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

Details

• Alternative Title:
  Nat Methods
• Personal Author:
  Knyazev, Sergey ; Chhugani, Karishma ; Sarwal, Varuni ; Ayyala, Ram ; Singh, Harman ; Karthikeyan, Smruthi ; Deshpande, Dhrithi ; Baykal, Pelin Icer ; Comarova, Zoia ; Lu, Angela ; Porozov, Yuri ; Vasylyeva, Tetyana I. ; Wertheim, Joel O. ; Tierney, Braden T. ; Chiu, Charles Y. ; Sun, Ren ; Wu, Aiping ; Abedalthagafi, Malak S. ; Pak, Victoria M. ; Nagaraj, Shivashankar H. ; Smith, Adam L. ; Skums, Pavel ; Pasaniuc, Bogdan ; Komissarov, Andrey ; Mason, Christopher E. ; Bortz, Eric ; Lemey, Philippe ; Kondrashov, Fyodor ; Beerenwinkel, Niko ; Lam, Tommy Tsan-Yuk ; Wu, Nicholas C. ; Zelikovsky, Alex ; Knight, Rob ; Crandall, Keith A. ; Mangul, Serghei
• Description:
  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 development of testing methods, and allowed 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 the efficient data driven COVID-19 response, advantages of democratization of viral sequencing around the world, and challenges associated with viral genome data collection and processing.
• Subjects:
  COVID-19 Genomics Humans Pandemics SARS-CoV-2
• Source:
  Nat Methods. 19(4):374-380
• Pubmed ID:
  35396471
• Pubmed Central ID:
  PMC9467803
• Document Type:
  Journal Article
• Funding:
  U01 CK000539/CK/NCEZID CDC HHSUnited States/ ; U19 AI135995/AI/NIAID NIH HHSUnited States/ ; U01 DA053941/DA/NIDA NIH HHSUnited States/ ; R01 AI125416/AI/NIAID NIH HHSUnited States/ ; R01 AI153044/AI/NIAID NIH HHSUnited States/ ; R00 AI139445/AI/NIAID NIH HHSUnited States/ ; R01 MH115676/MH/NIMH NIH HHSUnited States/ ; R21 AI129851/AI/NIAID NIH HHSUnited States/ ; 206298/Z/17/Z/WT_/Wellcome TrustUnited Kingdom/ ; R21 CA241044/CA/NCI NIH HHSUnited States/ ; U01 HG011715/HG/NHGRI NIH HHSUnited States/ ; R01 AI135992/AI/NIAID NIH HHSUnited States/ ; P20 GM103395/GM/NIGMS NIH HHSUnited States/ ; R01 AI151059/AI/NIAID NIH HHSUnited States/ ; DP2 AT011966/AT/NCCIH NIH HHSUnited States/ ; R01 HG009120/HG/NHGRI NIH HHSUnited States/ ; R01 AI167910/AI/NIAID NIH HHSUnited States/ ; R01 EB025022/EB/NIBIB NIH HHSUnited States/ ; R01 AI153827/AI/NIAID NIH HHSUnited States/ ; WT_/Wellcome TrustUnited Kingdom/
• Volume:
  19
• Issue:
  4
• Collection(s):
  CDC Public Access
• Main Document Checksum:
  urn:sha-512:9b334e8c166db8fd94a6b2aae476b3137ba5fd8dfdc7beb21e9c4aafff44c68d276f6c8bb8fb944def551edde52b1f505f6c7466ccc85ab9626542101e836759
• Download URL:
  https://stacks.cdc.gov/view/cdc/121208/cdc_121208_DS1.pdf
• File Type:
  [PDF - 636.80 KB ]