The global coronavirus disease COVID-19 pandemic is ravaging the world, affecting 185 countries and territories and infecting 2.4 million people. Now, a team of scientists aims to shed light on the variants of the novel coronavirus strains in India, showing how changes correspond to its transmission and how it causes disease. The research is published on the pre-print server bioRxiv.
The novel coronavirus, officially called severe acute respiratory coronavirus 2 (SARS-CoV-2), first emerged in a seafood market in Wuhan City, Hubei Province in China in December 2019. From February, the virus wreaked havoc across South Korea, Iran, Italy, and Spain. From there, it spread across Europe and on to the United States. The United States is now the epicenter of the virus, with more than 759,000 reported cases and more than 40,000 deaths. Spain, Germany, France, and the United Kingdom have all reported increasing cases as many countries are now in lockdowns to prevent the spread of the virus.
Novel Coronavirus SARS-CoV-2 Transmission electron micrograph of a SARS-CoV-2 virus particle, isolated from a patient. Image captured and color-enhanced at the NIAID Integrated Research Facility (IRF) in Fort Detrick, Maryland. Credit: NIAID
Variants of novel coronavirus
Knowing the variants of the virus can help scientists determine the virus's behavior and how it affects populations. This way, governments can impose health measures that are effective in stemming the virus spread, including social distancing measures.
As yet, there are no approved vaccines and drugs for SARS-CoV-2, the virus that causes COVID-19, and developing these is a significant challenge. The SARS-CoV-2 has RNA as its genetic material, and it gets mutated frequently. Understanding the nature of mutation may help in developing a potential drug. Also, it may give direction to understand the next cycle of mutation in the viral genome. Therefore, it is vital to understand the nature of variation in different strains of the novel virus.
The researchers from the Department of Bioscience and Bioengineering Indian Institute of Technology in India released their findings from the whole genome sequence analysis of viral genome sequences submitted from India. The data consists of 440 genome collective genome sequences, which were from the SRA, GISAID, and GenBank projects from across the globe. Twenty-eight different strains were identified in the report.
The team studied the sequence alignment of the genome sequences and found that there was a new mutation in the NSP3 gene of SARS-CoV-2 Indian strains. There are also regular and frequent changes from around the world. The changes were traced back to March, whereas these changes were not present in samples collected in January in Wuhan City, suggesting that the virus strain has mutated.
India has more than 17,000 confirmed cases of the coronavirus, with 559 deaths. However, the country is suspected of having more cases than what is reported since testing is limited. With the increasing number of cases, the virus might have changed to enhance its transmission and virulence, which describes the severity of the viral infection.
The team's observation shows that two of the early collected samples from patients with travel history to China underwent sampling with a gap of three days. The second sample from a patient had a change in the gene, suggesting the patient may have been infected with both as S-type and L-type of the virus strain.
The L type of strain is deemed more aggressive, while the S type was the one that has spread in China. The L type's prevalence decreased after early January, and the more common S type is more frequent today, thanks to quarantine measures that may have reduced the ability of the aggressive type to spread.
Analyzing genome sequences
Studying genome sequences and possible virus strains can guide scientists in the development of vaccines and treatments for the SARS-CoV-2 infection. In the Indian population, the new incorporation of one or more mutations can be linked to its transmission. The changes observed can be added to a group of changes in the virus in the country.
This information is crucial for the government to plan a series of steps to curb the spread of the virus in populated countries, with India being the second most populated country in the world. Scientists across the globe worry that if the virus can spread rapidly in the country, it will significantly overwhelm its health care system.
"There is an emergent need for more public data sharing from the Indian community to track new subtypes of the virus, the impact of the changes it is incorporating, and where the hotspot for therapeutics lies. India is observing the rapid increase in the number of cases despite country lockdown, it analyzes viral strains more crucial," the team concluded.
bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.