LOCUS       HPVCP141      455 bp ds-DNA             VRL       16-OCT-1994
DEFINITION  Human papillomavirus, isolate CP141, partial L1 cds, My09/My11
            region.
ACCESSION   U12476
SOURCE      Human papillomavirus DNA  derived from a cytologically normal
            cervical sample from a Hispanic woman, 20 years of age, isolate
            CP141.
  ORGANISM  Human papillomavirus
            Viridae; ds-DNA nonenveloped viruses; Papovaviridae;
            Papillomavirus.
REFERENCE   1  (bases 1 to 455)
  AUTHORS   Peyton,C.L. and Wheeler,C.M.
  TITLE     Identification of five novel human papillomaviruses in the New
            Mexico triethnic population
  JOURNAL   J. Infect. Dis. (1994) In press
  STANDARD  full staff_review
COMMENT     Data kindly provided prior to publication by Dr. C. Wheeler,
            University of New Mexico, School of Medicine, New Mexico
            Tumor Registry, 900 Camino del Salad NE, Albuquerque, NM, 
            87131-5306.

            Five novel HPV sequences were identified in a study in which 
            3655 cervical specimens were screened against known genital 
            HPV DNA [1].  The specimens were obtained from clinical 
            investigations conducted at the University of New Mexico.  
            The study subjects included Native Indians, Hispanics, and 
            non-Hispanic whites.  CP141 was derived from a cytologically normal
            cervical sample from a Hispanic woman, 20 years of age.  The viral
            DNA was PCR amplified using the L1 consensus primer MY09/MY11 pair, 
            which can hybridize to a broad spectrum of HPV types.  Resultant 
            fragments range from 449 to 458 nucleotides in length.  The 
            amplification products were initially screened against 2 sets of 
            type-specific probes and a generic probe.  If hybridization to the 
            generic probe and not to the type-specific probes ocurred, the 
            samples were further analyzed by restriction fragment length 
            polymorphisms.  RFLP patterns which did not match reference patterns
            were considered to be derived from novel HPVs.  The five novel 
            samples which were were identified in this study include CP8304,
            CP6108, CP8061, CP141, CP4173.   Peyton et al. also identified 
            two HPV45 subtypes and one HPV56 subtype.  They conclude that 
            since the existence of subtypes appears to be relatively rare, 
            it suggests that HPV45 and HPV56 are more divergent than many 
            HPV types. It should be noted that CP141 (U12476) is almost 
            identical to LVX160 (U12486) and HPVL1AE1 (U01535) and that CP4173 
            (U12477) is almost identical to LVX100 (U12485).  Both LVX160 and 
            LVX100 were identified by Ong et al. in a 1994 study which examined 
            Amazonian Indian subjects (Ong et al., J. Infect. Dis., 1994, in 
            press).  Primer regions are annotated in the sequence; information
            in this region is not accurate due to primer degeneracy.
 
            In a subsequent study Bernard et al. evaluated ten novel genital
            HPV types, including the five identified in the Peyton et al. study,
            and other known genital types to determine phylogenetic 
            relationships.  They observed that the genital types CP6108, CP8304,
            CP4173 and CP8061 form a branch with HPV types 61 and 62.  
            This emergent minor branch is positioned between two others which 
            contain cutaneous types.  Bernard et al. speculate as to whether 
            other low-risk genital types have escaped detection because of 
            considerable sequence divergence from the common genital types 
            (Bernard et al., J. Infect. Dis., 1994, in press).

            Bernard et al. also assessed the linear correlation coefficients
            for the MY9/MY11 fragments against the rest of L1 (.851) and against
            the E6 gene (.888).  Since these values are close, the authors
            suggest that the evolutionary distance information obtained for the
            primer pair region should be comparable to that available from the
            other regions of the genome (Bernard et al., J. Infect. Dis., 1994,
            in press).

FEATURES             Location/Qualifiers
     CDS             <1..>455
                     /note="putative"
                     /product="major capsid protein"
                     /gene="L1"
                     /note="putative"
                     /codon_start=1
                     /translation="AQGTNNGICWHNQLFITVVDTTRSTNFTLSACTETAIPAVYSPT
                     KFKEYTRHVEEYDLQFIFQLCTITLTADVMAYIHTMNPAILDNWNIGVTPPPSASLVD
                     TYRYLQSAAIVCQKDAPTPEKKDPYDDLKFWNVDLKEKFSTELDQFPLG"
BASE COUNT      142 a     86 c     90 g    137 t
ORIGIN      
        1 gcccagggaa ctaataatgg catttgttgg cataaccagt tgtttattac tgtggtggac
       61 actacacgta gtactaattt tacattgtct gcctgcaccg aaacggccat acctgctgta
      121 tatagcccta caaagtttaa ggaatatact aggcatgtgg aggaatatga tttacaattt
      181 atatttcaat tgtgtactat cacattaact gcagacgtta tggcctacat ccatactatg
      241 aatcctgcaa ttttggacaa ttggaatata ggagttaccc ctccaccatc tgcaagcttg
      301 gtggacacgt ataggtattt acaatcagca gctatagtat gtcaaaagga tgctcctaca
      361 cctgaaaaaa aggatcccta tgacgattta aaattttgga atgttgattt aaaggaaaag
      421 tttagtacag aactagatca gtttcctctg ggacg