Nucleocapsid mutation R203K/G204R increases the infectivity, fitness and virulence of SARS-CoV-2

Abstract

In addition to the mutations on the spike protein (S), co-occurring mutations on nucleocapsid (N) protein are also emerging in SARS-CoV-2 world widely. Mutations R203K/G204R on N, carried by high transmissibility SARS-CoV-2 lineages including B.1.1.7 and P.1, has a rapid spread in the pandemic during the past year. In this study, we performed comprehensive population genomic analyses and virology experiment concerning on the evolution, causation and virology consequence of R203K/G204R mutations. The global incidence frequency (IF) of 203K/204R has rose up from nearly zero to 76% to date with a shrinking from August to November in 2020 but bounced later. Our results show that the emergence of B.1.1.7 is associated with the second growth of R203K/G204R mutants. We identified positive selection evidences that support the adaptiveness of 203K/204R variants. The R203K/G204R mutant virus was created and compared with the native virus. The virus competition experiments show that 203K/204R variants possess a replication advantage over the preceding R203/G204 variants, possibly in relation to the ribonucleocapsid (RNP) assemble during the virus replication. Moreover, the 203K/204R virus increased the infectivity in a human lung cell line and induced an enhanced damage to blood vessel of infected hamsters' lungs. In consistence, we observed a positive association between the increased severity of COVID-19 and the IF of 203K/204R from in silicon analysis of global clinical and epidemic data. In combination with the informatics and virology experiment, our work suggested the contribution of 203K/204R to the increased transmission and virulence of the SARS-CoV-2. In addition to mutations on the S protein, the mutations on the N protein are also important to virus spread during the pandemic.

Disease waves of SARS-CoV-2 in Iran closely mirror global pandemic trends

“…ORF3a is an essential protein for viral cytotoxicity and is known to activate the inflammasome. This mutation causes a dramatic change in protein structure, affecting the binding affinity of Orf3a–S and Orf3a–Orf8 protein interactions, and finally may be correlated with enhanced viral virulence (Banoun 2021, Wu et al 2021). This dramatic change in protein structure is also reported for S194L and R203K/G204R in Nucleocapsid.…”

“…The R203/G204 amino acids are located in the serine/arginine-rich (SR-rich) linker region of Nucleocapsid, which is involved in modulating Nucleocapsid multimerization, and cellular localization. Therefore, R203K/G204R mutations may destabilize the protein, followed by a decrease in the overall structural flexibility, and finally can increase the virulence of SARS-CoV-2 (Leary et al 2021, Rahman et al 2021, Troyano-Hernáez et al 2021, Wu et al 2021)…”

Evidence for the dependence of the SARS-Cov-2 Delta high diffusivity on the associated N:G215C nucleocapsid mutation

“…Recently, other noteworthy mutations of the nucleocapsid of the SARS-CoV-2 have been detected and studied (Badua et al, 2021;Rahman et al, 2021). As an example, the mutation 203K/204R has been demonstrated to have competitive advantages as well as increased infectivity and virulence (Wu et al, 2021).…”

“…The immunological mechanisms concerning the nucleocapsid and the possible effects that the changes of this protein can have on transmissibility, replicability and pathogenicity of the virus are still mostly unclear. Recently, evidence has been found supporting the role played by certain nucleocapsid aminoacidic substitutions in promoting higher diffusivity, infectivity and virulence of SARS-CoV-2 (Wu et al, 2021).…”

“…It harbors nucloetidic variations in the gene encoding the SARS-CoV-2 spike protein (Shang et al, 2020) causing the aminoacidic substitutions T478K, P681R and L452R (Starr et al, 2021) which are supposed to affect transmissibility of the virus as well as a lower a nity for the neutralizing antibodies for previously circulating variants of the COVID-19 virus (ECDC, 2021). Till now, attention has been mainly paid to aminoacidic variations of the Spike gene of the virus, but some important aminoacidic variations affecting the Nucleocapside gene of the virus, together with corresponding antibodies, have been described (Brochot et al, 2020;Burbelo et al, 2020;Liang et al, 2021;Wu et al, 2021;Mourier et al, 2021).…”