North America has 87% of all unique SARS-CoV-2 S protein variants in the NCBI database among six continents

The spike (S) proteins on the surface of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are crucial in determining the infectivity and antigenicity of the virus. The spike protein has already undergone several mutations, and these mutations have influenced immune system evasion and boosted viral transmission. This has led to increased morbidity and mortality, and these negative changes caused by mutations are being investigated.

Study: Implications Derived from S-Protein Variants of SARS-CoV-2 from Six Continents. Image Credit: Limbitech / Shutterstock

Analyzing unique variants of S proteins across six continents

Spike proteins are of great interest to researchers from many angles, including pathogenicity and epidemiology. Recently, a team of researchers from various countries analyzed the unique variants of S proteins across six continents, including Africa, Asia, Oceania, Europe, South America, and North America. They wanted to characterize the unique S protein variants embedded in SARS-CoV-2 genomes infecting millions of people globally. This team has released their study as a preprint on the bioRxiv* server.

There are still many unique S protein variants in all continents that may spread from person to person through close communities or by spontaneous mutations caused a condition that may become alarming."

Africa has the highest percentage of unique S proteins compared to the other five continents

The team's findings show that Africa had the highest percentage (29.065%) of unique S proteins in comparison to the other continents part of the study. Interestingly, North America had 87% (14046) of all (16143) specific S proteins in the NCBI database across all continents. Also, S proteins from North America had mutations in nearly every amino acid residue position (1184 out of 1273), while unique S variants from other continents had mutations in only 16-20% of residues. Hence, even with limited international travel, the S proteins from these five continents will probably acquire mutations at other positions, where mutations already exist in the North American variants, through natural evolution.

Phylogenetic relationship implies that unique North American S proteins were considerably different from S proteins of other continents

Based on the distributions of amino acid frequency in the S protein variants across all the continents, a phylogenetic relationship was mapped. This relationship implied that unique S proteins from North America were considerably different from the S proteins from the other five continents.

The North American variants are likely to spread to other locations over time through naturally emerging mutations or travel. Hence, there is a high likelihood of the unique variants from North America spreading to the other continents via international travel.

Newer SARS-CoV-2 variants may emerge causing more waves of the COVID-19 pandemic

Even when a population reaches a high herd immunity threshold for one viral variant, there is a risk of resurgence of new variants with immunity-escape capabilities. This is concerning and raises important questions. Some of the important questions are: should post-infection herd immunity be combined with vaccination for better protection? and will WHO flag the new variants of concern to be included in "next-generation vaccines"?

Additionally, the possibility of more serious mutations in the viral RBD originating in India and the USA cannot be excluded. Therefore, the emergence of newer SARS-CoV-2 variants that may cause fourth and fifth waves of the COVID-19 pandemic is a possibility.

Vaccines under development need to be carefully reviewed for efficacy against new S protein variants

Based on the study's findings, the authors recommend international travel restrictions and mass vaccination programs as urgent measures to contain the spread of SARS-CoV-2. They also suggest a careful review of the efficacy of currently available vaccines and those under development. If needed, the vaccines should be further re-engineered based on the changing requirements due to the emerging S protein variants.

Massive vaccination is necessary to combat COVID-19, and of course, existing vaccines must be reviewed, and if needed further re-engineered may be required based on newly emerging S protein variants."

*Important Notice

bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Written by

Susha Cheriyedath

Susha has a Bachelor of Science (B.Sc.) degree in Chemistry and Master of Science (M.Sc) degree in Biochemistry from the University of Calicut, India. She always had a keen interest in medical and health science. As part of her masters degree, she specialized in Biochemistry, with an emphasis on Microbiology, Physiology, Biotechnology, and Nutrition. In her spare time, she loves to cook up a storm in the kitchen with her super-messy baking experiments.