Researchers Identify Three Separate Strains of SARS-CoV-2

Updated on 6 March 2020. 

According to scientists from Zhejiang University, Sun Yat-sen University and Saint Louis University in Missouri, rather than being a single virus strain, SARS-CoV-2 has already split into three separate strains, which can be grouped into two main strains.

The findings, which were published in a preprint on medRxiv.org, made the case for three SARS-CoV-2 strains, which the authors term Type IA, Type IB and Type II, and which may present with different symptoms.

The most important finding of this study is that COVID-19 strains form two well-supported clades (genotype I, or Type I, and Type II). Type II strains were likely evolved from Type I and are more prevalent than Type I among infected patients (68 Type II strains vs 29 Type I strains in total). Our results suggest the outbreak of type II COVID-19 likely occurred in the Huanan market, while the initial transmission of the type I virus to humans probably occurred at a different location in Wuhan. Second, by analyzing the three genomic sites distinguishing Type I and Type II strains, we found that the synonymous changes at two of the three sites confer higher protein translational efficiencies in Type II strains than in Type I strains, which might explain why Type II straints are more prevalent, implying that Type II is more contagious (transmissible) than Type I.

In another article in the National Science Review, genetic analysis of 103 SARS-CoV-2 genomes also indicated that the virus had evolved into two major types, which these authors’ designated the L type and S type.

Although the L type (∼70%) is more prevalent than the S type (∼30%), the S type was found to be the ancestral version. Whereas the L type was more prevalent in the early stages of the outbreak in Wuhan, the frequency of the L type decreased after early January 2020. Human intervention may have placed more severe selective pressure on the L type, which might be more aggressive and spread more quickly. On the other hand, the S type, which is evolutionarily older and less aggressive, might have increased in relative frequency due to relatively weaker selective pressure.

According to Shen et al, RNA viruses of which coronaviruses are a subtype have a high mutation rate “due to the lack of proofreading activity of polymerases.” As a consequence, they are more likely to evolve resistance to drugs and to escape efforts to monitor their transmission.

Iranian Case Count

Meanwhile, an epidemiological preprint published on medRxiv, has come to the startling conclusion that Iran is vastly underreporting the number of cases in the country.

While the official position of Iran is that there are only 245 cases and 26 deaths, the article’s authors have extrapolated a much wider epidemic in the country based on the number of those found to be infected who have recently travelled from Iran.

Tuite, Bogoch, Sherbo et al estimated that:

“18,3001 … COVID-19 cases would have had to occur in Iran, assuming an outbreak duration of 1.5 months in the country, in order to observe these three internationally exported cases reported at the time of writing.”

In a cruel irony, the Deputy Health Minister of Iran, Iraj Harirchi was announced to have contracted COVID-19, shortly after appearing on television with a colleague ostensibly to announce that everything was under control.

Denmark and Estonia have become the latest two countries to report cases of the coronavirus, taking the number of countries with cases to fifty.

An Iranian citizen who travelled from Riga to Tallinn by bus was hospitalised after arriving in the Estonian capital.

The Danish citizen meanwhile appears to have contracted COVID-19 while on holiday in Lombardy, Italy.

Picture by Mehr News Agency, CC BY 4.0, Link.

Footnotes

  1. (95% confidence interval: 3770 to 53,470)
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