Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic

被引:58
作者
Pillay, Sureshnee [1 ]
Giandhari, Jennifer [1 ]
Tegally, Houriiyah [1 ]
Wilkinson, Eduan [1 ]
Chimukangara, Benjamin [1 ,2 ,3 ]
Lessells, Richard [1 ,4 ]
Moosa, Yunus [4 ]
Mattison, Stacey [1 ]
Gazy, Inbal [1 ]
Fish, Maryam [1 ]
Singh, Lavanya [1 ]
Khanyile, Khulekani Sedwell [1 ]
San, James Emmanuel [1 ]
Fonseca, Vagner [1 ,5 ,6 ]
Giovanetti, Marta [6 ]
Alcantara, Luiz Carlos, Jr. [5 ,6 ]
de Oliveira, Tulio [1 ,2 ,7 ]
机构
[1] Univ KwaZulu Natal, KwaZulu Natal Res Innovat & Sequencing Platform K, Sch Lab Med & Med Sci, ZA-4001 Durban, South Africa
[2] Ctr AIDS Programme Res South Africa CAPRISA, ZA-4001 Durban, South Africa
[3] Univ KwaZulu Natal, Dept Virol, Natl Hlth Lab Serv, ZA-4001 Durban, South Africa
[4] Univ KwaZulu Natal, Nelson R Mandela Sch Med, Dept Infect Dis, ZA-4001 Durban, South Africa
[5] Univ Fed Minas Gerais, Lab Genet Celular & Mol, ICB, BR-31270901 Belo Horizonte, MG, Brazil
[6] Inst Oswaldo Cruz Fiocruz, Lab Flavivirus, BR-21045900 Rio De Janeiro, Brazil
[7] Univ Washington, Dept Global Hlth, Seattle, WA 98195 USA
基金
美国国家卫生研究院; 英国医学研究理事会;
关键词
sequencing; SARS-CoV2; Illumina; protocols; COVID-19; bioinformatics; ALGORITHM;
D O I
10.3390/genes11080949
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
The COVID-19 pandemic has spread very fast around the world. A few days after the first detected case in South Africa, an infection started in a large hospital outbreak in Durban, KwaZulu-Natal (KZN). Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes can be used to trace the path of transmission within a hospital. It can also identify the source of the outbreak and provide lessons to improve infection prevention and control strategies. This manuscript outlines the obstacles encountered in order to genotype SARS-CoV-2 in near-real time during an urgent outbreak investigation. This included problems with the length of the original genotyping protocol, unavailability of reagents, and sample degradation and storage. Despite this, three different library preparation methods for Illumina sequencing were set up, and the hands-on library preparation time was decreased from twelve to three hours, which enabled the outbreak investigation to be completed in just a few weeks. Furthermore, the new protocols increased the success rate of sequencing whole viral genomes. A simple bioinformatics workflow for the assembly of high-quality genomes in near-real time was also fine-tuned. In order to allow other laboratories to learn from our experience, all of the library preparation and bioinformatics protocols are publicly available at protocols.io and distributed to other laboratories of the Network for Genomics Surveillance in South Africa (NGS-SA) consortium.
引用
收藏
页码:1 / 13
页数:13
相关论文
共 24 条
[1]   SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing [J].
Bankevich, Anton ;
Nurk, Sergey ;
Antipov, Dmitry ;
Gurevich, Alexey A. ;
Dvorkin, Mikhail ;
Kulikov, Alexander S. ;
Lesin, Valery M. ;
Nikolenko, Sergey I. ;
Son Pham ;
Prjibelski, Andrey D. ;
Pyshkin, Alexey V. ;
Sirotkin, Alexander V. ;
Vyahhi, Nikolay ;
Tesler, Glenn ;
Alekseyev, Max A. ;
Pevzner, Pavel A. .
JOURNAL OF COMPUTATIONAL BIOLOGY, 2012, 19 (05) :455-477
[2]   Fast and sensitive protein alignment using DIAMOND [J].
Buchfink, Benjamin ;
Xie, Chao ;
Huson, Daniel H. .
NATURE METHODS, 2015, 12 (01) :59-60
[3]   Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes [J].
Cleemput, Sara ;
Dumon, Wim ;
Fonseca, Vagner ;
Karim, Wasim Abdool ;
Giovanetti, Marta ;
Alcantara, Luiz Carlos ;
Deforche, Koen ;
de Oliveira, Tulio .
BIOINFORMATICS, 2020, 36 (11) :3552-3555
[4]   Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California [J].
Deng, Xianding ;
Gu, Wei ;
Federman, Scot ;
Du Plessis, Louis ;
Pybus, Oliver G. ;
Faria, Nuno R. ;
Wang, Candace ;
Yu, Guixia ;
Bushnell, Brian ;
Pan, Chao-Yang ;
Guevara, Hugo ;
Sotomayor-Gonzalez, Alicia ;
Zorn, Kelsey ;
Gopez, Allan ;
Servellita, Venice ;
Hsu, Elaine ;
Miller, Steve ;
Bedford, Trevor ;
Greninger, Alexander L. ;
Roychoudhury, Pavitra ;
Starita, Lea M. ;
Famulare, Michael ;
Chu, Helen Y. ;
Shendure, Jay ;
Jerome, Keith R. ;
Anderson, Catie ;
Gangavarapu, Karthik ;
Zeller, Mark ;
Spencer, Emily ;
Andersen, Kristian G. ;
MacCannell, Duncan ;
Paden, Clinton R. ;
Li, Yan ;
Zhang, Jing ;
Tong, Suxiang ;
Armstrong, Gregory ;
Morrow, Scott ;
Willis, Matthew ;
Matyas, Bela T. ;
Mase, Sundari ;
Kasirye, Olivia ;
Park, Maggie ;
Masinde, Godfred ;
Chan, Curtis ;
Yu, Alexander T. ;
Chai, Shua J. ;
Villarino, Elsa ;
Bonin, Brandon ;
Wadford, Debra A. ;
Chiu, Charles Y. .
SCIENCE, 2020, 369 (6503) :582-+
[5]  
Eden J.S., 2020, VIRUS EVOL, V6, pv, DOI [10.1093/ve/veaa027, DOI 10.1093/ve/veaa027]
[6]   Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States [J].
Fauver, Joseph R. ;
Petrone, Mary E. ;
Hodcroft, Emma B. ;
Shioda, Kayoko ;
Ehrlich, Hanna Y. ;
Watts, Alexander G. ;
Vogels, Chantal B. F. ;
Brito, Anderson F. ;
Alpert, Tara ;
Muyombwe, Anthony ;
Razeq, Jafar ;
Downing, Randy ;
Cheemarla, Nagarjuna R. ;
Wyllie, Anne L. ;
Kalinich, Chaney C. ;
Ott, Isabel M. ;
Quick, Joshua ;
Loman, Nicholas J. ;
Neugebauer, Karla M. ;
Greninger, Alexander L. ;
Jerome, Keith R. ;
Roychoudhury, Pavitra ;
Xie, Hong ;
Shrestha, Lasata ;
Huang, Meei-Li ;
Pitzer, Virginia E. ;
Iwasaki, Akiko ;
Omer, Saad B. ;
Khan, Kamran ;
Bogoch, Isaac I. ;
Martinello, Richard A. ;
Foxman, Ellen F. ;
Landry, Marie L. ;
Neher, Richard A. ;
Ko, Albert, I ;
Grubaugh, Nathan D. .
CELL, 2020, 181 (05) :990-+
[7]  
Giandhari Jennifer, 2020, medRxiv, DOI 10.1101/2020.05.29.20116376
[8]   Whole-Genome Sequencing in Outbreak Analysis [J].
Gilchrist, Carol A. ;
Turner, Stephen D. ;
Riley, Margaret F. ;
Petri, William A., Jr. ;
Hewlett, Erik L. .
CLINICAL MICROBIOLOGY REVIEWS, 2015, 28 (03) :541-563
[9]   Introductions and early spread of SARS-CoV-2 in the New York City area [J].
Gonzalez-Reiche, Ana S. ;
Hernandez, Matthew M. ;
Sullivan, Mitchell J. ;
Ciferri, Brianne ;
Alshammary, Hala ;
Obla, Ajay ;
Fabre, Shelcie ;
Kleiner, Giulio ;
Polanco, Jose ;
Khan, Zenab ;
Alburquerque, Bremy ;
van de Guchte, Adriana ;
Dutta, Jayeeta ;
Francoeur, Nancy ;
Melo, Betsaida Salom ;
Oussenko, Irina ;
Deikus, Gintaras ;
Soto, Juan ;
Sridhar, Shwetha Hara ;
Wang, Ying-Chih ;
Twyman, Kathryn ;
Kasarskis, Andrew ;
Altman, Deena R. ;
Smith, Melissa ;
Sebra, Robert ;
Aberg, Judith ;
Krammer, Florian ;
Garcia-Sastre, Adolfo ;
Luksza, Marta ;
Patel, Gopi ;
Paniz-Mondolfi, Alberto ;
Gitman, Melissa ;
Sordillo, Emilia Mia ;
Simon, Viviana ;
van Bakel, Harm .
SCIENCE, 2020, 369 (6501) :297-+
[10]   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