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Microbes & Immunity Phylogenetic analysis of HPV16 L1 in Asia

Table 3. Presence inter-sequence variabilities of L1 protein retained their original lysine (K) composition. Thus, it can
sequences be concluded that lysine is conserved at these essential
positions, emphasizing their functional importance.
Residues
Accession 76 79 127 153 209 4. Discussion
QOI17574 P P D D N This study analyzed the L1 sequences of HPV-16, focusing
QOI17579 P P D D N on the major capsid protein at both the protein and nucleic
WKC12512 P P D D N acid levels. Sequences were sourced from a public database
QQL88061 P P N* N* N covering the period following the approval of HPV vaccines
AYV61481 P P D D N in Asia. The primary objective was to investigate sequence
QEG53826 P P D D N variations and assess their potential implications for viral
UNF16173 P P D D N entry mechanisms and host interactions, particularly in
binding with heparan sulfate.
UNF16181 P P D D N
BDO24711 P P D D T The phylogenetic analysis revealed that sequences
BEU33838 P P D D T in Figure 2C, uploaded from Japan between 2020 and
2022, exhibited close relationships, suggesting a potential
BEU33854 P P D D T common infectious source or a shared evolutionary
BEU33862 P P D D T lineage. These findings are supported by the clustering of
BEU33878 T* S* D D N sequences with phylogenetic similarities. However, this
BDO24681 P P D D N hypothesis is limited by the geographic expansion of isolates
BDO24695 P P D D N and the lack of detailed metadata on the individuals from
BDO24703 P P D D N whom the isolates were collected. Therefore, while these
BDO24719 P P D D T observations suggest a shared evolutionary trajectory;
further, validation through epidemiological and molecular
BDO24727 P P D D N studies is required.
BDO24735 P P D D N
Analysis of residue variability provided additional
BDO24743 P P D D N insights. Substitutions from proline to threonine or serine,
BEU33886 P P D D T* observed in specific sequences, were found to retain the
BEU33894 P P D D N hydrophilic properties of the R groups, as indicated by
Notes: In this table, protein sequences are compared, and amino acids their Kyte and Doolittle hydropathy indices (−1.6 for
are represented with one-letter codes. *Indicates residues that are proline, −0.7 for threonine, and −0.6 for serine). Despite
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detected in terms of their differences compared to the majority: 75, 77, the negative substitution scores in the BLOSUM62
127, 153, and 209.
matrix (−1), which suggest these changes are less likely
No amino acid substitutions were detected in the NLS to occur during evolutionary events, their presence
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region located at the C-terminus of the L1 protein sequence. indicates potential structural or functional adaptations.
This region, comprising approximately 22 amino acids, is Conversely, the substitution of aspartic acid to asparagine,
critical for recruiting karyopherin, which facilitates the with a positive BLOSUM62 score (+1), was more common
entry of the viral genome into the host cell. 26,27 and expected. This substitution maintained identical
hydropathy indices of −3.5, preserving the hydrophilic
To further elucidate amino acid variability, the L1 nature of the residues. 25,29
protein sequence was thoroughly compared with the
HPV16 reference sequence available on NCBI (NCBI The substitution from asparagine to threonine at position
Reference Sequence: NP_041332.2). Particular attention 209, observed in five isolates (accessions BDO24711,
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was given to amino acid residues at positions 54, 278, 356, BEU33838, BEU33838, BEU33862, and BDO24719),
further highlighted evolutionary dynamics. Although this
and 361, which play pivotal roles in attachment initiation. substitution is neutral in the BLOSUM62 matrix (score =
Except for 361K, these residues are located within hyper- 0), the significant difference in hydropathy indices (−3.5
variable loops as highlighted in the introduction: 54K in for asparagine and −0.7 for threonine) suggests a potential
the BC loop, 278K in the FG loop, and 356K in the HI functional impact on protein interactions or stability. While
loop. 14
both residues are hydrophilic, the reduced hydrophilicity of
Alignment analysis of the reference sequence revealed threonine may influence its interaction with surrounding
that the critical residues at positions 278, 356, and 361 molecules or the overall capsid structure.

Volume 2 Issue 2 (2025) 61 doi: 10.36922/mi.8410