Peer Review of the pre-print 'Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2'
This is a peer review of the pre-print “Endonuclease fingerprint indicates a synthetic origin of SARS-CoV2”, it is highly recommended that you go and read the pre-print in order to understand this review.
Introduction
The broad thread of the argument in the pre-print is that a synthetically engineered COVID-19 virus would be created using a process where ‘restriction’ enzymes cut the vaccine genome into roughly equal fragments so that they can be cloned in a bacterial system before being reassembled. Restriction enzymes cut the genome at very select sites where the DNA matches certain short sequences. These target sequences, called restriction sites, may appear in the genome by chance as natural nucleotide mutations occur. However, for a given genome the restriction sites will not usually be in the equally spaced locations needed for cutting the genome into equal chunks using restriction enzymes. To get around this, scientists create mutations in the viral genome to create new, more equally spaced restriction sites and remove old restriction sites which are too close together. Observing equally spaced restriction sites might be a marker of a synthetically engineered virus, since a wild-type viral genome has a small probability of having restriction sites so equally spaced throughout the genome.
Visualising microbial population structure with mandrake
Paper: https://doi.org/10.1098/rstb.2021.0237
(Joint work with Gerry Tonkin-Hill)
Dimensional reduction and embeddings
Dimension reduction methods are a popular way to understand large amounts of genetic data: PCA, t-SNE and UMAP have all been used to analyse and visualise large numbers of samples in two-dimensions (with the latter being particularly popular with single cell techniques).