In-depth investigation of the point mutation pattern of HIV-1

Nan Sun; Stephen S-T Yau

doi:10.3389/fcimb.2022.1033481

In-depth investigation of the point mutation pattern of HIV-1

Front Cell Infect Microbiol. 2022 Nov 15:12:1033481. doi: 10.3389/fcimb.2022.1033481. eCollection 2022.

Authors

Nan Sun¹, Stephen S-T Yau^{1

2}

Affiliations

¹ Department of Mathematical Sciences, Tsinghua University, Beijing, China.
² Yanqi Lake Beijing Institute of Mathematical Sciences and Applications, Beijing, China.

Abstract

Mutations may produce highly transmissible and damaging HIV variants, which increase the genetic diversity, and pose a challenge to develop vaccines. Therefore, it is of great significance to understand how mutations drive the virulence of HIV. Based on the 11897 reliable genomes of HIV-1 retrieved from HIV sequence Database, we analyze the 12 types of point mutation (A>C, A>G, A>T, C>A, C>G, C>T, G>A, G>C, G>T, T>A, T>C, T>G) from multiple statistical perspectives for the first time. The global/geographical location/subtype/k-mer analysis results report that A>G, G>A, C>T and T>C account for nearly 64% among all SNPs, which suggest that APOBEC-editing and ADAR-editing may play an important role in HIV-1 infectivity. Time analysis shows that most genomes with abnormal mutation numbers comes from African countries. Finally, we use natural vector method to check the k-mer distribution changing patterns in the genome, and find that there is an important substitution pattern between nucleotides A and G, and 2-mer CG may have a significant impact on viral infectivity. This paper provides an insight into the single mutation of HIV-1 by using the latest data in the HIV sequence Database.

Keywords: HIV; SNP; mutation; natural vector; nucleotide distribution.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Databases, Nucleic Acid
HIV-1* / genetics
Mutation
Mutation, Missense
Point Mutation