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Analysis of SARS-CoV-2 Temporal Molecular Networks Using Global and Local Topological Characteristics

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Computational Advances in Bio and Medical Sciences (ICCABS 2021)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 13254))

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Abstract

The global COVID-19 pandemic continues to have a devastating impact on human population health. In an effort to fully characterize the virus, a significant volume of SARS-CoV-2 genomes have been collected from infected individuals and sequenced. Comprehensive application of this molecular data toward epidemiological analysis in large parts has employed methods arising from phylogenetics. While undeniably valuable, phylogenetic methods have their limitations. For instance, due to their rooted structure, outgroup samples are often needed to contextualize genetic relationships inferred by branching. In this paper we describe an alternative: global and local topological characterization of neighborhood graphs relating viral genomes collected from samples in longitudinal studies. The applicability of our approach is demonstrated by constructing and analyzing such graphs using two distinct datasets from Israel and France, respectively.

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Acknowledgements

This research was funded in part by National Science Foundation grant IIS-1817239.

Genome sequences analyzed is this work were submitted and collected be the following laboratories: IDS was submitted by the Stern Lab and collected by Microbiology laboratory, Assuta Ashdod University-Affiliated Hospital (EPI_ISL_447258 - 80); Microbiology Division, Barzilai University Medical Center (EPI_ISL_447281-310); Clinical Virology Laboratory, Soroka Medical Center and the Faculty of Health Sciences, Ben-Gurion University of the Negev (EPI_ISL_447311-30); Clinical Virology Unit, Hadassah Hebrew University Medical Center (EPI_ISL_447331-82, EPI_ISL_447407-16), Clinical Microbiology Laboratory, The Baruch Padeh Medical Center, Poriya (EPI_ISL_447383-406, EPI_ISL_447417-8); and Clinical Microbiology Laboratory, Sheba Medical Center (EPI_ISL_447419-69).

FDS was submitted by two laboratories, namely the National Reference Center for Viruses of Respiratory Infections, Institut Pasteur, Paris. Samples were collected by the Centre Hositalier Universitaire de Rouen Laboratoire de Virologie (EPI_ISL_414624, EPI_ISL_416494); Centre Hospitalier Régional Universitaire de Nantes Laboratoire de Virologie (EPI_ISL_414625); Centre Hospitalier Compiègne Laboratoire de Biologie (EPI_ISL_414627, EPI_ISL_414629-30, EPI_ISL_414634-8, EPI_ISL_415653-4, EPI_ISL_416495-7, EPI_ISL_418218, EPI_ISL_418220-1, EPI_ISL_418223-5, EPI_ISL_418227-8, EPI_ISL_418231, EPI_ISL_418236-9); Hôpital Robert Debré Laboratoire de Virologie (EPI_ISL_414631-2); Centre Hospitalier René Dubois Laboratoire de Microbiologie - Bât A (EPI_ISL_414633); Hôpital Instruction des Armées - BEGIN (EPI_ISL_415650); CH Jean de Navarre Laboratoire de Biologie (EPI_ISL_416493, EPI_ISL_420044, EPI_ISL_420053); Institut Médico legal - Hop R. Poincaré (EPI_ISL_416498); LABM GH nord Essonne (EPI_ISL_416498); Hopital franco britannique - Service des Urgences (EPI_ISL_416501); CHRU Pontchaillou - Laboratoire de Virologie (EPI_ISL_416502, EPI_ISL_416504-6, EPI_ISL_416508-13); CHU - Hôpital Cavale Blanche - Labo. de Virologie (EPI_ISL_418219); CHRU Bretonneau - Serv. Bacterio-Virol. (EPI_ISL_418222); EHPAD - Résidences les Cèdres (EPI_ISL_418226); Hopital franco britannique - Laboratoire (EPI_ISL_418229); Clinique AVERAY LA BROUSTE, Med. Polyvalente (EPI_ISL_418230); Service des Urgences (EPI_ISL_418232-3); Cabinet médical (EPI_ISL_418235); Sentinelles network (EPI_ISL_420038, EPI_ISL_420045, EPI_ISL_420055, EPI_ISL_421514), L’Air du Temps (EPI_ISL_420039-40); CH Compiègne Laboratoire de Biologie (EPI_ISL_420041, EPI_ISL_420049-50, EPI_ISL_420056-7, EPI_ISL_421500, EPI_ISL_421509-11); Service de Biologie clinique (EPI_ISL_420042, EPI_ISL_421513); CMIP (EPI_ISL_420043, EPI_ISL_420061); Résidence Villa Caroline (EPI_ISL_420046-7); Service de Biologie Médicale - BP 125 (EPI_ISL_420048, EPI_ISL_420058-60, EPI_ISL_420062, EPI_ISL_420064, EPI_ISL_421501, EPI_ISL_421504-6, EPI_ISL_421512), Résidence Eleusis (EPI_ISL_420051); Résidence les Marines (EPI_ISL_420052); Résidence de maintenon (EPI_ISL_420054); Labo BM - Site de Juvisy - Hopital Général (EPI_ISL_420063); Parc des Dames (EPI_ISL_421502-3); Le Château de Seine-Port (EPI_ISL_421507-8), and unknown (EPI_ISL_414626, EPI_ISL_415649, EPI_ISL_415651-2, EPI_ISL_415649).

The second submitting laboratory was CNR Virus des Infections Respiratoires - France SUD. Samples were collected by CNR Virus des Infections Respiratoires – France SUD (EPI_ISL_416745-6); Institut des Agents Infectieux (IAI) Hospices Civils de Lyon (EPI_ISL_416747-8, EPI_ISL_416750, EPI_ISL_416754, EPI_ISL_416756, EPI_ISL_416758); Centre Hospitalier de Valence (EPI_ISL_416749, EPI_ISL_418414-5, EPI_ISL_418417, EPI_ISL_419168); CHU Gabriel Montpied (EPI_ISL_416751-2); Centre Hospitalier de Bourg en Bresse (EPI_ISL_416757, EPI_ISL_417340, EPI_ISL_418426, EPI_ISL_419183, EPI_ISL_419185-6, EPI_ISL_420620); Institut des Agents Infectieux (IAI), Hospices Civils de Lyon (EPI_ISL_417333-4, EPI_ISL_417336-7, EPI_ISL_417339, EPI_ISL_418420-5, EPI_ISL_418429-31, EPI_ISL_419169-73, EPI_ISL_419177-82, EPI_ISL_419184, EPI_ISL_420604-11, EPI_ISL_420615-6, EPI_ISL_420618-9, EPI_ISL_420621-5); Centre Hospitalier de Macon (EPI_ISL_417338, EPI_ISL_418413, EPI_ISL_419174-6, EPI_ISL_419187-8, EPI_ISL_420612-4); Centre Hospitalier des Vals d’Ardeche (EPI_ISL_418412); GH Les Portes du Sud (EPI_ISL_418416); Centre Hospitalier Saint Joseph Saint Luc (EPI_ISL_418418-9, EPI_ISL_420617); Hopital Privé de l’Est Lyonnais (EPI_ISL_418418-9, EPI_ISL_420617); and Centre Hospitalier Lucien Hussel (EPI_ISL_418428).

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  1. Department of Computer Science, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA, 94132, USA

    Fiona Senchyna & Rahul Singh

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  1. Fiona Senchyna
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  2. Rahul Singh
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Correspondence to Rahul Singh .

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Editors and Affiliations

  1. University of Connecticut, Storrs, CT, USA

    Mukul S. Bansal

  2. University of Connecticut, Storrs, CT, USA

    Ion Măndoiu

  3. University of Connecticut Health Center, Farmington, CT, USA

    Marmar Moussa

  4. Georgia State University, Atlanta, GA, USA

    Murray Patterson

  5. University of Connecticut, Storrs, CT, USA

    Sanguthevar Rajasekaran

  6. Georgia State University, Atlanta, GA, USA

    Pavel Skums

  7. Georgia State University, Atlanta, GA, USA

    Alexander Zelikovsky

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Senchyna, F., Singh, R. (2022). Analysis of SARS-CoV-2 Temporal Molecular Networks Using Global and Local Topological Characteristics. In: Bansal, M.S., et al. Computational Advances in Bio and Medical Sciences. ICCABS 2021. Lecture Notes in Computer Science(), vol 13254. Springer, Cham. https://doi.org/10.1007/978-3-031-17531-2_12

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  • DOI: https://doi.org/10.1007/978-3-031-17531-2_12

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