ID   HPVCP8304	STANDARD;	ds-DNA;	VRL;	4 bp.
XX
DE   Human papillomavirus, isolate CP8304, partial L1 cds, My09/My11 region. 
XX
AC   U12480
XX
DT   16-OCT-1994
XX
OS   Human papillomavirus, isolate CP8304. 
OC   Human papillomavirus;Viridae; ds-DNA nonenveloped viruses; 
OC   Papovaviridae;Papillomavirus.
XX
RN   [1]
RP   1 - 452
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: U12480.
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.  The viral DNA was PCR amplified using the 
XX   L1 consensus primer MY09/MY11 pair, which can hybridize to a 
XX   broad spectrum of HPV types.  Resultant fragments range from 
XX   449 to 458 nucleotides in length.  The amplification products 
XX   were initially screened against 2 sets of type-specific probes 
XX   and a generic probe.  If hybridization to the generic probe 
XX   and not to the type-specific probes ocurred, the samples were 
XX   further analyzed by restriction fragment length polymorphisms.
XX   RFLP patterns which did not match reference patterns were 
XX   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..>452
FT                   /note="putative"
FT                   /product="major capsid protein"
FT                   /gene="L1"
FT                   /note="putative"
FT                   /codon_start=1
XX
SQ   SEQUENCE  4 bp;  125 a;  93 c;  95 g;  139 t;
     gcacagggac ataataatgg tatttgttgg tttaatgaaa tgtttgttac agtggtggat        60
     actaccagaa gcaccaattt tactatttgc acagctacat ctgctgctgc agaatacaag       120
     gcctctaact ttaaggaatt tctgcgccat acagaggaat atgatttgca gtttattttc       180
     caattatgta aaatacagtt aacaccagaa attatggcct acttacataa tatgaacaag       240
     gcactgttgg atgattggaa ttttggtgtg ttgccacctc cttccaccag tttagatgac       300
     acatatcgct ttttacagtc tcgggccatt acctgtcaaa agggtgctgc tgcccctgcg       360
     cccaaagagg acccttatgc cgacatgtca ttttggacag ttgaccttaa ggacaagttg       420
     tctactgatt tggatcagta tcctctggga cg                                     452