The Power of Using Novel Nanopore Sequencing Technology for Diagnosis, Genomic and Pathological Studies of Covid-19

Chenghao Du,T Zhu,M Anpo,A Sharifi

doi:10.1051/e3sconf/202127104024

Chenghao Du, T Zhu + Show 2 more

Open Access

https://doi.org/10.1051/e3sconf/202127104024

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Abstract

The novel coronavirus disease 2019 (COVID‐19), originally identified in December 2019 Wuhan, China, has propagated to worldwide pandemic, causing many cases of death and morbidity. Since the development of COVID-19 vaccines is still under experimental stages without public access, different types of testing and detection ensuring rapid and accurate results are urgently required to prevent delaying isolation of infected patients. The traditional diagnostic and analytical methods of COVID-19 relied heavily on nucleic acid and antibody-antigen methods but are subject to assembly bias, restricted by reading length, showed some false positive/negative results and had a long turnaround time. Hence, three styles of nanopore sequencing techniques as complementary tools for COVID-19 diagnosis and analysis are introduced. The long-read nanopore sequencing technology has been adopted in metagenomic and pathological studies of virosphere including SARS-CoV-2 recently by either metagenomically, directly or indirectly sequencing the viral genomic RNA of SARS-CoV-2 in real-time to detect infected specimens for early isolation and treatment, to investigate the transmission and evolutionary routes of SARS-CoV-2 as well as its pathogenicity and epidemiology. In this article, the Nanopore-Based Metagenomic Sequencing, Direct RNA Nanopore Sequencing (DRS), and Nanopore Targeted Sequencing (NTS) become the main focus of the novel COVID-19 detecting analytical methods in sequencing platforms, which are discussed in comparison with other traditional and popular diagnostic methods. Finally, different types of nanopore sequencing platforms that are developed by Oxford Nanopore Technologies (ONT) due to various purposes and demands in viral genomic research are briefly discussed.

Highlights

The global outbreak of COVID-19 pandemic has resulted in many infections and mortality, and the infected population is still multiplying
All three nanopore sequencing platforms enable the genomic surveillance of viral RNA mutations and recombination, transmission pathway monitoring, and categorization of SARS-CoV-2 to enrich epidemiological and pathogenetic analyses of many viruses in the future with up-to-date data
Nanopore sequencing platforms for both clinical diagnosis and research is a novel, cutting-edge technology to study SARS‐CoV‐2, challenges, and difficulties related to SAR-CoV-2 detection remain unresolved using nanopore sequencing methods

Summary

Introduction

The global outbreak of COVID-19 pandemic has resulted in many infections and mortality, and the infected population is still multiplying. The diagnosis of COVID-19 relies heavily on nucleic acid testing, antibody-antigen test, and RT-PCR sequencing test, but the current suggested methods that are subject to assembly bias and restricted by reading length showed some rate of false negative/positive results, had long turnaround time, and failed to identify other respiratory diseases simultaneously. Real‐time reverse transcription polymerase chain reaction (RT‐qPCR) is currently the most prevalent diagnostic method to detect SARS‐CoV‐2, because RT‐qPCR has high specificity, is relatively economical and efficient that can generate results for numerous patients simultaneously in less than 2 days. It fails to accurately assess and analyze nucleic acid sequences of amplified gene fragments with long reading length. RT‐qPCR potentially demonstrates a relatively high false‐negative rate in clinical settings that promotes the spread of infection by delaying isolation of patients and cannot receive immediate treatment, causing more transmission of COVID‐19 [10]

Nanopore Sequencing Technology

Conclusion