Overview of sequence analysis methods in COVID-19 infections

ABSTRACT

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) was identified as the agent of COVID-19, and genomic data was first shared by China on January 10, 2020. Since then, tremendous effort has been devoted to sequencing the viral genome from samples collected around the world. In the recent past, next-generation sequencing (NGS) strategies have been used successfully to trace the origins, understand the evolution of infectious agents, to investigate the chains of the spread of epidemics, to facilitate the development of effective and rapid molecular diagnostic tests, and to contribute to the research of treatments and vaccines. Recent advances in technology and science have allowed the genomes of SARS-CoV-2, the agent of COVID-19, to be sequenced within hours or days after a case is identified. In this way, for the first time, the public health and epidemic size of a pandemic can be monitored in real-time. The early sharing of SARS-CoV-2 genome sequences has allowed the rapid development of molecular diagnostic tests, contributing to global preparedness and the design of countermeasures. Rapid, large-scale sequencing of the virus genome is essential in understanding the dynamics of viral outbreaks and assessing the effectiveness of control measures. SARS-CoV-2 gene sequencing can be used in many different areas, including improved diagnosis, development of countermeasures, and investigation of disease epidemiology. The development of effective and rapid sequencing methods to fully identify the genomic sequence of the etiologic agent of COVID-19 has been fundamental to the design of diagnostic molecular tests and the determination of effective measures and strategies to reduce the spread of the pandemic. Different approaches and sequencing methods can be applied to SARS-CoV-2 genomes, as evidenced by the number of sequences available. However, each technology and sequencing approach has its advantages and limitations. In this review, current platforms and methodological approaches for sequencing SARS-CoV-2 genomes will be discussed.