Open AccessVariation at Spike position 142 in SARS-CoV-2 Delta genomes is a technical artifact caused by dropout of a sequencing amplicon
Author(s) -
Theo Sanderson,
Jeffrey C. Barrett
Publication year - 2021
Publication title -
wellcome open research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.298
H-Index - 21
ISSN - 2398-502X
DOI - 10.12688/wellcomeopenres.17295.1
Subject(s) - biology , genome , spike (software development) , genetics , lineage (genetic) , computational biology , delta , mutation , evolutionary biology , gene , computer science , software engineering , engineering , aerospace engineering
Public SARS-CoV-2 genomes from the Delta lineage show complex and confusing patterns of mutations at Spike codon 142, and at another nearby position, Spike codon 95. It has been hypothesised that these represent recurrent mutations with interesting evolutionary dynamics, and that these mutations may affect viral load. Here we show that these patterns, and the relationship with viral load, are artifacts of sequencing difficulties in this region of the Delta genome caused be a deletion in the binding site for the 72_RIGHT primer of the ARTIC V3 schema. Spike G142D should be considered a lineage-defining mutation of Delta.