Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Reporting Two SARS-CoV-2 Strains Based on A Unique Trinucleotide-Bloc Mutation and Their Potential Pathogenic Difference

Version 1 : Received: 16 April 2020 / Approved: 19 April 2020 / Online: 19 April 2020 (07:14:52 CEST)

How to cite: Ibn Ayub, M. Reporting Two SARS-CoV-2 Strains Based on A Unique Trinucleotide-Bloc Mutation and Their Potential Pathogenic Difference. Preprints 2020, 2020040337. Ibn Ayub, M. Reporting Two SARS-CoV-2 Strains Based on A Unique Trinucleotide-Bloc Mutation and Their Potential Pathogenic Difference. Preprints 2020, 2020040337.


SARS-CoV-2, the novel coronavirus behind COVID-19 pandemic is acquiring new mutations in its genome. Although some mutations provide benefits to the virus against human immune response, a number of them may result in their reduced pathogenicity and virulence. By analyzing more than 3000 high-coverage, complete genome sequences deposited in the GISAID database, here I report a unique 28881-28883:GGG>AAC trinucleotide-bloc mutation in the SARS-CoV-2 genome that results in two sub-strains, described here as SARS-CoV-2g (28881-28883:GGG genotype) and SARS-CoV-2a (28881-28883:AAC genotype). Computational analysis and literature review suggest that this bloc mutation would bring 203-204:RG(arginine-glycine)>KR(lysine-arginine) amino acid changes in the nucleocapsid (N) protein affecting the SR (serine-arginine)-rich motif of the protein, a critical region for the transcription of viral RNA and replication of the virus. Thus, 28881-28883:GGG>AAC bloc-mutation is expected to modulate the pathogenicity of the SARS-CoV-2. Remarkably, SARS-CoV-2g and SARS-CoV-2a strains can be linked with the heterogeneity of COVID-19 cases across different regions within and between countries by analyzing existing data. Sequence analysis suggests that severely affected cities, such as Milan, Lombardy, New York, Paris have the predominant presence of SARS-CoV-2g strains, whereas less affected places like Abruzzo, Lyon, Valencia have a relatively higher presence of SARS-CoV-2a, an indication that the latter strain may contribute to the reduced cases of COVID-19. A similar relationship is observed when Netherlands, Portugal are compared with Spain, France and Germany. These analyses suggest that the SARS-CoV-2 has already evolved into a less infective SARS-CoV-2a affecting COVID-19 cases in different regions. The time a country or region needs to acquire SARS-CoV-2a strains may be indicative to the time it would need to overcome the peak of the COVID-19 cases. To confirm these assumptions, prompt retrospective and prospective epidemiological studies should be conducted in different countries to understand the course of pathogenicity of the SARS-CoV-2a and SARS-CoV-2g. Potential drugs can be designed targeting 28881-28883 region of the N protein to modulate virus pathogenicity.


SARS-CoV-2; COVID-19; strains of SARS-CoV-2


Biology and Life Sciences, Virology

Comments (0)

Comment 1
Received: 24 April 2020
Commenter: Hemayet Ullah
The commenter has declared there is no conflict of interests.
Comment: Excellent investigative work Mustak....This shows that motivation and initiative can produce excellent results....we always complain that a lot of funding is needed to do research but this shows we fail to utilize all the online resources.....This is encouraging that less virulent ones maybe in Bangladesh....Sequence just the Spike gene after amplifying by me it is the variation in the Spike protein that may be more involved in the virulence...

See this paper...Chinese team showed almost 270 fold more virulence associated with specific variations
My lab has developed a broad based antiviral drug targeting a host protein. We believe these drugs will be effective against this coronavirus as well. NIH/NIAID of USA has accepted my proposal to test the drug against the SARS-CoV-2 virus but the pipeline is so long will take 2 months (they informed me). Now using a private antiviral testing facility..will take three weeks. We have tested them against HIV-1 and Hepatitis C IRES based replication and these drugs also inhibit HIV-1 and Hepatitis C replication... We are submitting the manuscript on Monday to Virus Journal.
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