ID   HPVCP141	STANDARD;	ds-DNA;	VRL;	455 bp.
XX
DE   Human papillomavirus, isolate CP141, partial L1 cds, My09/My11 region. 
XX
AC   U12476
XX
DT   16-OCT-1994
XX
OS   Human papillomavirus DNA  derived from a cytologically normal cervical 
OS   sample from a Hispanic woman, 20 years of age, isolate CP141. 
OC   Human papillomavirus;Viridae; ds-DNA nonenveloped viruses; 
OC   Papovaviridae;Papillomavirus.
XX
RN   [1]
RP   1 - 455
RA   Peyton,C.L. and Wheeler,C.M;
RT   "Identification of five novel human papillomaviruses in the New Mexico 
RT   triethnic population;"
RL   J. Infect. Dis. (1994) In press.
XX
XX   Created by HPV database on 21-APR-1995 from GenBank: U12476.
XX
XX   Data kindly provided prior to publication by Dr. C. Wheeler,
XX   University of New Mexico, School of Medicine, New Mexico
XX   Tumor Registry, 900 Camino del Salad NE, Albuquerque, NM, 
XX   87131-5306.
XX
XX   Five novel HPV sequences were identified in a study in which 
XX   3655 cervical specimens were screened against known genital 
XX   HPV DNA [1].  The specimens were obtained from clinical 
XX   investigations conducted at the University of New Mexico.  
XX   The study subjects included Native Indians, Hispanics, and 
XX   non-Hispanic whites.  CP141 was derived from a cytologically normal
XX   cervical sample from a Hispanic woman, 20 years of age.  The viral
XX   DNA was PCR amplified using the L1 consensus primer MY09/MY11 pair, 
XX   which can hybridize to a broad spectrum of HPV types.  Resultant 
XX   fragments range from 449 to 458 nucleotides in length.  The 
XX   amplification products were initially screened against 2 sets of 
XX   type-specific probes and a generic probe.  If hybridization to the 
XX   generic probe and not to the type-specific probes ocurred, the 
XX   samples were further analyzed by restriction fragment length 
XX   polymorphisms.  RFLP patterns which did not match reference patterns
XX   were considered to be derived from novel HPVs.  The five novel 
XX   samples which were were identified in this study include CP8304,
XX   CP6108, CP8061, CP141, CP4173.   Peyton et al. also identified 
XX   two HPV45 subtypes and one HPV56 subtype.  They conclude that 
XX   since the existence of subtypes appears to be relatively rare, 
XX   it suggests that HPV45 and HPV56 are more divergent than many 
XX   HPV types. It should be noted that CP141 (U12476) is almost 
XX   identical to LVX160 (U12486) and HPVL1AE1 (U01535) and that CP4173 
XX   (U12477) is almost identical to LVX100 (U12485).  Both LVX160 and 
XX   LVX100 were identified by Ong et al. in a 1994 study which examined 
XX   Amazonian Indian subjects (Ong et al., J. Infect. Dis., 1994, in 
XX   press).  Primer regions are annotated in the sequence; information
XX   in this region is not accurate due to primer degeneracy.
XX   
XX   In a subsequent study Bernard et al. evaluated ten novel genital
XX   HPV types, including the five identified in the Peyton et al. study,
XX   and other known genital types to determine phylogenetic 
XX   relationships.  They observed that the genital types CP6108, CP8304,
XX   CP4173 and CP8061 form a branch with HPV types 61 and 62.  
XX   This emergent minor branch is positioned between two others which 
XX   contain cutaneous types.  Bernard et al. speculate as to whether 
XX   other low-risk genital types have escaped detection because of 
XX   considerable sequence divergence from the common genital types 
XX   (Bernard et al., J. Infect. Dis., 1994, in press).
XX
XX   Bernard et al. also assessed the linear correlation coefficients
XX   for the MY9/MY11 fragments against the rest of L1 (.851) and against
XX   the E6 gene (.888).  Since these values are close, the authors
XX   suggest that the evolutionary distance information obtained for the
XX   primer pair region should be comparable to that available from the
XX   other regions of the genome (Bernard et al., J. Infect. Dis., 1994,
XX   in press).
XX
XX
FT  KEY              Location/Qualifiers
FT   CDS             <1..>455
FT                   /note="putative"
FT                   /product="major capsid protein"
FT                   /gene="L1"
FT                   /note="putative"
FT                   /codon_start=1
XX
SQ   SEQUENCE  455 bp;  142 a;  86 c;  90 g;  137 t;
     gcccagggaa ctaataatgg catttgttgg cataaccagt tgtttattac tgtggtggac        60
     actacacgta gtactaattt tacattgtct gcctgcaccg aaacggccat acctgctgta       120
     tatagcccta caaagtttaa ggaatatact aggcatgtgg aggaatatga tttacaattt       180
     atatttcaat tgtgtactat cacattaact gcagacgtta tggcctacat ccatactatg       240
     aatcctgcaa ttttggacaa ttggaatata ggagttaccc ctccaccatc tgcaagcttg       300
     gtggacacgt ataggtattt acaatcagca gctatagtat gtcaaaagga tgctcctaca       360
     cctgaaaaaa aggatcccta tgacgattta aaattttgga atgttgattt aaaggaaaag       420
     tttagtacag aactagatca gtttcctctg ggacg                                  455