Cervical cancer is reported as the fourth most frequent cancer among women worldwide [
1]. Human papillomavirus (HPV) is considered as the etiological agent of cervical cancer. Although more than 40 HPV types can infect the anogenital tract, 14 HPV types, designated as the high-risk HPV types including 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 68 and 73, associate with progression to cervical cancer [
2‐
6]. Among high-risk HPV types, HPV 16 and 18 are leading cause and responsible for almost 72% of cervical cancer [
7]. Most studies on the prevalence of HPV types has indicated that HPV 16 and 18 are the most prevalent types in women with normal cervical cytology and invasive cervical cancer in Iran [
8‐
13]. A meta-analysis was revealed that the five most common HPV types are HPV 16, 18, 31, 39, and 45 in Iranian women with cervical cancer [
14]. Indeed, HPV 16, 18, 31, 39, and 45 are account for 52%, 14.1%, 5%, 3.3%. and 3.3% of cervical cancer, respectively [
14].
A distinct HPV type is considered when the DNA sequence of the L1 gene was differ from that of any other characterized type by at least 10%. Isolates of the same HPV type are designated to as lineage and sublineage when the nucleotide sequences of the L1 gene differ by less than 1–10% and 0.5–1%, respectively. Up to date, HPV 39 has two distinct lineages A and B; which lineage A include 2 different sublineages A1 and A2 [
15].
While the co-evolution of HPV 16 and HPV 18 variants and human populations is well characterized [
4,
16‐
19], the geographic associations for variants of other types remains to be inconclusive. To better understand of an association between the distinct variants of HPV 39 and ethnicity further studies are needed in the world.
The data with regards to the regional variants of distinct HPV types is of great value as it would provide a rational for future studies on their evolution, epidemiology, pathogenicity, and biology. Whereas the spreading of HPV types is identified in Iran, there is much less known about HPV variants. Previous studies were investigated the common HPV 16, 18, 31, and 45 variants in Iran [
19‐
21]. Regard to above-mentioned data that HPV 39 is one of the five most common HPV types in Iranian women with cervical cancer [
14], this study aimed to investigate the frequent HPV 39 variants circulating in Iran. According to this fact that E6 gene can only separate A and B lineages from each other, long control region (LCR) were analyzed to distinguish two distinctive sublineages A1 and A2.