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.

Keywords

• COVID-19
• PANDEMIC
• SARS-CoV-2
• SEQUENCE

COVID-19 Enfeksiyonlarında Dizi Analizi Yöntemlerine Genel Bakış

Abstract

Şiddetli akut solunum sendromu koronavirüs 2 (SARS-CoV-2), koronavirüs hastalığı 2019'un (COVID-19) etkeni olarak tanımlandı ve genomik veriler ilk olarak 10 Ocak 2020'de Çin tarafından paylaşıldı. O tarihten itibaren, dünya genelinde toplanan örneklerden viral genomu dizilemek için çok büyük çaba harcandı. Yakın geçmişte, kökenleri izlemek ve bulaşıcı ajanların evrimini anlamak, salgınların yayılma zincirlerini araştırmak, hem etkili ve hızlı moleküler tanı testlerinin geliştirilmesini kolaylaştırmak hem de tedavi ve aşıların araştırılmasına katkıda bulunmak için, yeni nesil dizileme (NGS) stratejileri, başarıyla kullanılmıştır. Teknoloji ve bilimdeki son gelişmeler, COVID-19'un etkeni olan ağır akut solunum sendromu koronavirüsü-2'nin (SARS-CoV-2) genomlarının, bir vakanın tanımlanmasından sonraki saatler veya günler içinde dizilenmesine olanak sağlamıştır. Bu sayede, ilk kez, bir pandeminin halk sağlığı ve epidemi boyutu gerçek zamanlı olarak izlenebilmektedir. SARS-CoV-2 genom dizilerinin erken paylaşımı, moleküler tanı testlerinin hızla geliştirilmesine olanak sağlayarak, küresel hazırlığa ve karşı önlemlerin tasarımına katkıda bulunmuştur. Hızlı, büyük ölçekli virüs genom dizilimi, viral salgınların dinamiklerini anlama ve kontrol önlemlerinin etkinliğini değerlendirmede oldukça önemlidir. SARS-CoV-2 gen dizilimi, gelişmiş tanılar, karşı önlemlerin geliştirilmesi ve hastalık epidemiyolojisinin araştırılması dahil olmak üzere birçok farklı alanda kullanılabilir. COVID-19'un etiyolojik ajanının genomik dizisini tam olarak tanımlamak için etkili ve hızlı dizileme yöntemlerinin geliştirilmesi, tanısal moleküler testlerin tasarımı ve pandemi yayılımını azaltmada etkili önlemlerin alınması ve stratejilerin belirlenmesinde temel olmuştur. Mevcut dizilerin sayısından anlaşıldığı gibi, SARS-CoV-2 genomlarına, farklı yaklaşımlar ve dizileme yöntemleri uygulanabilir. Bununla birlikte, her teknoloji ve dizileme yaklaşımının kendi avantajları ve sınırlamaları vardır. Bu derlemede, SARS-CoV-2 genomlarının dizilenmesi için şu andaki mevcut platformlar ve metodolojik yaklaşımlardan bahsedilecektir.

Keywords

• COVID-19
• PANDEMİ
• SARS-CoV-2
• SEKANS

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