Unlocking capacities of genomics for the COVID-19 response and future pandemics

Sergey Knyazev, Karishma Chhugani, Varuni Sarwal, Ram Ayyala, Harman Singh, Smruthi Karthikeyan, Dhrithi Deshpande, Pelin Icer Baykal, Zoia Comarova, Angela Lu, Yuri Porozov, Tetyana I Vasylyeva, Joel O Wertheim, Braden T Tierney, Charles Y Chiu, Ren Sun, Aiping Wu, Malak S Abedalthagafi, Victoria M Pak, Shivashankar H NagarajAdam L Smith, Pavel Skums, Bogdan Pasaniuc, Andrey Komissarov, Christopher E Mason, Eric Bortz, Philippe Lemey, Fyodor Kondrashov, Niko Beerenwinkel, Tommy Tsan-Yuk Lam, Nicholas C Wu, Alex Zelikovsky, Rob Knight, Keith A Crandall, Serghei Mangul

Research output: Contribution to journalArticlepeer-review


During the COVID-19 pandemic, genomics and bioinformatics have emerged as essential public health tools. The genomic data acquired using these methods have supported the global health response, facilitated the development of testing methods and allowed the timely tracking of novel SARS-CoV-2 variants. Yet the virtually unlimited potential for rapid generation and analysis of genomic data is also coupled with unique technical, scientific and organizational challenges. Here, we discuss the application of genomic and computational methods for efficient data-driven COVID-19 response, the advantages of the democratization of viral sequencing around the world and the challenges associated with viral genome data collection and processing.
Original languageEnglish (US)
Pages (from-to)374-380
Number of pages7
JournalNature Methods
Issue number4
StatePublished - Apr 2022


  • COVID-19
  • Genomics
  • Humans
  • Pandemics
  • SARS-CoV-2/genetics


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