bootstrap support (Figure 3). However, most of the Peruvian VEEV isolates from the Iquitos region grouped into the ID Panama/Peru genotype and were obtained from humans, rodents, and mosquitoes. The VEE complex subtype IIIC strain, first isolated in 1971 from mosquitoes collected near Iquitos (12,13), was isolated again in 2002 from a sentinel hamster in the Amazon region. Several other isolates from mosquitoes, humans, and rodents also grouped into subtype III (88% bootstrap support) but were quite distinct from the subtype IIIC isolates (18% nucleotide sequence, 8% amino acid sequence divergence in the PE2 protein genes). These lev- els of divergence are equal to or greater than those of other VEE complex antigenic subtypes, so we propose the des- ignation of subtype IIID for these strains. To further document these relationships within subtype III and to investigate possible recombination, phylogenet- ic trees on the basis of the nsP1 gene were also construct- ed. The nsP1 trees did not show any evidence of recombination and also supported the sister-group relation- ship between subtype IIIC and the related IIID isolates (data not shown). To further genetically characterize this new subtype III strains, trees based on the complete 26S structural gene sequences were generated. All trees, including the neighbor-joining tree shown in Figure 4, confirmed the close relationship between the IIIC and IIID subtypes, as well as their level of divergence. Antigenic Characterization of Proposed Subtype IIID To characterize antigenically the putative new VEEV subtype IIID, PRNTs were performed to determine the antigenic relationships among the subtype III viruses (Table 4). Mucambo virus (subtype IIIA) versus Tonate virus (subtype IIIB) showed a fourfold difference in only one direction, which, based on the traditional serologic classification criteria (26), indicates that these are virus subtypes. When subtype IIIC was compared with the IIIA and IIIB subtypes, a fourfold or greater difference was observed in both directions, indicating that IIIC is a differ- ent virus. However, only a twofold difference existed in endpoint titers between subtype IIIC and the new IIID, which indicated that they are not distinct subtypes accord- ing to traditional antigenic criteria (28). Discussion VEEV is considered an emerging human pathogen in Latin America because a resurgence of VEE disease has occurred in Mexico and South America during the past decade (8). Our results indicate that VEEV is also endem- ic in Peru, with cases occurring regularly in the Iquitos area from 1993 through 2002. Analysis of a larger number of VEEV isolates allowed us to generate a more accurate and complete description of VEE complex circulating in Endemic Venezuelan Equine Encephalitis in Northern Peru Figure 3. Phylogenetic tree of the Venezuelan equine encephalitis virus (VEEV) complex derived from partial PE2 gene sequences of Peruvian VEEV isolates and homologous sequences published previously, using the neighbor joining program implemented in PAUP 4.0 (22). The tree was rooted using an outgroup comprised of four major lineages of Eastern Equine Encephalitis virus (26). Virus strains are labeled by VEE complex subtype, abbreviated country (FL=Florida, USA) and year of isolation, followed by strain designation. Numbers indicate bootstrap values for clades to the right. the Amazon Basin of Peru than was possible previously (9). Most human isolates belong to subtype ID, and phylo- genetic analyses distinguish two distinct ID genotypes: the Colombia/Venezuela genotype, which is currently circulat- ing in Peru, contrary to previous suggestions (9), and the Panama/Peru genotype, which represents most human iso- lates. Several hypotheses explain the apparently higher rate of human infection in the Iquitos area by the ID Panama/Peru genotype: 1) viruses from the Colombia/Venezuela genotype are not transmitted effi- ciently to humans compared to those in the Panama-Peru genotype; 2) the Panama/Peru genotype circulates at high- er levels in urban areas such as Iquitos, resulting in more infections; 3) the Panama/Peru genotype causes more severe disease, with more patients visiting clinics and par- ticipating in the NMRCD febrile illness study, resulting in more virus isolations and; 4) the Panama/Peru genotype produces higher titer human viremia, resulting in more human isolates. Further ecologic, epidemiologic, and ento- mologic studies are needed to test these hypotheses. The mosquito vector(s) that transmit VEEV to humans in Peru are unknown. VEEV has been isolated from Culex (Melanoconion) spp. mosquitoes in Peru, known vectors Emerging Infectious Diseases • www.cdc.gov/eid • Vol. 10, No. 5, May 2004 885