Phylogeographic Analysis Of Humam Papillomavirus 58

Human papillomavirus 58(HPV58) is one of the high-risk types for anogenital cancer.Worldwide,HPV58 infection is not very common.Unusual high prevalence, however,has been reported in Southeast Asia,Western Africa,and some other areas. Nevertheless,due to the global scattered distribution of HPV58 data and lacking of data for some developing countries or regions with high HPV58 incidence(like the Mainland of China),so far,the global special geographical distribution of HPV58 has not yet been well explored by more comprehensive analysis.Genetic phylogeography is good method for analysis of virus's unique geographic diffusion by bioinformatic technique.It can avoid largely clinical tracing from the perspective of the virus's victim(women),whose infection has been identified by clinical tests.And it tracks the migration from the perspective of the virus alone using virus genetic sequences. Genetic phylogeograpy not only represents the "gold standard" in characterizing viral genealogy,transmission,and ancient spread,but also provides a powerful epidemiological tool to reveal the association of HPV 58 with cervical cancer.This method recently has been successfully used for the analysis of H5N1 virus.Mainland China is the high incidence area of HPV58,so it is particularly important to integrate the mainland of China into the global data system to conduct a comprehensive analysis of phylogeography.However,the existing sequence data of HPV58 coming from this place quite lack(GenBank included only two sequences,up to 2008.8). Therefore,in order to collect more primordial data and explore global phylogeograpy of HPV58 comprehensively,in this issue we collect more HPV-positive cervical cancer tissue in the Chinese mainland,type and sequencing,for expansion of the Mainland Chinese HPV58 sequence library;we merge the received HPV58 sequence data of Chinese Mainland into the existing global data;using some bioinformatic methods(the geography,the phylogeography,adaptive evolution,etc.),we integrate scattered data based on distinct genes of HPV58 and reconstruct HPV58 global evolution path;we explore characteristics of Mainland Chinese HPV58 variants and the important role of Mainland China in the global HPV58 migration process.The issue divided into the following four-part study.PartⅠ:HPV-E6 and L1 genes' compatibility and incorporation of typing potential Objective:To explore E6 gene's typing potential of Human papillomavirus,to confirm the compatibility and incorporation for data of E6 gene and L1 gene.Methods:We downloaded 158 isolates sequences in HPV16 phylogenic group (including seven types:HPV16,HPV31,HPV33,HPV35,HPV52,HPV58,HPV67) whose E6 region sequence are functional and complete(450bp) or nearly complete (≥385bp) from GenBank Database.We make phylogeny analysis of 158 sequences and HPV16 single based on E6 gene.Results:We found that E6 nucleotide sequence similarity within HPV16 group is higher than 90 percent,similar to L1 gene,with high homology;three phylogenic trees of HPV16 group respectively using three algorithms present similar topologic patterns,demonstrating excellent stability,in which various types of HPV can be very distinguished,(the boots strap value in each branch of trees reached 99 percent);the phylogenic analysis of HPV16 single also show similar to previous L1 gene analysis.Conclusions:E6 gene and L1 gene may be under the equalized pressure of evolution,both of them may be more conservative coding region;although the data of the two gene sequence is fragmented,independent,but the two gene carrying evolutional information may be phylogenetically compatible and can be combined together.PartⅡ:Detection and analysis of HPV58 sequence in some region of Chinese Mainland and phylogenic relationship analysisObjective:TO detect HPV58 sequence(E6 genes and gene L1) in mainland China and mutation of the sequence characteristics;to explore the HPV58 phylogenic relationship between Chinese mainland and the rest of the world.Methods:We collect human cervical cancer tissue embedded in paraffin in the Chinese mainland(1996 to 2007,Jiangsu Province,Sichuan Province,Shanghai city, etc.).After the DNA extraction,amplification,sequencing,and other steps,we detect E6 and L1 gene sequence in HPV58 positive samples.Then we make phylogenic analysis of HPV58-E6 and L1,based on merging sequence data obtained from test into GenBank's sequence.Results:We have detected five HPV58-E6 complete sequence(450 bp),two nearly complete sequence(435 bp,436bp) and seven HPV58-L1 nearly complete sequence(1124-1480 bp).From phylogenic analysis based on merging sequence data obtained from test into GenBank's sequence,we found that HPV58 sequences from mainland of China are more homologous with sequences from Hong Kong,China Xian,Japan,the Philippines and other Southeast Asian strains,and they are prone to gathered in the lower part of the tree.Conclusions:Mainland China and Southeast Asia may format the unique "transit point" of HPV58 strains dissemination after receiving variants from the "root" source. And Mainland China and Southeast Asia may play an important role in the spread and migration of HPV58 in the world,PartⅢ:Global phylogenic evolution and movement path of HPV58-E6 and L1Objective:To integrate Mainland China data into the global data in GenBank, reconstruct HPV58 global evolution path;to explore the important role of Mainland China in the global HPV58 spread and migration process.Methods:According to the two phylogenic trees of the HPV58-E6,L1,we matched the two trees through geographic mapping,and superimpose the information of tree on the markers in map of the world,marking one or more historic migration of HPV58 virus in a period,to reconstruct the global evolution path of HPV58.Results:We found that the two trees of E6 and L1 complementally reinforced each other;and migration path of E6 prompted the important relocated source of the Southeast Asia(Hong Kong,Xi'an of China);while migration path of L1 show clearly initial origin of Africa in migration path of the HPV58.Conclusions:Western Africa is probably the original source of ancient HPV58 variant,while Southeast Asia appears to be another new and important source;The unusual high prevalence in Africa and Southest Asia probably is extremely likely related to an earlier preoccupant existence(or introduction) of HPV58 variants,but also probably because the ancient variants(closer to "root") are usually more virulent.PartⅣ:adaptive evolution of HPV58 and the relationship between cervical cancer and HPV58Objective:To explore the causes for unique distribution of HPV58,and whether adaptive evolution of this virus exist;to discuss the relationship between HPV58 and cervical cancer.Methods:We calculate every variation of the incident(of sequence variation between February 2) dn/ ds ratio(that is,non-synonymous with the replacement rate of occurrence than the alternative synonymous),using self-development software; Then,we integrate HPV58's migration path into the 2005 WHO statistic map of global distribution of cervical cancer incidence and make contrast.Results:For HPV58-E6 and L1 gene,we respectively detected dn/ds＞1 in seven and eight migration events,where adaptive evolution probably exist.When HPV58 invaded Southest Asia from West Africa,within the region of Southest Asia itself,and then when variants "transit" into Latin America from South Asian,variants turned to make adaptive evolution obviously.Africa,India and Mongolia of Asia, Southeast Asian island,and Latin America suffer severer cervical cancer burden all over the world.These distribution of cervical carcinoma surprisingly coincide with successive migration of HPV58 variants "Africa→Southest Asia→Europe,North America".Conclusions:The phenomenon of adaptive evolution possibly exists in variants scattered in distinct ethnic groups and geographic environment,causing the differences in prevalence HPV58;Migration and involution of HPV58's variants may be related to the global prevalence and spread of cervical cancer,both of which may be closely associated.In summary,Mainland China and Southeast Asia may play an important role in the spread and migration of HPV58 in the world,which may format the unique "transit point" of strains dissemination;Beyond our previous concept,HPV58 variants significantly play an important role in the global spread of cervical carcinoma. HPV58 is conceivably a leading type associated to cervical carcinoma risk,like HPV16,HPV18.