Machine Learning Model to Track SARS-CoV-2 Viral Mutation Evolution and Speciation Using Next-generation Sequencing Data

被引：0

作者：

Derecichei, Iulian ^{[1
]}

Atikukke, Govindaraja ^{[2
]}

机构：

[1] Univ Windsor, Windsor, ON, Canada

[2] ITOS Oncol, Windsor, ON, Canada

来源：

ACM-BCB 2020 - 11TH ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY, AND HEALTH INFORMATICS | 2020年

关键词：

D O I：

10.1145/3388440.3415991

中图分类号：

TP39 [计算机的应用];

学科分类号：

081203 ; 0835 ;

摘要：

RNA sequence analysis of emerging SARS-CoV-2 infection is valuable for tracking viral evolution and developing novel diagnostic tools. Furthermore, SARS-CoV-2 sequence analysis can provide insight into potential antigenic drift events that lead to strain speciation and changing clinical outcomes. In this work, we aim to develop a pipeline using next-generation sequencing (NGS) technology in addition to machine learning/bioinformatics to track the accumulation of mutations and viral evolution.

引用

页数：1

共 50 条

[1] Accurate Detection of SARS-CoV-2 by Next-Generation Sequencing in Low Viral Load Specimens
Ilie, Marius
Benzaquen, Jonathan
Hofman, Veronique
Long-Mira, Elodie
Lassalle, Sandra
Boutros, Jacques
Bontoux, Christophe
Lespinet-Fabre, Virginie
Bordone, Olivier
Tanga, Virginie
Allegra, Maryline
Salah, Myriam
Fayada, Julien
Leroy, Sylvie
Vassallo, Matteo
Touitou, Irit
Courjon, Johan
Contenti, Julie
Carles, Michel
Marquette, Charles-Hugo
Hofman, Paul
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2023, 24 (04)
[2] Identification of SARS-CoV-2 Variants of Concern Using Amplicon Next-Generation Sequencing
Nasereddin, Abdelmajeed
Berman, Hadar Golan
Wolf, Dana G.
Oiknine-Djian, Esther
Adar, Sheera
MICROBIOLOGY SPECTRUM, 2022, 10 (04):
[3] Benchmarking and Assessment of Eight De Novo Genome Assemblers on Viral Next-Generation Sequencing Data, Including the SARS-CoV-2
Gupta, Amit Kumar
Kumar, Manoj
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 2022, 26 (07) : 372 - 381
[4] High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing
Bhoyar, Rahul C.
Jain, Abhinav
Sehgal, Paras
Divakar, Mohit Kumar
Sharma, Disha
Imran, Mohamed
Jolly, Bani
Ranjan, Gyan
Rophina, Mercy
Sharma, Sumit
Siwach, Sanjay
Pandhare, Kavita
Sahoo, Swayamprabha
Sahoo, Maheswata
Nayak, Ananya
Mohanty, Jatindra Nath
Das, Jayashankar
Bhandari, Sudhir
Mathur, Sandeep K.
Kumar, Anshul
Sahlot, Rahul
Rojarani, Pallavali
Lakshmi, Juturu Vijaya
Surekha, Avileli
Sekhar, Pulala Chandra
Mahajan, Shelly
Masih, Shet
Singh, Pawan
Kumar, Vipin
Jose, Blessy
Mahajan, Vidur
Gupta, Vivek
Gupta, Rakesh
Arumugam, Prabhakar
Singh, Anjali
Nandy, Ananya
Ragavendran, P., V
Jha, Rakesh Mohan
Kumari, Anupama
Gandotra, Sheetal
Rao, Vivek
Faruq, Mohammed
Kumar, Sanjeev
Reshma, Betsy G.
Varma, Narendra G.
Roy, Shuvra Shekhar
Sengupta, Antara
Chattopadhyay, Sabyasachi
Singhal, Khushboo
Pradhan, Shalini
PLOS ONE, 2021, 16 (02):
[5] SARS-CoV-2 tracking in Tunisia through next-generation sequencing: lessons for the future
Rebai, Ahmed
Souissi, Amal
Abid, Nabil
Masmoudi, Saber
EURO-MEDITERRANEAN JOURNAL FOR ENVIRONMENTAL INTEGRATION, 2021, 6 (02)
[6] Detection of SARS-COV-2 variants and their proportions in wastewater samples using next-generation sequencing in Finland
Lipponen A.
Kolehmainen A.
Oikarinen S.
Hokajärvi A.-M.
Lehto K.-M.
Heikinheimo A.
Halkilahti J.
Juutinen A.
Luomala O.
Smura T.
Liitsola K.
Blomqvist S.
Savolainen-Kopra C.
Pitkänen T.
Scientific Reports, 14 (1) : 7751
[7] Detection of SARS-COV-2 variants and their proportions in wastewater samples using next-generation sequencing in Finland
Lipponen, Anssi
Kolehmainen, Aleksi
Oikarinen, Sami
Hokajarvi, Anna-Maria
Lehto, Kirsi-Maarit
Heikinheimo, Annamari
Halkilahti, Jani
Juutinen, Aapo
Luomala, Oskari
Smura, Teemu
Liitsola, Kirsi
Blomqvist, Soile
Savolainen-Kopra, Carita
Pitkanen, Tarja
SCIENTIFIC REPORTS, 2024, 14 (01):
[8] SARS-CoV-2 tracking in Tunisia through next-generation sequencing: lessons for the future
Ahmed Rebai
Amal Souissi
Nabil Abid
Saber Masmoudi
Euro-Mediterranean Journal for Environmental Integration, 2021, 6
[9] Evaluation of next generation sequencing approaches for SARS-CoV-2
Curini, Valentina
Ancora, Massimo
Jurisic, Lucija
Di Lollo, Valeria
Secondini, Barbara
Mincarelli, Luana Fiorella
Caporale, Marialuigia
Puglia, Ilaria
Di Gialleonardo, Luigina
Mangone, Iolanda
Di Domenico, Marco
Di Pasquale, Adriano
Lorusso, Alessio
Marcacci, Maurilia
Camma, Cesare
HELIYON, 2023, 9 (11)
[10] A decontamination strategy for resolving SARS-CoV-2 amplicon contamination in a next-generation sequencing laboratory
Peter Mwangi
Milton Mogotsi
Ayodeji Ogunbayo
Teboho Mooko
Wairimu Maringa
Hlengiwe Sondlane
Kelebogile Nkwadipo
Olusesan Adelabu
Philip Armand Bester
Dominique Goedhals
Martin Nyaga
Archives of Virology, 2022, 167 : 1175 - 1179

← 1 2 3 4 5 →