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

Author(s)

Justo Arevalo, Santiago ^{[1, 2]} ; Zapata Sifuentes, Daniela ^[2] ; Huallpa, Cesar J. ^[3] ; Landa Bianchi, Gianfranco ^[2] ; Castillo Chavez, Adriana ^[2] ; Garavito-Salini Casas, Romina ^[2] ; Uceda-Campos, Guillermo ^[4] ; Pineda Chavarria, Roberto ^[2]

Affiliation

^[1] Univ Sao Paulo, Inst Chem, Dept Biochem, Sao Paulo - Brazil

^[2] Univ Ricardo Palma, Fac Ciencias Biol, Lima - Peru

^[3] Univ Nacl Agr Molina, Fac Ciencias, Lima - Peru

^[4] Univ Nacl Pedro Ruiz Gallo, Fac Ciencias Biol, Lambayeque - Peru

• Document type: Journal article
• Source: FRONTIERS IN MICROBIOLOGY; v. 12, FEB 17 2021.
• Web of Science Citations: 3

Abstract

Since the identification of SARS-CoV-2, a large number of genomes have been sequenced with unprecedented speed around the world. This marks a unique opportunity to analyze virus spreading and evolution in a worldwide context. Currently, there is not a useful haplotype description to help to track important and globally scattered mutations. Also, differences in the number of sequenced genomes between countries and/or months make it difficult to identify the emergence of haplotypes in regions where few genomes are sequenced but a large number of cases are reported. We propose an approach based on the normalization by COVID-19 cases of relative frequencies of mutations using all the available data to identify major haplotypes. Furthermore, we can use a similar normalization approach to tracking the temporal and geographic distribution of haplotypes in the world. Using 171,461 genomes, we identify five major haplotypes or operational taxonomic units (OTUs) based on nine high-frequency mutations. OTU\_3 characterized by mutations R203K and G204R is currently the most frequent haplotype circulating in four of the six continents analyzed (South America, North America, Europe, Asia, Africa, and Oceania). On the other hand, during almost all months analyzed, OTU\_5 characterized by the mutation T85I in nsp2 is the most frequent in North America. Recently (since September), OTU\_2 has been established as the most frequent in Europe. OTU\_1, the ancestor haplotype, is near to extinction showed by its low number of isolations since May. Also, we analyzed whether age, gender, or patient status is more related to a specific OTU. We did not find OTU's preference for any age group, gender, or patient status. Finally, we discuss structural and functional hypotheses in the most frequently identified mutations, none of those mutations show a clear effect on the transmissibility or pathogenicity. (AU)

• FAPESP's process: 15/13318-4 - Structural engineering of the active site of diguanylate cyclase (GGDEF) domains to produce new second messengers
• Grantee: Santiago Justo Arevalo
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)