Characterization of major capsid protein (L1) variants of Human papillomavirus type 16 by cervical neoplastic status in Indian women: Phylogenetic and functional analysis

Abstract

The etiological role of infection with Human papillomavirus type 16 (HPV16) in cervical cancer is well established. HPV16 variants, classified based on less than 10% nucleotide variations in the major capsid (L1 ORF) are known to contribute to persistent infection leading to cancer development. L1 protein forms the cornerstone of HPV structure and antigenicity. In the present study, HPV16 L1 variants were characterized by cervical lesion grade and variations in sequences were correlated to structure and function. The L1 gene was analyzed in 152 HPV16 positive cervical samples obtained from Indian women using polymerase chain reaction‐directed sequencing. Phylogenetic analysis was carried out for lineage typing. Sixty‐one SNPs were detected in L1 genes resulting in 20 nonsynonymous amino acid substitutions of which N56T, N92T, L158F, V178G, N181I, K236T, K443Q, K454T, and K475R are reported in Indian isolates for the first time. The substitutions N181T, T353P, and T389S were significantly associated with high‐grade cervical disease. The predominance of lineage A (A1‐A4, 84.96%) was observed among the isolates, while the D3 sublineage showed significant association with high‐grade cervical lesions. No evidence for recombination and the positive selection was obtained. These substitutions, when mapped on three‐dimensional structure, revealed that 11 and 4 substitutions are part of experimentally validated B‐ and T‐cell epitopes, of which T266A and N285T were common to both types of epitopes and may impact HPV vaccine efficacy. The variants identified through this study have the potential to serve as translational leads for designing diagnostic probes and vaccines.

Genetic diversity in L1 ORF of human papillomavirus in women with cervical cancer with and without human immunodeficiency virus in Botswana and Kenya

“…Changes in the L1 region of the HPV genome may be important for discriminating the infectious potential of different variants, as well as in defining epitopes relevant to vaccine design. Some previous studies investigating HPV-16 full-length sequences in cervical specimens have shown that the contiguous deletions identified to be highly associated with cancer are suggestive of a pattern of HPV integration [ 30 – 37 ]. The findings of this study indicate that there could be variants of HPV circulating within sub-Saharan Africa.…”

Genetic variations in the long control region of human papillomavirus type 16 isolates from India: implications for cervical carcinogenesis

“…Phylogenetic analysis of 171 sequences was carried out to identify the clustering pattern using both the alignment-based maximum likelihood (ML) method implemented in the IQTREE [24] server (http://iqtree.cibiv.univie.ac.at/) for 1000 bootstrap runs and the return time distribution (RTD) (http://bioinfo.unipune.ac.in/RTD/home.htm) based alignment-free method developed in-house [25]. Lineage and sub-lineage assignment of isolates was carried out based on the L1 gene as described previously [17], and these were assigned to the LCR sequences of the respective isolates. Phylogenetic trees were visualized using the iTOL server (https://itol.embl.de/) [26].…”

“…These variants exhibit differential risks of persistence and progression to cervical pre-cancer/cancer [12–16]. The lineage distribution of HPV16 variants from the Indian population was reported on the basis of the L1 gene by our group [17].…”

Heparan Sulfate and Sialic Acid in Viral Attachment: Two Sides of the Same Coin?

“…The capsid of HPVs is mainly composed of the L1 protein, which can be recognized by several receptors and confers alternative pathways for cell entry [ 103 ]. Although there is no mandatory receptor for HPV entry, host heparan sulfates are essential factors that provide the microenvironment necessary for the initial attachment of virions, either by direct binding to the cell surface through syndecan-1 or by transient binding to laminin-5 of the extracellular matrix.…”