Omicron was circulating globally for months – remaining undetected due to sequencing artifacts

The first thing one does is think – how? Things have to make sense

1. How did a slow mutating virus like Cov2 suddenly accrue so many mutations – how did such a jump come about? One of the possibilities is of course lab-editing – or maybe recombination
2. But then how is it across the globe so quickly after detection in Nov – escaping the strict PCR regimes across airports. Is it that transmissible?
3. And how did the variants mutate so fast and differently in these countries?

The problem with sequencing primers

Cov2 sequences submitted at GISAID use a set of primers called Artic, small fragments of the genome. But these primers are known to have problems, especially as the virus mutates – which lead to stretches of the genome that are not sequenced. And large swathes of dark-matter which will mask real mutations in these genomic regions, and where/when some mutations arose. This is exactly what happened with omicron – the mutations led to sequencing black-boxes, and the virus was mutating under the radar. This Oct pre-print said the same about G142D mutation. So, sequencing was not catching these mutations.

The trail left across the globe

And as expected, it left its footprints across the globe as intermediates or different linages – the EPE insertion which caught everyone’s eye was a much later entrant. It is not possible that a variant of omicron with many more mutations is present in Australia & England & Denmark having left SA in November.

GISAID entries – and their deletion

The first GISAID entry (now deleted, see Fig) was collected in June, 2021-06-17, Western Cape, 73 female, Id: EPI_ISL_7543999.

As explained above, there are “Long stretches of NNN’s” (see last part of Fig) – but it has the characteristic mutations in the first and last part of the spike protein. Since then GISAID has deleted multiple entries from SA (Aug), Nigeria (Oct) and Italy (Oct)- but there is no way out of this.

There is no other theory which fits the observations – so many mutations, in so many countries. And the further we go back in time, the lesser dangerous omicron becomes. And the world needs that reassurance