Trace the samples from 22 African countries
Omickron variant strain BA.1 was first reported in a patient in South Africa on November 11, 2021. Compared with the ancestor SARS-CoV-2 strain, BA.1 has more than 50 non-synonymous mutations, most of which are located in the viral spike protein-encoded genes. In the BA.1 spike protein critical amino acid replacement, the unique combination of K417N, S477N, E484A and N501Y in the receptor binding domain leads to BA.1 being able to escape the immune barrier cast by vaccination or previous infection, suggesting that BA.1 has unique serotype characteristics compared to several previous novel coronavirus variants.
So the research team designed a highly specific real-time RT-PCR detection method, which is to target specific markers on BA.1 (the insertion of three amino acids of EPE at the 214 site of the spike protein) and Delta-specific markers (the amino acids at the 157/158 site of the spike protein). A total of 13,097 samples collected from 200 cities in 22 African countries from mid-2021 to early 2022 were included in the study. These samples were from laboratory-confirmed patients with COVID-19 .
As early as August 2021, the ancestral strain of BA.1 appeared in West Africa .
. Based on the BA.1 specific marker used in this study, the research team first systematically searched 6 million sequencing results in GISAID (Global Coronavirus Data Sharing Website), ruled out the possibility that the potential ancestors of BA.1 exist outside Africa. Although BA.1 cases were first detected in South Africa and Botswana , the earliest BA.1-specific PCR signal was detected in this study, 25 patients who were sampled from 6 different West and East African countries ( Mali , Benin , Kenya , Uganda , Ghana and Niger ) from August to September 2021.
researchers also sequenced the viral genomes of 670 samples, making it possible to detect new mutations and identify new viral lineages, with the highest similarity from the Benin Republic of West Africa with Omickron BA.1. The researchers then conducted a complete analysis of SARS-CoV-2 genome characteristics on 247 patient samples from Benin and 424 patient samples from South Africa. Phylogenetic analysis results show that five PCR-positive samples collected from Benin from August 22 to October 27, 2021 (called Ben-1 ~ Ben-5) belonged to the ancestors of Omickron BA.1. The proximal ancestors Ben-4 and Ben-5 contained 67.7% and 75.0% of BA.1-specific mutations, respectively, and had 38.3% to 66.7% of BA.1-specific mutations compared with the distal ancestor (Ben-1-Ben-3). The result of supports that BA.1 originated in West Africa and gradually spread to southern Africa . Interestingly, these viruses that are highly similar to BA.1 also differ greatly from each other. The main leader of this study, Professor Jan Felix Drexler from the Institute of Virology at Charité University, Berlin, explained: " Our data show that Omickron has different ancestors, they interact and spread in Africa, sometimes simultaneously for several months ." This suggests that the BA.1 Omickron variant strain was gradually evolved during which the virus gradually adapted to existing human immunity.
Summary and Outlook
This study shows that Omickron's ancestors have long existed in patients across Africa, and thus have extensive evolution, so that when South Africa first reported Omickron, the whole world was shocked by so many mutation sites of Omickron. This also warns us that we need to establish shared monitoring mechanisms globally to detect threats early and take effective interventions.
