A widely reported study published in Science that presented evidence for a distributed, ‘stepwise’ origin for Omicron across the African continent has drawn criticism from a number of prominent scientists.
Dr Tulio Oliveira, the director of CERI (Centre for Epidemic Response & innovation) and KRISP (KZN Research Innovation & Sequencing Platform) was one of these scientists expressing their doubts over Twitter.
Dr Oliveira tweeted that, like many other scientists, he was sceptical of the Science paper’s narrative of a stepwise emergence of Omicron in Africa.
“First, the ‘fishing’ of intermediates in Africa should also have been performed in Europe and the USA, which were the regions of the world that introduced the majority of Omicron lineages to Africa -“
He also questioned the accuracy of their results due to possible contamination, and also the strength of their analyses, noting that phylogenetic analyses are weak.
For his fourth point, he says that “the Benin sequences could be recombinants of Delta and Omicron, real recombination, or recombination through contamination of the sequencing process.” He was unable to check for the prevalence of mutations.
He also makes a very simple observation regarding the timing of waves: if Omicron arose first in West Africa, why then did South Africa experience the Omicron wave before them?
The paper was also not presented as a preprint to allow for the research community to give feedback and improved the manuscript, a criticism echoed by biologist and physicist Richard Neher.
“Lastly, the results presented do not reject any of the three hypotheses of Omicron evolution (i.e. unsampled location, immune suppressed individual, animal reservoir).”
Nevertheless, he says that “I have many colleagues and collaborators in this paper and would like to recognize that the allele qPCR system to identify BA.1 is a great tool. Also that their mutation analyses are also good.”
