Virus strain of a mild COVID-19 patient in Hangzhou represents a new trend in SARS-CoV-2 evolution related to Furin cleavage site

Abstract

The outbreak of COVID-19 become enormous threat to human beings, showing unclear virus mutation during dissemination. We found, in our 788 confirmed COVID-19 patients, the decreased rate of severe/critical type, increased liver/kidney damage and prolonged period of nuclear acid positivity, when compared with Wuhan.To investigate underlining mechanisms, we isolated one strain of SARS-CoV-2 (ZJ01) in mild COVID-19 patient and found the existence of 35 specific gene mutation by gene alignment. Further phylogenetic analysis and RSCU heat map results suggested that ZJ01 may be a potential evolutionary branch of SARS-CoV-2. We classified 54 strains of viruses worldwide (C/T type) based on the base (C or T) at positions 8824 and 28247. ZJ01 has both T at those sites, becoming the only TT type currently identified in the world. The prediction of Furin cleavage site (FCS) and the sequence alignment of virus family indicated that FCS may be an important site of coronavirus evolution. ZJ01 had mutations near FCS (F1-2), which caused changes in the structure and electrostatic distribution of S protein surface, further affecting the binding capacity of Furin. Single cell sequencing and ACE2-Furin co-expression results confirmed that Furin level was higher in the whole body, especially in glands, liver, kidney and colon while FCS may help SARS-CoV-2 infect these organs. The evolutionary pattern of SARS-CoV-2 towards FCS formation may result in its clinical symptom becoming closer to HKU-1 and OC43 (the source of FCS sequence-PRRA) caused influenza, further showing potential in differentiating into mild COVID-19 subtypes.

A review on the cleavage priming of the spike protein on coronavirus by angiotensin-converting enzyme-2 and furin

“…In another study, Xi et al (2020) isolated one strain of SARS-CoV-2 (ZJ01) in mild COVID-19 patient and reported the presence of more than 30 specific gene mutation. The theoretical analysis of FCS and the case alignment of CoV family determined that FCS may be a crucial site of CoV evolution.…”

“…GZ02 presented a number of negative charge distribution in F3 site while limited negative charge distribution was observed in SARS-CoV-2-associated virus (Figure 4a). Hence, they deduced that, the mutation close to FCS site lead to a significant change in the protein conformation and surface charges, which further affected its interaction with the ligands (Xi et al, 2020). Hoffmann et al (2020) depicted that SARS-CoV-2 cell entry relied on ACE-2 and TMPRSS2 and is limited by a protease inhibitor.…”

“…Also, based on the crystal structure of furin, some potent inhibitors like 2,5-dideoxystreptamine-mediated inhibitor (Xi et al, 2020). The similarity between SARS-CoV and SARS-CoV-2 (Hoffmann et al, 2020).…”

A comprehensive germline variant and expression analyses ofACE2,TMPRSS2and SARS-CoV-2 activatorFURINgenes from the Middle East: Combating SARS-CoV-2 with precision medicine

“…The genetic susceptibility to has also been explored by scrutinizing Angiotensin converting enzyme 2 (ACE2) genetic variations in different populations. ACE2 is the functional receptor mediating entry of SARS-CoV-2 into the host cells 5 , which is facilitated by FURIN cleavage [6][7][8] . Transmembrane serine protease 2 (TMPRSS2) is another candidate gene that has been linked to COVID-19 disease [8][9][10] .…”

“…The hallmark of the novel SARS-CoV-2, as compared to other SARS viruses, is the presence of a polybasic FURIN cleavage site. FURIN has been reported to facilitate the transport of SARS-CoV-2 into or from the host cell [6][7][8] . Notably, a recent study has highlighted the presence of a unique functional polybasic FURIN cleavage consensus site between the two spike subunits S1 and S2 by the insertion of 12 nucleotides encoding PRRA in the S protein of SARS-CoV-2 virus 12 .…”