A New Approach to Dengue Fatal Cases Diagnosis: NS1 Antigen Capture in Tissues

Dengue manifestations may vary from asymptomatic to potentially fatal complications. With an increasing number of Dengue Hemorrhagic fever (DHF) and fatal cases, the availability of new approaches useful for cases confirmation plays an important role for the disease surveillance. The diagnosis of fatal cases in frozen and fixed tissues from autopsies can be determined by techniques such as viral RT-PCR, in situ hybridization, viral proteins detection by immunohistochemistry and NS3 specific immunostaining. We aimed to assess for the first time the usefulness of NS1 capture tests as a diagnostic technique to demonstrate DENV antigens in human tissue specimens. The highest sensitivity was obtained by a rapid ICT which was also the most sensitive in liver, lung, kidney, brain, spleen and thymus. Despite a number of studies demonstrating the usefulness of DENV NS1 antigen detection by different ELISAs in plasma and/or sera of dengue patients, no research has been done previously to demonstrate NS1 presence in tissues of fatal dengue cases. Moreover, the application of NS1 kits to demonstrate the presence of DENV may provide a better understanding of viral tropism in fatal cases and may be useful for studies of pathogenesis in vivo and in experimental animals

Identification of Close Relatives in the HUGO Pan-Asian SNP Database

The HUGO Pan-Asian SNP Consortium has recently released a genome-wide dataset, which consists of 1,719 DNA samples collected from 71 Asian populations. For studies of human population genetics such as genetic structure and migration history, this provided the most comprehensive large-scale survey of genetic variation to date in East and Southeast Asia. However, although considered in the analysis, close relatives were not clearly reported in the original paper. Here we performed a systematic analysis of genetic relationships among individuals from the Pan-Asian SNP (PASNP) database and identified 3 pairs of monozygotic twins or duplicate samples, 100 pairs of first-degree and 161 second-degree of relationships. Three standardized subsets with different levels of unrelated individuals were suggested here for future applications of the samples in most types of population-genetics studies (denoted by PASNP1716, PASNP1640 and PASNP1583 respectively) based on the relationships inferred in this study. In addition, we provided gender information for PASNP samples, which were not included in the original dataset, based on analysis of X chromosome data

Population Genetic Structure of Peninsular Malaysia Malay Sub-Ethnic Groups

Patterns of modern human population structure are helpful in understanding the history of human migration and admixture. We conducted a study on genetic structure of the Malay population in Malaysia, using 54,794 genome-wide single nucleotide polymorphism genotype data generated in four Malay sub-ethnic groups in peninsular Malaysia (Melayu Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis). To the best of our knowledge this is the first study conducted on these four Malay sub-ethnic groups and the analysis of genotype data of these four groups were compiled together with 11 other populations' genotype data from Indonesia, China, India, Africa and indigenous populations in Peninsular Malaysia obtained from the Pan-Asian SNP database. The phylogeny of populations showed that all of the four Malay sub-ethnic groups are separated into at least three different clusters. The Melayu Jawa, Melayu Bugis and Melayu Minang have a very close genetic relationship with Indonesian populations indicating a common ancestral history, while the Melayu Kelantan formed a distinct group on the tree indicating that they are genetically different from the other Malay sub-ethnic groups. We have detected genetic structuring among the Malay populations and this could possibly be accounted for by their different historical origins. Our results provide information of the genetic differentiation between these populations and a valuable insight into the origins of the Malay sub-ethnic groups in Peninsular Malaysia

Mapping human genetic diversity in Asia

Asia harbors substantial cultural and linguistic diversity, but the geographic structure of genetic variation across the continent remains enigmatic. Here we report a large-scale survey of autosomal variation from a broad geographic sample of Asian human populations. Our results show that genetic ancestry is strongly correlated with linguistic affiliations as well as geography. Most populations show relatedness within ethnic/linguistic groups, despite prevalent gene flow among populations. More than 90% of East Asian (EA) haplotypes could be found in either Southeast Asian (SEA) or Central-South Asian (CSA) populations and show clinal structure with haplotype diversity decreasing from south to north. Furthermore, 50% of EA haplotypes were found in SEA only and 5% were found in CSA only, indicating that SEA was a major geographic source of EA populations

Mitochondrial DNA variation of Tai Speaking Peoples in Northern Thailand

The genetic structure and genetic affinity of Tai ethnic populations in northern Thailand has never been investigated, therefore their biological ancestor as well as their history is not clearly resolved. In this study, we examined the D-loop fragment of the mitochondrial DNA in 496 unrelated individuals belonging to 4 Tai ethnic groups from 10 villages: 4 Yuan, 4 Lue, 1 Yong and 1 Khuen. Based on a comparison of 522- bp sequences at the position 16048-16569, 195 distinct haplotypes defined by 130 polymorphic sites were distinguished. Of these, 154 types were unique to their respective populations, whereas 41 were shared by two or more populations. The studied Tai populations showed evidence of demographic expansion with corresponding estimated expansion times of more than 66,000 years before the present. During historical migration and settlement, intensive genetic drift and founder effects left their imprint as population differentiation. Genetic affinity among the populations was not consistent with their linguistic classification. The Yuan or Khon Muang in northern Thailand exhibited a close relationship to the Tai groups in South and Southeast China, which supported the immigrant hypothesis and their ancestor’s origin. However, an admixture between the Khon Muang and the Lawa and Mon, the long existing populations of northern Thailand, needs to be investigated

Genetic structure of Khon Mueang populations along a historical Yuan migration route in Northern Thailand

The genetic structure and diversity of the Khon Mueang, who constitute the majority of the current northern Thai populations, is poorly understood. In present study, 433 unrelated individuals from 10 Khon Mueang villages, located in different geographic areas along historical Yuan migration route, were analyzed using the mtDNA hypervariable region (HVR) 1 and 17 Y chromosome short tandem repeats (Y-STRs) as markers. The studied populations from the Chiang Mai-Lamphun basin showed the evidence of demographic expansion and gene flow process in this area. Genetic structure of the geographically diverse Khon Mueang was driven by geography, while genetic differentiation of Chiang Mai-Lamphun populations was shaped by genetic exchange with the neighbouring populations in the area. Contrasting patterns of mtDNA and Y chromosome variations, influenced by sex-bias rates of migration and admixture, suggests that male and female Khon Mueang do not have identical demographic histories

Complete mitochondrial genomes of Thai and Lao populations indicate an ancient origin of Austroasiatic groups and demic diffusion in the spread of Tai–Kadai languages

The Tai–Kadai (TK) language family is thought to have originated in southern China and spread to Thailand and Laos, but it is not clear if TK languages spread by demic diffusion (i.e., a migration of people from southern China) or by cultural diffusion, with native Austroasiatic (AA) speakers switching to TK languages. To address this and other questions, we obtained 1234 complete mtDNA genome sequences from 51 TK and AA groups from Thailand and Laos. We find high genetic heterogeneity across the region, with 212 different haplogroups, and significant genetic differentiation among different samples from the same ethnolinguistic group. TK groups are more genetically homogeneous than AA groups, with the latter exhibiting more ancient/basal mtDNA lineages, and showing more drift effects. Modeling of demic diffusion, cultural diffusion, and admixture scenarios consistently supports the spread of TK languages by demic diffusion