Massive-scale SARS-CoV-2 spike protein mutants evaluation identifies subclonal variants indicative of within-host viral variety

Because the first reported coronavirus illness 2019 (COVID-19) case in December 2019, the extreme acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome has continued to mutate and evolve. Some mutations within the SARS-CoV-2 genome may affect the event of efficient intervention methods.

Study: Large-scale analysis of SARS-CoV-2 spike-glycoprotein mutants demonstrates the need for continuous screening of virus isolates. Image Credit: Dotted Yeti/ ShutterstockExamine: Massive-scale evaluation of SARS-CoV-2 spike-glycoprotein mutants demonstrates the necessity for steady screening of virus isolates. Picture Credit score: Dotted Yeti/ Shutterstock

Coronaviruses are genetically secure in comparison with different RNA viruses resulting from their inherent 3′ to five’ exoribonuclease exercise. Nevertheless, mutations of vital residues within the receptor-binding area (RBD) of the spike protein (S protein) may improve the virus transmissibility. Moreover, mutations in RBD may intervene with the efficacy of vaccines and coverings focusing on the S protein.

Of their latest research revealed on PLOS ONE, researchers from Germany have investigated an unlimited SARS-CoV-2 meeting and next-generation sequencing (NGS) information set, collected throughout the globe, to detect non-synonymous S protein mutations and to guage their impact on potential antibody binding websites and identified T cell epitopes.


The S protein consists of the S1 subunit at N-terminal and the S2 subunits at C-terminal. The receptor-binding area (RBD) within the S1 subunit engages with human angiotensin-converting enzyme 2 (ACE2) as its entry receptor on the host cell floor. Subsequently, the S2 subunit helps fuse the viral envelope with the host cell membrane.

The genomic area encoding the RBD is extremely conserved, making it a gorgeous vaccine goal because it elicits high-quality, protecting antibodies. Mutation N501 in RBD has been proven to reinforce viral infectivity by enhancing the binding between SARS-CoV-2 and the human ACE2 receptor.

What did the researchers do?

The workforce based mostly their investigation on greater than one million SARS-CoV-2 genomic assemblies and 30,806 NGS datasets.

Pairwise alignments to the SARS-CoV-2 Wuhan-Hu-1 reference genomic sequence (MN908947.3) have been carried out on genomic assemblies downloaded from the worldwide initiative on sharing avian influenza information (GISAID) database in April 2021.

The workforce moreover downloaded all NGS information obtainable for SARS-CoV-2 in June 2021 from the European Nucleotide Archive (ENA). The human genome sequence was filtered out, and information have been aligned to the reference MN908947.3. Variants within the S gene sequence have been retrieved from the alignment information.

NGS variants with a sequencing depth of protection of at the very least 30 reads protection have been chosen to determine high-confidence sub-clonal mutations.

What did the researchers discover?

The workforce found that solely 2.5% of virus sequences contained the wild-type (WT) S protein. Mutant viruses exhibited just a few mutations within the S protein with lower than ten mutations for all however 4,193 sequences.

Nevertheless, the imply and median variety of mutations elevated over time from December 2019 (imply: 0.14, median: 0) to April 2021 (imply: 7.2, median: 7).

In complete, the workforce detected 5,472 distinct non-synonymous mutations within the S protein. Solely 22.4% of the mutations within the meeting and NGS information units have been singular occasions. The remainder of them have been recurrently distributed all through the entire S protein.

The most typical recurrent mutation was D614G, positioned simply exterior the RBD, in each the genome assemblies and the NGS information units, adopted by the Y501N mutation, positioned inside RBD. Within the area encoding RBD, the workforce detected 852 mutations (646 recurrent) from the meeting sequences and 259 mutations (105 recurrent) from the NGS datasets.

P681H/D614G was the commonest co-occurring mutation detected in 345,808 samples from mixed meeting and NGS information units. One other often co-occurring mutation was P681H/T716I, noticed in 324,269 samples.

Subclonal S protein mutations, which point out both a co-infection with a number of SARS-CoV-2 strains or an intra-host evolution of the virus pressure, have been detected in 2.59% of the NGS information units. Most of those subclonal occasions have been recurrent.


Researchers from Germany recognized an general low mutation burden within the SARS-CoV-2 S protein. Nevertheless, the imply and median variety of mutations per pattern elevated over time.

We recognized round 99.1% of the samples with a D614G variant, which helps a earlier principle of an growing frequency of the D614G variant within the world pandemic”, say Sahin and colleagues.

S477N mutation probably impacts the RBD stability and strengthens the binding with the human ACE2 receptor. The workforce discovered a frequent co-occurrence of S477N with D614G. As per a earlier report, this mixture has been estimated to unfold much more quickly than the D614G mutant alone, highlighting the necessity to always observe new SARS-CoV-2 variants and their illness transmission patterns for knowledgeable preventive and therapeutic methods.

The workforce additionally means that subclonal variants, indicative of viral variety throughout the host, might stop full clearance after remedy, leading to resistant strains.

Recurrent mutations in subclonal variants may level to co-infection with a number of strains. Pattern-specific variants in flip may reasonably point out that the mutation occurred after an infection throughout the host.”

Journal reference:

  • Schrörs, B. et al. (2021) “Massive-scale evaluation of SARS-CoV-2 spike-glycoprotein mutants demonstrates the necessity for steady screening of virus isolates”, PLOS ONE, 16(9), p. e0249254. doi: 10.1371/journal.pone.0249254.

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