Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level

• DOI: 10.20411/pai.v6i2.460
• Publication Date: 2021-11-12T11:06:10Z
• Authors: Shay Leary; Silvana Gaudieri; Matthew Parker; Abha Chopra; Ian James; Suman Pakala; Eric Alves; Mina John; Benjamin Lindsey; Alexander Keeley; Sarah Rowland-Jones; Maurice Swanson; David Ostrov; Jodi Bubenik; Suman Das; John Sidney; Alessandro Sette; ; Thushan De Silva; Elizabeth Phillips; Simon Mallal
• Keywords: SARS-CoV-2;; 0303 health sciences; SARS-CoV-2; sub-genomic RNA transcript;; COVID-19; transcription-regulating sequence; homologous recombination;; homologous recombination; transcription-regulating sequence;; C500; RC581-607; 3. Good health; 03 medical and health sciences; COVID-19;; Pathology; RB1-214; sub-genomic RNA transcript; viral polymorphism; Immunologic diseases. Allergy; Research Article

Background: Genetic variations across the SARS-CoV-2 genome may influence transmissibility of the virus and the host’s anti-viral immune response, in turn affecting the frequency of variants over time. In this study, we examined the adjacent amino acid polymorphisms in the nucleocapsid (R203K/G204R) of SARS-CoV-2 that arose on the background of the spike D614G change and describe how strains harboring these changes became dominant circulating strains globally. Methods: Deep-sequencing data of SARS-CoV-2 from public databases and from clinical samples were analyzed to identify and map genetic variants and sub-genomic RNA transcripts across the genome. Results: Sequence analysis suggests that the 3 adjacent nucleotide changes that result in the K203/R204 variant have arisen by homologous recombination from the core sequence of the leader transcription-regulating sequence (TRS) rather than by stepwise mutation. The resulting sequence changes generate a novel sub-genomic RNA transcript for the C-terminal dimerization domain of nucleocapsid. Deep-sequencing data from 981 clinical samples confirmed the presence of the novel TRS-CS-dimerization domain RNA in individuals with the K203/R204 variant. Quantification of sub-genomic RNA indicates that viruses with the K203/R204 variant may also have increased expression of sub-genomic RNA from other open reading frames. Conclusions: The finding that homologous recombination from the TRS may have occurred since the introduction of SARS-CoV-2 in humans, resulting in both coding changes and novel sub-genomic RNA transcripts, suggests this as a mechanism for diversification and adaptation within its new host.