Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases during the Pandemic

摘要: ABSTRACT Since the identification of SARS-CoV-2, a large number genomes have been sequenced with unprecedented speed around world. This marks unique opportunity to analyze virus spreading and evolution in worldwide context. Currently, there is not useful haplotype description help track important globally scattered mutations. Also, differences between countries and/or months make it difficult identify emergence haplotypes regions where few are but cases reported. We propose an approach based on normalization by COVID-19 relative frequencies mutations using all available data major haplotypes. Furthermore, we can use similar tracking temporal geographic distribution Using 171 461 genomes, five (OTUs) nine high-frequency OTU_3 characterized R203K G204R currently most frequent circulating four six continents analyzed. On other hand, during almost analyzed, OTU_5 mutation T85I nsp2 North America. Recently (since September), OTU_2 has established as Europe. OTU_1, ancestor near extinction showed its low isolations since May. analyzed whether age, gender, or patient status more related specific OTU. did find OTU’s preference for any age group, status. Finally, discuss structural functional hypotheses frequently identified mutations, none those show clear effect transmissibility pathogenicity.