The Philippines is generally believed to have been established by various peoples who migrated from neighboring areas. To gain new insights into the peopling of the Philippines, we used the JC virus (JCV) genotyping approach. We collected about 50 urine samples on each of two representative islands of the Philippines, Luzon and Cebu. DNA was extracted from the urine samples and used to amplify the 610-bp region (IG region) of the viral genome. For each island, we determined about 20 IG sequences, from which a neighbor-joining phylogenetic tree was constructed to classify the JCV isolates detected into distinct genotypes. The predominant genotype detected was SC, the Southeast Asian genotype. Minor JCV genotypes were SC/Phi, B1-a, and B3. SC/Phi was a subcluster of SC and has not been detected in areas other than the Philippines. B1-a was detected previously in mainland China, Pamalican Island (Palawan, Philippines), and Taiwan (an aboriginal tribe). B3 was classified in this study into two subgroups, one (B3-a) containing three Luzon isolates and several Chinese, Thai, and Uzbek isolates, the other (B3-b) containing two Luzon, one Cebu, and one Indonesian isolate. These findings suggest that the modern Filipino population was formed not only by Southeast Asians carrying SC but also by a few distinct ethnic groups carrying SC/Phi, B1-a, and B3-a or -b.

JC virus (JCV) genotyping is a novel method of tracing human migrations.

No abstract

JC virus (JCV) is ubiquitous in the human population, usually being transmitted from parents to children during cohabitation. JCV genotyping is a useful means of elucidating the origins of various ethnic groups in the world. We used this method to gain insights into the origin of the Mamanwa, a Philippine Negrito tribe in Northeast Mindanao. We found that the Mamanwa carried two major JCV genotypes, B3-b/2E and SC-f/7A. This was in contrast with the JCV genotype profile of modern Filipinos who carry up to five genotypes, with B3-b/2E showing only a low frequency. B3-b/ 2E is spread throughout Oceania but rare on the Asian continent. In contrast, SC-f/7A is spread throughout Southeast Asia (including neighboring Oceanic islands) but rare in Remote Oceania. The present findings thus suggest that the Mamanwa tribe was formed by early colonization by people carrying B3-b/2E followed by an admixture of more recent immigrants carrying SC-f/7A. As the indigenous tribe (the Chamorro) in the Mariana Islands has essentially the same JCV genotype profile as the Mamanwa, other indigenous tribes in Southeast Asian and Oceanic islands may have a population history analogous to that suggested for the Mamanwa.

An A --> G single nucleotide polymorphism (SNP) at nucleotide 153,104 in the retinoblastoma susceptibility locus (RB1) at 13q14 was previously reported to be present only in Asians. In this study, we determined the distribution of this SNP in normal Southeast Asian populations (Chinese, Malay, Javanese, Thai, Filipino), in South Asian populations (Bangladeshi, Pakistani Pushtun and Indian) and in Chinese retinoblastoma cases and control subjects. The RB1 SNP was present in all populations at an overall frequency of =/< 0.18. Heterozygosity was higher in the Southeast Asian groups (0.14-0.34) than in the South Asian groups (Bangladeshi and Indian) (0.04-0.06). Significant differences in allele frequencies were found between the two population groups. Interestingly, our Pakistani population comprised of ethnic Pushtuns from northwest Pakistan was significantly different from the neighbouring Bangladeshi and Indian populations. No significant difference was found between Chinese case patients and control subjects. This RB1 SNP appears to be an ethnic variant prevalent in Southeast Asian populations and may be useful for studying RB1 inheritance by pedigree analysis.