Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients

ABSTRACT

The SARS-CoV-2 spike (S) protein, the viral mediator for binding and entry into the host cell, has sparked great interest as a target for vaccine development and treatments with neutralizing antibodies. Initial data suggest that the virus has low mutation rates, but its large genome could facilitate recombination, insertions, and deletions, as has been described in other coronaviruses. Here, we deep-sequenced the complete SARS-CoV-2 S gene from 18 patients (10 with mild and 8 with severe COVID-19), and found that the virus accumulates deletions upstream and very close to the S1/S2 cleavage site (PRRAR/S), generating a frameshift with appearance of a stop codon. These deletions were found in a small percentage of the viral quasispecies (2.2%) in samples from all the mild and only half the severe COVID-19 patients. Our results suggest that the virus may generate free S1 protein released to the circulation. We suggest that natural selection has favoured a “Don’t burn down the house” strategy, in which free S1 protein may compete with viral particles for the ACE2 receptor, thus reducing the severity of the infection and tissue damage without losing transmission capability.

KEYWORDS:

• SARS-CoV-2
• deletions
• quasispecies
• NGS
• respiratory virus
• diversity

Acknowledgements

The authors thank Celine Cavallo for English language support.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Author contributions

CA, DG-C, MP and MCM have significantly contributed to designing the experimental work and performed the technical work involving RNA extraction, amplification, and deep sequencing

JG and MG-M developed the software and statistics used in the study

FRF, JE, AR, LG, BA, RF and MGC collected samples and actively participated in discussions and corrections related to the draft

SQ designed the graphics and actively participated in the draft discussion and corrections.

MC, LG, BA, RF, JIE, and TP participated in the analysis and interpretation of the data, and substantially revised the draft

AA and JQ conceived the work, designed the primers, led the data analysis, wrote the draft, and led the discussion.

Conflicts of interest

We declare that no public or private company has had any role in the study design, data collection, experimental work, data analysis, decision to publish, or preparation of the manuscript. Roche Diagnostics S.L. provided support in the form of a salary for one of the authors (Josep Gregori), but the company did not have any role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.

No other competing interests to declare. Thus, our adherence to policies on sharing data and materials is not altered.

Ethics Committee approval

The work has been approved by Vall d'Hebron Hospital Universitary Ethical Committee reference number PR(AG)259-2020.

Additional information

Funding

This study was partially supported by the Direcció General de Recerca i Innovació en Salut (DGRIS) Catalan Health Ministry Generalitat de Catalunya through Vall d'Hebron Institut de Recerca (VHIR); European Development Regional Fund (ERDF) “A way to achieve Europe” by Spanish Network for Research in Infectious Diseases (REIPI RD16/0016/0003); and Centro para el Desarrollo Tecnológico Industrial (CDTI) from the Spanish Ministry of Economy and Business, grant number IDI-20200297.