Why is delta different? The delta variant with all its characteristic mutations and deletions in the spike protein. The delta variant belongs to clade 21A, under the NextStrain phylogenetic classification system, and is designated B.1.617.2 under the Pangolin lineages nomenclature. The P681R substitution may boost the variant’s cell-level infectivity.Ĭuriously, the delta doesn’t have the N501Y substitution, which is an integral part of the alpha, beta and gamma variants, and is known to enhance the virus’s transmission capability. In particular, the L452R substitution increases the spike protein’s affinity for the ACE2 receptor and affects the immune system’s ability to recognise the invader. The delta variant’s genome has 13 mutations, including significant ones in the gene encoding the spike protein, known to affect the virus’s transmissibility and whether it can be neutralised by antibodies for previously circulating variants of the virus. More recent evidence suggests that N has a crucial role in evading the cell’s innate immune response, and amino-acid replacements in this region may increase the virus’s replication capacity.
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(Think of the genome as an instruction manual that each cell ‘reads’ to produce the proteins needed for the virus’s function.)Īll VOCs have an amino-acid replacement at position 203, 204 or 205 of the N protein. Mutations in the virus’s genome alter the amino-acid sequences of the proteins that the genome encodes. The one exception to these characteristics is the alpha variant, which has only one mutation associated with immune evasion. NS substitutions in the spike are located mostly in the NTD and receptor binding domain.NS substitutions predominantly in the spike protein.More non-synonymous (NS) substitutions (or point mutations) compared to non-VOCs.WHO classifies the variants that have these characteristics as variants of concern (VOC), variants of interest (VOI) or variants under monitoring/investigation (VUM).Īn additional 12 variants previously classified as VOIs, such as the B.1.427/9 that originated in California, have now been reclassified as VUMs.Īt the genome level, all the VOCs have three key features: having a common ancestor – and classified based on the available evidence for increased transmissibility, virulence, or immune escape. So antibody-evasion substitutions could confer a significant advantage on the virus’s survival.Īt the genomic level, variants are characterised by phylogenetic clade – i.e. The delta variant is currently spreading in a different scenario, with more immunised and recovered individuals in the population. So antibody-evasion substitutions bore no selective advantage in infections of naïve individuals.
This is in line with the timeline in which the alpha began to spread, around the last quarter of 2020 – when the global population hadn’t been vaccinated and less than a large fraction of the same population had been infected and recovered. These substitutions are abundant in all other key variants.
We know that the alpha variant does not have substitutions associated with immune evasion (except for one amino-acid deletion at the N-terminal domain, or NTD, of the spike protein). Its current global cumulative prevalence is 15%. At present, the delta variant seems to be displacing all other variants. As of August 10, 2021, 378,405 sequences of the delta variant had been detected since the lineage was first identified. In the last few months, our focus has been on the delta variant (B.1.617.2), first detected in India last year but which has since emerged in almost every country. In contrast, the second year of the pandemic has been punctuated by the emergence of several variants, signalling more and faster changes. Photo: NIAID/Flickr, CC BY 2.0ĭuring the first few months of the COVID-19 pandemic, the evolution of the causative novel coronavirus was relatively predictable, with substitutions accumulating at a fixed pace of about one every second week. A colorised scanning electron micrograph of a cell (teal and green) infected with SARS-CoV-2 virus particles (purple and pink).
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