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Coronavirus Resource

Genome Medicine - Guest editor: Junhua Li

Given the highly evolving landscape of SARS-CoV-2 and COVID-19 research and to capture significant advances in this field, Genome Medicine is pleased to announce a call for papers for our Coronavirus Resource, guest edited by Dr Junhua Li from BGI Research. We encourage work from academic-industry partnerships and collaboration among scientists from multi-disciplinary fields.

We are now inviting the submission of Research, Method, Software, Database and Guideline manuscripts of outstanding interest covering the breadth of the multi-disciplinary work and advances made in this area, covering all aspects of: 

-SARS-CoV-2 evolution, infection and immune response,

-Detection and diagnostics,

-Vaccine development,

-Novel treatment strategies,

-Epidemiology,

-Public health genomics and surveillance.

To submit your manuscript, please use the Genome Medicine online submission system and indicate in your covering letter that you would like the article to be considered for the Coronavirus Resource. If you would like to enquire about the suitability of a manuscript for consideration, please email editorial@genomemedicine.com.

This collection of articles has not been sponsored and articles will undergo the journal’s standard peer-review process. The Guest Editor declares that they have no competing interests. The Guest Editor serves an advisory role to guide the scope of the collection and commissioned content; final editorial decisions lie with the Editor.’


  1. The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alteration...

    Authors: Long H. Nguyen, Daniel Okin, David A. Drew, Vincent M. Battista, Sirus J. Jesudasen, Thomas M. Kuntz, Amrisha Bhosle, Kelsey N. Thompson, Trenton Reinicke, Chun-Han Lo, Jacqueline E. Woo, Alexander Caraballo, Lorenzo Berra, Jacob Vieira, Ching-Ying Huang, Upasana Das Adhikari…
    Citation: Genome Medicine 2023 15:49
    Content type: Research Published on:

  2. The emergence of SARS-CoV-2 Omicron subvariants has raised questions regarding resistance to immunity by natural infection or immunization. We examined the sensitivity of Delta and Omicron subvariants (BA.1, B...

    Authors: Xue-Jun Wang, Lin Yao, Hong-Yun Zhang, Ka-Li Zhu, Jing Zhao, Bing-Dong Zhan, Yi-Ke Li, Xue-Juan He, Cong Huang, Zhuang-Ye Wang, Ming-Dong Jiang, Peng Yang, Yang Yang, Guo-Lin Wang, Sheng-Qi Wang, Er-Hei Dai…
    Citation: Genome Medicine 2022 14:146
    Content type: Research Published on:

  3. The COVID-19 pandemic, which has a prominent social and economic impact worldwide, shows a largely unexplained male bias for the severity and mortality of the disease. Loss of chromosome Y (LOY) is a risk fact...

    Authors: Bożena Bruhn-Olszewska, Hanna Davies, Daniil Sarkisyan, Ulana Juhas, Edyta Rychlicka-Buniowska, Magdalena Wójcik, Monika Horbacz, Marcin Jąkalski, Paweł Olszewski, Jakub O. Westholm, Agata Smialowska, Karol Wierzba, Åsa Torinsson Naluai, Niklas Jern, Lars-Magnus Andersson, Josef D. Järhult…
    Citation: Genome Medicine 2022 14:139
    Content type: Research Published on:

  4. COVID-19 manifests with a wide spectrum of clinical phenotypes, ranging from asymptomatic and mild to severe and critical. Severe and critical COVID-19 patients are characterized by marked changes in the myelo...

    Authors: Gerard Godoy-Tena, Anis Barmada, Octavio Morante-Palacios, Carlos de la Calle-Fabregat, Ricardo Martins-Ferreira, Anna G. Ferreté-Bonastre, Laura Ciudad, Adolfo Ruiz-Sanmartín, Mónica Martínez-Gallo, Ricard Ferrer, Juan Carlos Ruiz-Rodriguez, Javier Rodríguez-Ubreva, Roser Vento-Tormo and Esteban Ballestar
    Citation: Genome Medicine 2022 14:134
    Content type: Research Published on:

  5. Since the start of the coronavirus disease 2019 (COVID-19) pandemic, important insights have been gained into virus biology and the host factors that modulate the human immune response against severe acute res...

    Authors: Caspar I. van der Made, Mihai G. Netea, Frank L. van der Veerdonk and Alexander Hoischen
    Citation: Genome Medicine 2022 14:96
    Content type: Review Published on:

  6. The continuous emergence of SARS-CoV-2 variants of concern (VOC) with immune escape properties, such as Delta (B.1.617.2) and Omicron (B.1.1.529), questions the extent of the antibody-mediated protection again...

    Authors: Enrico Lavezzo, Monia Pacenti, Laura Manuto, Caterina Boldrin, Margherita Cattai, Marco Grazioli, Federico Bianca, Margherita Sartori, Federico Caldart, Gioele Castelli, Michele Nicoletti, Eleonora Nieddu, Elisa Salvadoretti, Beatrice Labella, Ludovico Fava, Maria Cristina Vanuzzo…
    Citation: Genome Medicine 2022 14:61
    Content type: Research Published on:

  7. In early 2021, the SARS-CoV-2 lineage B.1.1.7 (Alpha variant) became dominant across large parts of the world. In Denmark, comprehensive and real-time test, contact-tracing, and sequencing efforts were applied...

    Authors: Thomas Y. Michaelsen, Marc Bennedbæk, Lasse E. Christiansen, Mia S. F. Jørgensen, Camilla H. Møller, Emil A. Sørensen, Simon Knutsson, Jakob Brandt, Thomas B. N. Jensen, Clarisse Chiche-Lapierre, Emilio F. Collados, Trine Sørensen, Celine Petersen, Vang Le-Quy, Mantas Sereika, Frederik T. Hansen…
    Citation: Genome Medicine 2022 14:47
    Content type: Research Published on:

  8. Natural killer (NK) cells are innate lymphoid cells that mediate antitumour and antiviral responses. However, very little is known about how ageing influences human NK cells, especially at the single-cell level.

    Authors: Chuang Guo, Mingming Wu, Beibei Huang, Rui Zhao, Linlin Jin, Binqing Fu, Ping Wang, Dongyao Wang, Meijuan Zheng, Jingwen Fang, Haiming Wei, Kun Qu and Fang Ni
    Citation: Genome Medicine 2022 14:46
    Content type: Research Published on:

    The Research Highlight to this article has been published in Genome Medicine 2022 14:57

  9. Breast milk is a vehicle to transfer protective antibodies from the lactating mother to the neonate. After SARS-CoV-2 infection, virus-specific IgA and IgG have been identified in breast milk, however, there a...

    Authors: Marta Selma-Royo, Christine Bäuerl, Desirée Mena-Tudela, Laia Aguilar-Camprubí, Francisco J. Pérez-Cano, Anna Parra-Llorca, Carles Lerin, Cecilia Martínez-Costa and Maria Carmen Collado
    Citation: Genome Medicine 2022 14:42
    Content type: Research Published on:

  10. Understanding the host genetic architecture and viral immunity contributes to the development of effective vaccines and therapeutics for controlling the COVID-19 pandemic. Alterations of immune responses in pe...

    Authors: Yunlong Ma, Fei Qiu, Chunyu Deng, Jingjing Li, Yukuan Huang, Zeyi Wu, Yijun Zhou, Yaru Zhang, Yichun Xiong, Yinghao Yao, Yigang Zhong, Jia Qu and Jianzhong Su
    Citation: Genome Medicine 2022 14:16
    Content type: Research Published on:

  11. The COVID-19 pandemic has resulted in 275 million infections and 5.4 million deaths as of December 2021. While effective vaccines are being administered globally, there is still a great need for antiviral ther...

    Authors: Marco Grodzki, Andrew P. Bluhm, Moritz Schaefer, Abderrahmane Tagmount, Max Russo, Amin Sobh, Roya Rafiee, Chris D. Vulpe, Stephanie M. Karst and Michael H. Norris
    Citation: Genome Medicine 2022 14:10
    Content type: Research Published on:

  12. Clinical metagenomics (CMg) has the potential to be translated from a research tool into routine service to improve antimicrobial treatment and infection control decisions. The SARS-CoV-2 pandemic provides add...

    Authors: Themoula Charalampous, Adela Alcolea-Medina, Luke B. Snell, Tom G. S. Williams, Rahul Batra, Christopher Alder, Andrea Telatin, Luigi Camporota, Christopher I. S. Meadows, Duncan Wyncoll, Nicholas A. Barrett, Carolyn J. Hemsley, Lisa Bryan, William Newsholme, Sara E. Boyd, Anna Green…
    Citation: Genome Medicine 2021 13:182
    Content type: Research Published on:

  13. Québec was the Canadian province most impacted by COVID-19, with 401,462 cases as of September 24th, 2021, and 11,347 deaths due mostly to a very severe first pandemic wave. In April 2020, we assembled the Cor...

    Authors: Carmen Lía Murall, Eric Fournier, Jose Hector Galvez, Arnaud N’Guessan, Sarah J. Reiling, Pierre-Olivier Quirion, Sana Naderi, Anne-Marie Roy, Shu-Huang Chen, Paul Stretenowich, Mathieu Bourgey, David Bujold, Romain Gregoire, Pierre Lepage, Janick St-Cyr, Patrick Willet…
    Citation: Genome Medicine 2021 13:169
    Content type: Research Published on:

  14. The receptor-binding domain (RBD) variants of SARS-CoV-2 could impair antibody-mediated neutralization of the virus by host immunity; thus, prospective surveillance of antibody escape mutants and understanding...

    Authors: Chunyan Yi, Xiaoyu Sun, Yixiao Lin, Chenjian Gu, Longfei Ding, Xiao Lu, Zhuo Yang, Yaguang Zhang, Liyan Ma, Wangpeng Gu, Aidong Qu, Xu Zhou, Xiuling Li, Jianqing Xu, Zhiyang Ling, Youhua Xie…
    Citation: Genome Medicine 2021 13:164
    Content type: Research Published on:

  15. The emergence of SARS-CoV-2 underscores the need to better understand the evolutionary processes that drive the emergence and adaptation of zoonotic viruses in humans. In the betacoronavirus genus, which also ...

    Authors: Juan Ángel Patiño-Galindo, Ioan Filip, Ratul Chowdhury, Costas D. Maranas, Peter K. Sorger, Mohammed AlQuraishi and Raul Rabadan
    Citation: Genome Medicine 2021 13:124
    Content type: Research Published on:

  16. Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, has been associated with neurological and neuropsychiatric illness in many individuals. We...

    Authors: John F. Fullard, Hao-Chih Lee, Georgios Voloudakis, Shengbao Suo, Behnam Javidfar, Zhiping Shao, Cyril Peter, Wen Zhang, Shan Jiang, André Corvelo, Heather Wargnier, Emma Woodoff-Leith, Dushyant P. Purohit, Sadhna Ahuja, Nadejda M. Tsankova, Nathalie Jette…
    Citation: Genome Medicine 2021 13:118
    Content type: Research Published on:

  17. Early in the pandemic, we designed a SARS-CoV-2 peptide vaccine containing epitope regions optimized for concurrent B cell, CD4+ T cell, and CD8+ T cell stimulation. The rationale for this design was to drive bot...

    Authors: Christof C. Smith, Kelly S. Olsen, Kaylee M. Gentry, Maria Sambade, Wolfgang Beck, Jason Garness, Sarah Entwistle, Caryn Willis, Steven Vensko, Allison Woods, Misha Fini, Brandon Carpenter, Eric Routh, Julia Kodysh, Timothy O’Donnell, Carsten Haber…
    Citation: Genome Medicine 2021 13:101
    Content type: Research Published on:

  18. While genome-wide associations studies (GWAS) have successfully elucidated the genetic architecture of complex human traits and diseases, understanding mechanisms that lead from genetic variation to pathophysi...

    Authors: Liuyang Wang, Thomas J. Balmat, Alejandro L. Antonia, Florica J. Constantine, Ricardo Henao, Thomas W. Burke, Andy Ingham, Micah T. McClain, Ephraim L. Tsalik, Emily R. Ko, Geoffrey S. Ginsburg, Mark R. DeLong, Xiling Shen, Christopher W. Woods, Elizabeth R. Hauser and Dennis C. Ko
    Citation: Genome Medicine 2021 13:83
    Content type: Software Published on:

  19. The large airway epithelial barrier provides one of the first lines of defense against respiratory viruses, including SARS-CoV-2 that causes COVID-19. Substantial inter-individual variability in individual dis...

    Authors: Silva Kasela, Victor E. Ortega, Molly Martorella, Suresh Garudadri, Jenna Nguyen, Elizabeth Ampleford, Anu Pasanen, Srilaxmi Nerella, Kristina L. Buschur, Igor Z. Barjaktarevic, R. Graham Barr, Eugene R. Bleecker, Russell P. Bowler, Alejandro P. Comellas, Christopher B. Cooper, David J. Couper…
    Citation: Genome Medicine 2021 13:66
    Content type: Research Published on:

  20. Immunosuppressive and anti-cytokine treatment may have a protective effect for patients with COVID-19. Understanding the immune cell states shared between COVID-19 and other inflammatory diseases with establis...

    Authors: Fan Zhang, Joseph R. Mears, Lorien Shakib, Jessica I. Beynor, Sara Shanaj, Ilya Korsunsky, Aparna Nathan, Laura T. Donlin and Soumya Raychaudhuri
    Citation: Genome Medicine 2021 13:64
    Content type: Research Published on:

  21. The genome of SARS-CoV-2 is susceptible to mutations during viral replication due to the errors generated by RNA-dependent RNA polymerases. These mutations enable the SARS-CoV-2 to evolve into new strains. Vir...

    Authors: Billy T. Lau, Dmitri Pavlichin, Anna C. Hooker, Alison Almeda, Giwon Shin, Jiamin Chen, Malaya K. Sahoo, Chun Hong Huang, Benjamin A. Pinsky, Ho Joon Lee and Hanlee P. Ji
    Citation: Genome Medicine 2021 13:62
    Content type: Research Published on:

  22. ChAdOx1 nCoV-19 is a recombinant adenovirus vaccine against SARS-CoV-2 that has passed phase III clinical trials and is now in use across the globe. Although replication-defective in normal cells, 28 kbp of ad...

    Authors: Abdulaziz Almuqrin, Andrew D. Davidson, Maia Kavanagh Williamson, Philip A. Lewis, Kate J. Heesom, Susan Morris, Sarah C. Gilbert and David A. Matthews
    Citation: Genome Medicine 2021 13:43
    Content type: Research Published on:

  23. Since early February 2021, the causative agent of COVID-19, SARS-CoV-2, has infected over 104 million people with more than 2 million deaths according to official reports. The key to understanding the biology ...

    Authors: Yanqun Wang, Daxi Wang, Lu Zhang, Wanying Sun, Zhaoyong Zhang, Weijun Chen, Airu Zhu, Yongbo Huang, Fei Xiao, Jinxiu Yao, Mian Gan, Fang Li, Ling Luo, Xiaofang Huang, Yanjun Zhang, Sook-san Wong…
    Citation: Genome Medicine 2021 13:30
    Content type: Research Published on:

  24. We present CoronaHiT, a platform and throughput flexible method for sequencing SARS-CoV-2 genomes (≤ 96 on MinION or > 96 on Illumina NextSeq) depending on changing requirements experienced during the pandemic...

    Authors: Dave J. Baker, Alp Aydin, Thanh Le-Viet, Gemma L. Kay, Steven Rudder, Leonardo de Oliveira Martins, Ana P. Tedim, Anastasia Kolyva, Maria Diaz, Nabil-Fareed Alikhan, Lizzie Meadows, Andrew Bell, Ana Victoria Gutierrez, Alexander J. Trotter, Nicholas M. Thomson, Rachel Gilroy…
    Citation: Genome Medicine 2021 13:21
    Content type: Method Published on:

  25. The SARS-CoV-2 pandemic is currently leading to increasing numbers of COVID-19 patients all over the world. Clinical presentations range from asymptomatic, mild respiratory tract infection, to severe cases wit...

    Authors: Anna C. Aschenbrenner, Maria Mouktaroudi, Benjamin Krämer, Marie Oestreich, Nikolaos Antonakos, Melanie Nuesch-Germano, Konstantina Gkizeli, Lorenzo Bonaguro, Nico Reusch, Kevin Baßler, Maria Saridaki, Rainer Knoll, Tal Pecht, Theodore S. Kapellos, Sarandia Doulou, Charlotte Kröger…
    Citation: Genome Medicine 2021 13:7
    Content type: Research Published on:

  26. During COVID-19, diagnostic serological tools and vaccines have been developed. To inform control activities in a post-vaccine surveillance setting, we have developed an online “immuno-analytics” resource that...

    Authors: Daniel Ward, Matthew Higgins, Jody E. Phelan, Martin L. Hibberd, Susana Campino and Taane G. Clark
    Citation: Genome Medicine 2021 13:4
    Content type: Database Published on:

  27. The identification of genetic variation that directly impacts infection susceptibility to SARS-CoV-2 and disease severity of COVID-19 is an important step towards risk stratification, personalized treatment pl...

    Authors: Yu-Chung Lin, Jennifer D. Brooks, Shelley B. Bull, France Gagnon, Celia M. T. Greenwood, Rayjean J. Hung, Jerald Lawless, Andrew D. Paterson, Lei Sun and Lisa J. Strug
    Citation: Genome Medicine 2020 12:115
    Content type: Correspondence Published on:

  29. Genomic studies of patients with COVID-19, or exposed to it, are underway to delineate host factors associated with variability in susceptibility, infectivity, and disease severity. Here, we highlight the ethi...

    Authors: Gail Geller, Priya Duggal, Chloe L. Thio, Debra Mathews, Jeffrey P. Kahn, Lisa L. Maragakis and Brian T. Garibaldi
    Citation: Genome Medicine 2020 12:95
    Content type: Comment Published on:

  30. The ongoing COVID-19 pandemic has created an urgency to identify novel vaccine targets for protective immunity against SARS-CoV-2. Early reports identify protective roles for both humoral and cell-mediated imm...

    Authors: Asaf Poran, Dewi Harjanto, Matthew Malloy, Christina M. Arieta, Daniel A. Rothenberg, Divya Lenkala, Marit M. van Buuren, Terri A. Addona, Michael S. Rooney, Lakshmi Srinivasan and Richard B. Gaynor
    Citation: Genome Medicine 2020 12:70
    Content type: Research Published on:

  31. SARS-CoV-2 is a recently emerged respiratory pathogen that has significantly impacted global human health. We wanted to rapidly characterise the transcriptomic, proteomic and phosphoproteomic landscape of this...

    Authors: Andrew D. Davidson, Maia Kavanagh Williamson, Sebastian Lewis, Deborah Shoemark, Miles W. Carroll, Kate J. Heesom, Maria Zambon, Joanna Ellis, Philip A. Lewis, Julian A. Hiscox and David A. Matthews
    Citation: Genome Medicine 2020 12:68
    Content type: Research Published on:

  32. COVID-19 (coronavirus disease 2019) has caused a major epidemic worldwide; however, much is yet to be known about the epidemiology and evolution of the virus partly due to the scarcity of full-length SARS-CoV-...

    Authors: Minfeng Xiao, Xiaoqing Liu, Jingkai Ji, Min Li, Jiandong Li, Lin Yang, Wanying Sun, Peidi Ren, Guifang Yang, Jincun Zhao, Tianzhu Liang, Huahui Ren, Tian Chen, Huanzi Zhong, Wenchen Song, Yanqun Wang…
    Citation: Genome Medicine 2020 12:57
    Content type: Research Published on: