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Background  Cervical cancer is associated with infection by certain subtypes of human papillomavirus (HPV). The  L1  protein comprising HPV vaccine formulations elicits high-titre neutralizing antibodies and confers protection against specific HPV subtypes. HPV  L2  protein is an attractive candidate for cross-protective vaccines. HPV-33 and HPV-58 are very prevalent among Chinese women.    Methods  To study the gene intratypic variations and polymorphisms of HPV-33 and HPV-58  L1/L2  in Sichuan China, HPV-33 and HPV-58  L1  and  L2  genes were sequenced and compared with other genes submitted to GenBank. Phylogenetic trees were constructed by maximum-likelihood and the Kimura 2-parameters methods (MEGA 6). The secondary structure was analyzed by PSIPred software, and HPV-33 and HPV-58 L1 homology models were created by SWISS-MODEL software. The selection pressures acting on the  L1/L2  genes were estimated by PAML 4.8.    Results  Among 124 HPV-33  L1  sequences 20 single nucleotide mutations were observed included 8/20 non-synonymous and 12/20 synonymous mutations. The 101 HPV-33  L2  sequences included 12 single nucleotide mutations comprising 7/12 non-synonymous and 5/12 synonymous mutations. The 223 HPV-58  L1  sequences included 32 single nucleotide mutations comprising 9/32 non-synonymous and 23/32 synonymous mutations. The 201 HPV-58  L2  sequences comprised 26 single nucleotide mutations including 9/26 non-synonymous and 17/26 synonymous mutations. Selective pressure analysis showed that most of the common non-synonymous mutations showed a positive selection. HPV-33 and HPV-58  L2  were more stable than HPV-33 and HPV-58  L1 .    Conclusions  HPV-33 and HPV-58  L2  were better candidates as clinical diagnostic targets compared with HPV-33 and HPV-58  L1 . Clinical diagnostic probes and second-generation polyvalent vaccines should be designed on the basis of the unique sequence of HPV-33 and 58  L1/L2  variations in Sichuan, to improve the accuracy of clinical detection and the protective efficiency of vaccines.    Electronic supplementary material  The online version of this article (doi:10.1186/s12985-016-0629-9) contains supplementary material, which is available to authorized users.

L1 and L2 gene polymorphisms in HPV-58 and HPV-33: implications for vaccine design and diagnosis