Journal
PLOS ONE
Volume 17, Issue 9, Pages -Publisher
PUBLIC LIBRARY SCIENCE
DOI: 10.1371/journal.pone.0260331
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Funding
- National Institute of General Medical Sciences of the NIH [R01GM123314]
- Indo-U.S. Science and Technology Forum [IUSSTF/VN-COVID/005/2020]
- IUPUI's Office of the Vice Chancellor for Research COVID-19 Rapid Response Grant
- NIH [R01GM123314]
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SARS-CoV-2 has different spreading capacities and mortality rates compared to SARS-CoV-1. Research has found long-range RNA-RNA interactions in the Spike region of SARS-CoV-2, which may impact the viral life cycle.
SARS-CoV-2 has affected people worldwide as the causative agent of COVID-19. The virus is related to the highly lethal SARS-CoV-1 responsible for the 2002-2003 SARS outbreak in Asia. Research is ongoing to understand why both viruses have different spreading capacities and mortality rates. Like other beta coronaviruses, RNA-RNA interactions occur between different parts of the viral genomic RNA, resulting in discontinuous transcription and production of various sub-genomic RNAs. These sub-genomic RNAs are then translated into other viral proteins. In this work, we performed a comparative analysis for novel long-range RNA-RNA interactions that may involve the Spike region. Comparing in-silico fragment-based predictions between reference sequences of SARS-CoV-1 and SARS-CoV-2 revealed several predictions amongst which a thermodynamically stable long-range RNA-RNA interaction between (23660-23703 Spike) and (28025-28060 ORF8) unique to SARS-CoV-2 was observed. The patterns of sequence variation using data gathered worldwide further supported the predicted stability of the sub-interacting region (23679-23690 Spike) and (28031-28042 ORF8). Such RNA-RNA interactions can potentially impact viral life cycle including sub-genomic RNA production rates.
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