ;

Theze, Julien ;

Magnani, Diogo M. ;

Prieto, Karla ;

Reyes, Daniel ;

Bingham, Andrea M. ;

Paul, Lauren M. ;

Robles-Sikisaka, Refugio ;

Oliveira, Glenn ;

Pronty, Darryl ;

Barcellona, Carolyn M. ;

Metsky, Hayden C. ;

Baniecki, Mary Lynn ;

Barnes, Kayla G. ;

Chak, Bridget ;

Freije, Catherine A. ;

Gladden-Young, Adrianne ;

Gnirke, Andreas ;

Luo, Cynthia ;

MacInnis, Bronwyn ;

Matranga, Christian B. ;

Park, Daniel J. ;

Qu, James ;

Schaffner, Stephen F. ;

Tomkins-Tinch, Christopher ;

West, Kendra L. ;

Winnicki, Sarah M. ;

Wohl, Shirlee ;

Yozwiak, Nathan L. ;

Quick, Joshua ;

Fauver, Joseph R. ;

Khan, Kamran ;

Brent, Shannon E. ;

Reiner, Robert C., Jr. ;

Lichtenberger, Paola N. ;

Ricciardi, Michael J. ;

Bailey, Varian K. ;

Watkins, David I. ;

Cone, Marshall R. ;

Kopp, Edgar W. ;

Hogan, Kelly N. ;

Cannons, Andrew C. ;

Jean, Reynald .

NATURE, 2017, 546 (7658) :401-+

[9] Spread of SARS-CoV-2 in the Icelandic Population [J].

Gudbjartsson, Daniel F. ;

Helgason, Agnar ;

Jonsson, Hakon ;

Magnusson, Olafur T. ;

Melsted, Pall ;

Norddahl, Gudmundur L. ;

Saemundsdottir, Jona ;

Sigurdsson, Asgeir ;

Sulem, Patrick ;

Agustsdottir, Arna B. ;

Eiriksdottir, Berglind ;

Fridriksdottir, Run ;

Gardarsdottir, Elisabet E. ;

Georgsson, Gudmundur ;

Gretarsdottir, Olafia S. ;

Gudmundsson, Kjartan R. ;

Gunnarsdottir, Thora R. ;

Gylfason, Arnaldur ;

Holm, Hilma ;

Jensson, Brynjar O. ;

Jonasdottir, Aslaug ;

Jonsson, Frosti ;

Josefsdottir, Kamilla S. ;

Kristjansson, Thordur ;

Magnusdottir, Droplaug N. ;

le Roux, Louise ;

Sigmundsdottir, Gudrun ;

Sveinbjornsson, Gardar ;

Sveinsdottir, Kristin E. ;

Sveinsdottir, Maney ;

Thorarensen, Emil A. ;

Thorbjornsson, Bjarni ;

Loeve, Arthur ;

Masson, Gisli ;

Jonsdottir, Ingileif ;

Moeller, Alma D. ;

Gudnason, Thorolfur ;

Kristinsson, Karl G. ;

Thorsteinsdottir, Unnur ;

Stefansson, Kari .

NEW ENGLAND JOURNAL OF MEDICINE, 2020, 382 (24) :2302-2315

[10] Nextstrain: real-time tracking of pathogen evolution [J].

Hadfield, James ;

Megill, Colin ;

Bell, Sidney M. ;

Huddleston, John ;

Potter, Barney ;

Callender, Charlton ;

Sagulenko, Pavel ;

Bedford, Trevor ;

Neher, Richard A. .

BIOINFORMATICS, 2018, 34 (23) :4121-4123

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