AIDS RESEARCH AND HUMAN RETROVIRUSES Volume 16, Number 13, 2000, pp. 1319–1324 Mary Ann Liebert, Inc. Sequence Note Presence of Diverse Human Immunodeficiency Virus Type 1 Viral Variants in Cameroon PETER N. FONJUNGO, 1 EITEL N. MPOUDI, 2 JUDITH N. TORIMIRO, 2 GEORGE A. ALEMNJI, 2 LAURA T. ENO, 2 JOHN N. NKENGASONG, 3 FENG GAO, 4 MARK RAYFIELD, 1 THOMAS M. FOLKS, 1 DANUTA PIENIAZEK, 1 and RENU B. LAL 1 ABSTRACT Phylogenetic analysis of the gp41 region of 123 HIV-1-seropositive specimens from Cameroon showed that 89 were subtype A (71% of these sequences were IbNg-like), 12 (10%) were subtype D, 11 (9%) were subtype G, 5 (4%; closely related to subtype F2) were subtype F, 1 was subtype H, 2 (1.6%) remained unclassifiable, while 3 were group O. Further analysis of the two unclassifiable specimens in gag p24 , pol prot , and env (C2V3 or gp41) showed that one (98CM19) was a complex mosaic between subtype A in p24 and subtype J prot, and unclassifiable in env (C2V3 or gp41). The second, 98CM63, clustered distinctly from all known subtypes in p24, prot, C2V3, or gp41. 98CM63 clustered with a specimen from Cyprus and these two geographically and epidemiologically unlinked specimens, with their distinct clustering pattern, may represent a new subcluster of subtype A. In conclusion, these findings confirm the high HIV-1 genetic variability and further suggest the continuous appearance of new viral strains in this population. 1319 INTRODUCTION H IV-1 ACCOUNTS FOR approximately 33 million infections worldwide, with more than 90% of these infections oc- curring among persons in Africa and Asia. 1 HIV-1 has been di- vided into three distinct major groups; M (major), O (outlier) and N (non-M, non-O). 2,3 HIV-1 group M has been further sub- divided into 11 subtypes (subtypes A–K) on the basis of phy- logenetic analysis of the env region, with each subtype being approximately equidistant from each other. 2,4,5 In contrast, group O, which is genetically divergent from group M, repre- sents less than 5% of infections worldwide and has been de- tected almost exclusively in West Central Africa. 6–8 Studies have provided evidence of distinct subtypes within group O viruses. 9,10 Further, HIV-1 group N infection has been identi- fied in only a handful of patients from Cameroon. 3 Further- more, a molecular epidemiological survey of African-born per- sons in the United States, as well as a limited survey carried out in Cameroon, did not identify any group N virus. 11,12 This suggests that infections due to group N virus are not resulting in a rapidly expanding epidemic such as observed with group M viruses. Cameroon is endemic for HIV-1, with all the major groups in cocirculation. Three epidemiological situations make Cameroon an appropriate area in which to study HIV-1 genetic diversity. First, Cameroon has an unusually high circulation of multiple HIV-1 groups and subtypes. 6–8 Second, HIV-1 groups O and N were originally reported from this region. 3,6,7 Third, the geo- graphic coincidence of the high HIV-1 prevalence and the pres- ence of chimpanzee subspecies Pan troglodytes troglodytes in this region, 13 including further implications for zoonotic trans- mission from such subspecies, suggest that Cameroon may be the focal point for emergence of these variants. With the contin- uous emergence of HIV-1 variants, it is important to study HIV- 1 HIV/AIDS and Retrovirology Branch, Division of AIDS, STD and TB Laboratory Research, National Center for Infectious Diseases, Cen- ters for Disease Control and Prevention, Atlanta, Georgia 30333. 2 Hopital Militaire de Yaoundé, Yaoundé, Cameroon. 3 Projet RETRO-CI, Abidjan, Ivory Coast and International Activity Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS/TB/STD, CDC, Atlanta, Georgia 30333. 4 Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294.