Fs Test Research Articles

Population structure of leishmania major in southeastern morocco

Cutaneous leishmaniasis (CL) is an infectious disease caused by various Leishmania species. It is among the most neglected tropical diseases and has been considered a major health threat over the past decades in the country. Its zoonotic form caused by Leishmania (L) major is the most prevalent in Morocco. This study investigated the population structure of L. major in southeastern Morocco. Samples (n = 67) were collected from patients with CL in five different endemic areas located in three provinces (Ouarzazate, Tinghir, and Zagora). These samples were then sequenced using two nuclear markers: internal transcribed spacer 1 (ITS1) and a fragment of the virulence factor GP63. Next, the sequences were edited and analyzed. Molecular diversity indices showed a high population genetic diversity but an overall low haplotype diversity. Our results suggest small population differentiation, indicating a low geographic structure. Tajima's D and Fu's Fs tests both suggested recent population expansion based on the significant deviations from neutrality in both tests for all populations except Tinghir, which may be due to a small sample size. Based on our findings, the region is experiencing rapid population expansion caused by recent CL outbreaks, and one of them has been recently studied. In addition, analysis of molecular variance and FST suggested gene flow between Zagora and both Ouarzazate and Tinghir. Nonetheless, no gene flow was observed between Tinghir and Ouarzazate. To the best of our knowledge, this is the first analysis of the population structure of L. major in Morocco. The results of this study provide crucial background information for epidemiological studies by showing the presence of gene flow between populations and clonal expansion in cases of an outbreak. This will drive authorities to reconsider the implemented control strategies.

Genetic diversity of Echinococcus granulosus sensu stricto in Sardinia (Italy).

Cystic echinococcosis (CE) is a severe parasitic zoonosis caused by the metacestode of the tapeworm Echinococcus granulosus sensu lato (s.l.). The disease has a global distribution representing a significant public health concern. Based on mitochondrial DNA analysis E. granulosus s.l. has been subdivided into five species: E. granulosus sensu stricto (s.s.) (G1, G3 genotype), E. equinus (G4 genotype), E. ortleppi (G5 genotype), E. canadensis (G6-G8, G10 genotype) and E. felidis. E. granulosus s.s., and in particular G1, is the most widespread genotype and the major responsible of human CE cases worldwide. In Italy G1 genotype is higly represented with larger percentages in some hyperendemic areas such as Sardinia. Molecular studies represent a valuable tool to improve our understanding of the E. granulosus epidemiology and CE control strategies. In the present study we investigated genetic variability of E. granulosus s.s. in Sardinia. To this purpose 83 hydatid cysts were collected from different animal species including humans and the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene was partially sequenced (720bp). Nucleotide sequences from Mediterranean basin were also analyzed for comparison. The phylogenetic network revealed 30 haplotypes grouped around a predominant isolate that had been already reported from other world regions. Haplotype diversity (0.8495±0.0336) and nucleotide diversity (0.003305±0.002014) were similar in Sardinia respect to other Mediterranean countries. Neutrality indices obtained by Tajima's D and Fu's Fs test were significantly negative (p≤.01) suggesting expansion of Sardinian population. Low Fixation indices (Fst), ranging from negative values (Algeria, Greece, Spain, other part of Italy) to 0.089 (Albania, France), indicated absence of genetic differentiation, and gene flow between Sardinia and other Mediterranean countries.

Genetic analysis and population structure of the Anopheles gambiae complex from different ecological zones of Burkina Faso

The Anopheles gambiae complex (Diptera: Culicidae) is the most important vector for malaria in Sub-Saharan Africa, besides other vectors such as Anopheles funestus. Malaria vector control should encompass specific identification, genetic diversity and population structure of An. gambiae to design vector control strategies.The aim of this study was to determine the distribution of sibling species of the An. gambiae complex according to climatic regions related to cotton-growing or cotton-free areas by using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Then, variation in mitochondrial cytochrome c oxidase 1 (COI) was used to assess the genetic structure within and between populations from our selected ecological zones.At the sibling species level, the following proportions were found across all samples (n = 180): An. coluzzii 65.56%, An. gambiae stricto sensu (s.s). 21.11%, and An. arabiensis 3.33%. Hybrids between An. gambiae s.s. and An. coluzzii (7.78%) and hybrids between An. coluzzii and An. arabiensis (2.22%) were found. The phylogenetic tree and Integer Neighbour-Joining (IntNJ) haplotype network did not reveal any distinct genetic structure pattern related to climatic or agricultural conditions in Burkina Faso. The Fst (Wright's F-statistic) values close to zero showed a free gene flow and no differentiation in An. gambiae complex populations. Furthermore, neutrality indices calculated by Tajima's D, Fu and Li's D⁎, Fu and Li's F⁎, Fu's Fs tests suggested an excess of rare mutations in the populations.Overall, variation in the proportions of An. gambiae s.s., An. coluzzii and An. arabiensis was found according to climatic regions, but COI analysis did not evidence any population structuring of the An. gambiae complex. These scientific contributions can be used as a basis for further in-depth study of the genetic diversity of the An. gambiae complex for epidemiological risk assessment of malaria in Burkina Faso.

Time to Detection of Hepatitis C Virus Infection With the Xpert HCV Viral Load Fingerstick Point-of-Care Assay: Facilitating a More Rapid Time to Diagnosis.

Xpert HCV Viral Load Fingerstick assay (Xpert HCV VL FS) is a point-of-care test quantifying HCV RNA in <1 hour, enabling same-visit diagnosis and treatment. This study evaluated time to HCV RNA detection using the Xpert HCV VL FS assay. Fingerstick whole-blood samples were collected from participants in an observational cohort in Australia. In May 2018-2019, 1468 participants were enrolled, 1426 had Xpert HCV VL FS testing performed, and 1386 had a valid result. HCV RNA was detected in 23% (325/1386). Among people with undetectable HCV RNA (n = 1061), median time to result was 57 minutes. Among people with detectable HCV RNA (n = 325), median time to HCV RNA detection was 32 minutes and 80% (261/325) had a detectable HCV RNA result in ≤40 minutes. Median time to HCV RNA detection was dependent on HCV RNA level. A quicker HCV diagnosis could be achieved by monitoring the time when HCV RNA is first detected with the Xpert HCV VL FS test, rather than HCV RNA quantification, although the current platform does not allow for this. These findings could facilitate new strategies to reduce waiting times for an HCV diagnosis and improve linkage to treatment.

Molecular characterization and genetic diversity of Ornithonyssus sylviarum in chickens (Gallus gallus) from Hainan Island, China

BackgroundThe northern fowl mite (NFM), Ornithonyssus sylviarum, is an obligatory hematophagous ectoparasite of birds and one of the most important pests in the poultry industry on several continents. Although NFM poses a serious problem, it remains a neglected pest of poultry in China and other Asian countries. Therefore, a molecular analysis was conducted to provide baseline information on the occurrence, genetic diversity and emergence of NFM in poultry farms from China.MethodsThis study focused on morphological description and identification of adults based on electron microscopy, molecular sequencing of the mitochondrial cox1 gene and phylogenetic analysis. We have also used the DNA sequences of the cox1 gene to study the genetic diversity, population structure and demographic history. The neutrality tests were used to analyze signatures of historical demographic events.ResultsThe mites collected were identified as the northern fowl mite Ornithonyssus sylviarum based on external morphological characterization using electron microscopy. Molecular analysis using a 756-bp long partial fragment of the cox1 gene revealed 99–100% sequence identity with NFM and phylogenetic inferences showed a bootstrap value of 99% indicating a well-supported monophyletic relationship. Molecular diversity indices showed high levels of haplotype diversity dominated by private haplotypes, but low nucleotide divergence between haplotypes. The Tajima’s D test and Fu’s Fs test showed negative value, indicating deviations from neutrality and both suggested recent population expansion of mite populations supported by a star-like topology of the isolates in the network analysis. Our genetic data are consistent with a single introduction of NFM infestations and the spread of NFM infestation in Hainan poultry farms and a private haplotype dominance, which suggest that infestations are recycled within the farms and transmission routes are limited between farms.ConclusionsTo our knowledge, this is the first time a molecular report of NFM in chicken from China including other Asian countries using DNA barcoding. The findings have potential implications with respect to understanding the transmission patterns, emergence and populations trends of parasitic infestations of poultry farms that will help for setting the parameters for integrated pest management (IPM) tactics against mite infestations.

Diversity of two Theileria parva CD8+ antigens in cattle and buffalo-derived parasites in Tanzania

Theileria parva is a tick-transmitted protozoan parasite that causes a disease called East Coast fever (ECF) in cattle. This important tick borne-disease (TBD) causes significant economic losses in cattle in many sub-Saharan countries, including Tanzania. Cattle immunization using Muguga cocktail has been recommended as an effective method for controlling ECF in pastoral farming systems in Tanzania. However, immunity provided through immunization is partially strain-specific. Therefore, the control of ECF in Tanzania is still a challenge due to inadequate epidemiological information. This study was conducted to assess genetic diversity of Tp1 and Tp2 genes from T. parva isolates that are recognized by CD8 + T-cells in cattle and buffalo. The Tp1 and Tp2 genes are currently under evaluation as candidates for inclusion in a subunit vaccine. A total of 130 blood samples collected from cattle which do not interact with buffalo (98), cattle co-grazing with buffalo (19) and buffalo (13) in Mara, Mbeya, Morogoro, Tanga, and Coast regions in Tanzania were used in this study. Genomic DNA was extracted from the blood samples, Tp1 and Tp2 genes were amplified using nested PCR and the PCR products were purified and sequenced. The partial sequencing of the Tp1 and Tp2 genes from T. parva isolates exhibited polymorphisms in both loci, including the epitope-containing regions. Results for sequence analysis showed that the overall nucleotide polymorphism (π) was 0.7% and 13.5% for Tp1 and Tp2, respectively. The Tajima’s D and Fu’s Fs test showed a negative value for both Tp1 and Tp2 genes, indicating deviations from neutrality due to a recent population expansion. The study further revealed a low to high level of genetic differentiations between populations and high genetic variability within populations. The study also revealed that most samples from the seven populations possessed several epitopes in antigens that were identical to those in the T. parva Muguga reference stock, which is the main component of the widely used live vaccine cocktail. Therefore, different strategic planning and cost-effective control measures should be implemented in order to reduce losses caused by ECF in the study areas.

Molecular characterization and genetic diversity study of Vibrio parahaemolyticus isolated from aquaculture farms in India

Vibrio parahaemolyticus is known to cause disease and infection in humans. This study was conducted to understand the prevalence of V. parahaemolyticus and the presence of virulence factors in environmental isolates of V. parahaemolyticus, collected from three major shrimp producing states viz, West Bengal, Andhra Pradesh and Gujarat of India during February 2014 to June 2017. Total 183 V. parahaemolyticus were isolated from moribund shrimp and identified using toxR and 16S rRNA gene. Polymerase Chain Reaction (PCR) was performed to detect virulence genes under T3SS1 and T3SS2 along with AHPND. All the isolates showed presence of vcrD1, vp1680 and vopD1 gene under T3SS1 but negative for AHPND. Only 3% of isolates showed presence of all the virulence genes (vcrD2, vopD2, vopB2 and vopC) used in the present study under T3SS2. The isolates were also tested for the presence of tdh, trh or both the genes; 8% of the isolates had trh gene and 3% of the isolates had tdh gene. The genetic diversity within and between V. parahaemolyticus isolated from three different geographical locations, was analyzed by using 16S rRNA gene. Though the biotype diversity (h) was high for all three populations, phylogenetic study of V. phaemolyticus revealed an admixture of biotypes. Tajima's D (−2.59470; p < .001) test of selective neutrality and Fu's Fs (−32.422; p < .001) test were negative and significant, suggesting a sudden population expansion with limited time for population differentiation.

Genetic diversity of Oecomys (Rodentia, Sigmodontinae) from the Tapajós River basin and the role of rivers as barriers for the genus in the region

The genus Oecomys is one of the most speciose within the subfamily Sigmodontinae, with most species found in the Amazon region. Recent studies have shown that the diversity, recognition of specific boundaries and geographical distribution is still imprecise for the genus. Herein, we investigate the genetic diversity of Oecomys in the Tapajós River basin and determine whether its rivers (Tapajós, Teles Pires, and Juruena) act as barriers for some species or populations in this genus based on phylogenetic analyzes with the mitochondrial marker cytochrome b (cytb) and the nuclear marker intron 7 β-fibrinogen, and on populational analysis with cytb. The phylogenetic relationships showed the presence of seven species in the region, namely O. bicolor, Oecomys aff. catherinae, O. catherinae, O. cleberi, O. paricola, O. roberti, and O. tapajinus. The geographic distributions of O. bicolor and O. cleberi seem to be shaped by the Tapajós and Teles Pires Rivers, with the former species occurring on the right bank and the latter species on the left bank of both rivers. Moreover, O. cleberi was the only Oecomys species to be recorded on the left bank of the Tapajós River. Our results also indicate that gene flow occurs between O. cleberi populations from the west Juruena and Tapajós Rivers and is absent between opposite banks of the Juruena River. The isolation by distance was discarded for this species. No evidence of gene flow was found for O. bicolor populations, and the isolation by distance was positive for this species. The spatial distribution of specimens and haplotypes of O. paricola indicates that the Teles Pires River does not act as a barrier for this species. Finally, Fs test significant results for O. cleberi and O. paricola showed that species population expansion cannot be discarded for these species.

Pleistocene climate change and phylogeographic structure of the Gymnocarpos przewalskii (Caryophyllaceae) in the northwest China: Evidence from plastid DNA, ITS sequences, and Microsatellite.

Northwestern China has a wealth of endemic species, which has been hypothesized to be affected by the complex paleoclimatic and paleogeographic history during Quaternary. In this paper, we used Gymnocarpos przewalskii as a model to address the evolutionary history and current population genetic structure of species in northwestern China. We employed two chloroplast DNA fragments (rps16 and psbB‐psbI), one nuclear DNA fragment (ITS), and simple sequence repeat (SSRs) to investigate the spatial genetic pattern of G. przewalskii. High genetic diversity (cpDNA: h S = 0.330, h T = 0.866; ITS: h S = 0.458, h T = 0.872) was identified in almost all populations, and most of the population have private haplotypes. Moreover, multimodal mismatch distributions were observed and estimates of Tajima's D and Fu's FS tests did not identify significantly departures from neutrality, indicating that recent expansion of G. przewalskii was rejected. Thus, we inferred that G. przewalskii survived generally in northwestern China during the Pleistocene. All data together support the genotypes of G. przewalskii into three groups, consistent with their respective geographical distributions in the western regions—Tarim Basin, the central regions—Hami Basin and Hexi Corridor, and the eastern regions—Alxa Desert and Wulate Prairie. Divergence among most lineages of G. przewalskii occurred in the Pleistocene, and the range of potential distributions is associated with glacial cycles. We concluded that climate oscillation during Pleistocene significantly affected the distribution of the species.

Genetic Analysis of Populations of the Peach Fruit Fly, Bactrocera zonata (Diptera: Tephritidae), in Iran.

Bactrocera zonata (Saunders) as one of the most devastating species of the genus Bactrocera is a notorious polyphagous fruit fly pest attacking lots of commercially important host plant species in many parts of the world including Iran. Despite economic importance, the population genetics of B. zonata have remained relatively unexplored in the country. In this study, the genetic structure, genetic diversity, and demographic history of this pest in Iran were investigated on the basis of cytochrome oxidase c subunit 1 (COI) sequences. A total of 21 haplotypes were identified from 66 individuals collected from seven locations. Genetic diversity indices (number of haplotypes, haplotype diversity, and nucleotide diversity) revealed high genetic diversity without any isolation by distance among the geographic areas. An overall low level of genetic differentiation between populations revealed by genetic structure analysis reinforces the hypothesis of free movement of flies throughout the geographic areas. Non-significant correlation between genetic distances and geographic distances was an indication of a high level of gene flow among the studied populations of the pest. In addition, the recent population expansion following a recent past bottleneck could be a factor that might be contributed to the overall low level of the genetic structure. Mismatch distribution analysis as well as Tajima's D and Fu's FS tests strengthens the likelihood of a recent expanded population following a population bottleneck.

Phylogeography Approach of Diloboderus abderus (Coleoptera: Melolonthidae) in the Southern Cone of America.

Diloboderus abderus (Sturm, 1826) (Coleoptera: Melolonthidae) is a serious soil pest of corn, wheat, oat, and natural and cultivated pastures in Argentina, Paraguay, Uruguay, and southern Brazil. Despite its economic importance, the genetic diversity and population structure of D. abderus remain unknown. We sequenced a fragment of the mitochondrial gene cytochrome oxidase I region (COI), of six populations of D. abderus from the Southern Cone of America. The mtDNA marker revealed a high haplotype diversity, high pairwise FST values, and significant genetic variations among populations. No correlation was found between genetic and geographical distances, yet the most common haplotype (Dab01) was present in four out of the six populations. Analysis of molecular variance showed that most of the variation was within populations of D. abderus. Tajima's D and Fu's FS tests indicated no evidence that D. abderus populations are under recent expansion. Our results indicate that genetic-based traits will likely remain localized or spread slowly, and management strategies need to be undertaken on a small scale.

Mitochondrial variation in subpopulations of Anopheles balabacensis Baisas in Sabah, Malaysia (Diptera: Culicidae).

Anopheles balabacensis, the primary vector of Plasmodium knowlesi in Sabah, Malaysia, is both zoophilic and anthropophilic, feeding on macaques as well as humans. It is the dominant Anopheles species found in Kudat Division where it is responsible for all the cases of P. knowlesi. However there is a paucity of basic biological and ecological information on this vector. We investigated the genetic variation of this species using the sequences of cox1 (1,383 bp) and cox2 (685 bp) to gain an insight into the population genetics and inter-population gene flow in Sabah. A total of 71 An. balabacensis were collected from seven districts constituting 14 subpopulations. A total of 17, 10 and 25 haplotypes were detected in the subpopulations respectively using the cox1, cox2 and the combined sequence. Some of the haplotypes were common among the subpopulations due to gene flow occurring between them. AMOVA showed that the genetic variation was high within subpopulations as compared to between subpopulations. Mantel test results showed that the variation between subpopulations was not due to the geographical distance between them. Furthermore, Tajima’s D and Fu’s Fs tests showed that An. balabacensis in Sabah is experiencing population expansion and growth. High gene flow between the subpopulations was indicated by the low genetic distance and high gene diversity in the cox1, cox2 and the combined sequence. However the population at Lipasu Lama appeared to be isolated possibly due to its higher altitude at 873 m above sea level.

Identity and genetic structure of eggplant fruit and shoot borer, Leucinodes orbonalis Guenée (Lepidoptera:Crambidae) populations in the Philippines inferred from morphological traits and COI sequence data

Abstract Morphological and molecular analysis of 15 Philippine populations of eggplant fruit and shoot borer (EFSB), Leucinodes orbonalis Guenee were conducted to determine if these populations are constituted singly by L. orbonalis or by different species and to assess the level of variability among them. Morphometric analysis of five genital traits of 850 male adult EFSB from field populations and analysis of the COI gene sequence of 879 F1 EFSB larvae from 15 main eggplant-producing provinces identified all individuals as belonging to L. orbonalis. Principal Component Analysis of five morphometric genital characters revealed high similarity among the EFSB populations regardless of geographic location. Thirteen (13) sequence variants (haplotypes) were identified, with one haplotype predominant and widespread throughout the country. The remaining haplotypes occurred rarely and differed from the widespread haplotype by one mutation. Overall, the EFSB populations from Philippines exhibited low nucleotide and haplotype diversity, indicating low genetic diversity. Topologies from a maximum likelihood tree indicate all thirteen haplotypes cluster in a single clade with EFSB populations from India and other South-East Asian countries. Further analysis with the Generalized Mixed Yule Coalescent (GMYC) method classified the different haplotypes into a single GMYC entity. Combined with morphometric analysis, differences between haplotypes are not suggestive of any subspecies. Negative values of Tajima's D and Fu's Fs tests combined with the phylogenetic analysis and overall low genetic diversity of Philippine populations support the hypothesis that EFSB is not endemic but introduced to the Philippines.

Phylogenetic and phylogeographic inferences based on two DNA markers reveal geographic structure of the orangeclaw hermit crab Calcinus tibicen (Anomura: Diogenidae) in the western Atlantic

ABSTRACTThe hermit crab Calcinus tibicen has an extensive distribution along the coasts of the western Atlantic Ocean, from the USA to southern Brazil. The present study aimed to test the hypothesis of the presence of phylogeographic structure of C. tibicen throughout its distribution, evaluating the genetic and morphological variabilities of the species. The molecular data, genetic diversity and demographic history were inferred from 16 different localities for the mitochondrial genes cytochrome oxidase subunit I (COI) (75 specimens) and 16S rRNA (20). The morphological information was based on 99 individuals from the same 16 localities. Results were obtained by the construction of haplotype networks and a phylogenetic tree, an Analysis of Molecular Variance (AMOVA), Tajima’s D and Fu’s Fs tests, pairwise mismatch distributions under the sudden expansion model, and by estimating divergence times. The haplotype networks show the existence of two genetically well-defined groups that do not share haplotypes. The phylogenetic tree and the matrix of genetic distances suggest lack of gene between North and South Atlantic groups, also corroborated by AMOVA for the COI gene. The genetic distance can be attributed to at least two ecological factors: the existence of a physiological barrier caused by the Amazon River freshwater plume, and the effect of the bifurcation of the westerly flowing South Atlantic oceanic currents creating a gap along the Brazilian coastline. Demographic history analyses suggest that C. tibicen experienced population expansion, probably after the Amazon River changed its direction. Despite the molecular evidence for the existence of a phylogeographic structure, no morphological pattern for each genetic group was observed. Therefore, based on the described molecular differences and the ecological and historical factors suggested, the question arises whether a cryptic species should be recognized for some of the populations of C. tibicen.

Genetic structure analysis of mantis shrimp Oratosquilla oratoria based on mitochondrial DNA control region sequence.

The genetic relationships of mantis shrimp Oratosquilla oratoria between the coastal waters of China and Japan were not well studied. To reveal the genetic differentiation and genetic structure among populations, we collected populations of mantis shrimp O. oratoria from the coastal waters of China and Japan to analyze the mtDNA control region variation. A total of 309 individuals of O. oratoria were collected from 13 localities (11 from China and 2 from Japan) and a segment of mitochondrial DNA control region was sequenced. Three hundred nine haplotypes were defined, yielding a very high haplotype diversity and nucleotide diversity. Two lineages of O. oratoria were revealed and displayed strong differences in the geographical distribution. In the coastal waters of China, the geographic distribution of the two lineages was completely separated by the Yangtze River estuary; however, the lineages showed geographic sympatry in two populations from Japan. Based on the lineage distribution, three groups were defined. There was no significant genetic differentiation among the populations within the three groups, indicating high gene flow within each group. Significant and negative values for Tajima D and Fu's Fs tests, and mismatch distributions for two lineages indicated population expansion. The present result confirmed that the freshwater outflow from the Yangtze River formed a physical barrier and affected gene exchange. The different distribution patterns of the two lineages in coastal waters of China and Japan indicated that the larvae of O. oratoria were transferred from China to the coastal waters of Japan with a one-way gene flow.

Phylogenetic relationship and genetic diversity of citrus psyllid populations from China and Pakistan and their associated Candidatus bacterium

Asian citrus psyllid (ACP), Diaphorina citri Kuwayama (Hemiptera: Liviidae), is a severely devastating pest of Rutaceae plants, mainly citrus, across the globe, and causal agent of Huanglongbing (HLB) disease. To find out the genetic relationship and diversity among the populations of ACP and associated Candidatus Liberibacter asiaticus (CLas) from two countries (China and Pakistan), sequence data of three different genes, cytochrome oxidase subunit I (COI), Cu-transporting protein (ATOX1) and 16S rRNA, were used to characterize all populations. In the present study, MEGA-7 and statistical parsimony software (TCS-1.2) were used to depict the phylogenetic relationship among all populations under both genes, whereas diversity was calculated by DnaSP v5. All analyses were done for country wise and overall relationship among all populations. For ACP populations, both genes presented a significant strong intermingled relationship among all populations and put all population into a single haplotype (Dcit-2), which proved similarity between Chinese and Pakistani populations. Moreover, for CLas strains, 16S gene also presented strong relationship for all sampled populations. All three genes of ACP and CLas populations elucidated more than 95% resemblance to each other. On the other hand, a significant genetic variation was observed by three genes for overall populations, although, country wise variation was non-significant between all collected populations. ATOX1 gene presented higher diversity through Fu’s Fs test (π = 0.01081, p < 0.003) whereas COI gene gave less diversity under Fu’s Fs and Tajima’s D test (π = 0.00512, p < 0.000 and 0.05, respectively). Similarly, nucleotide mismatch distribution also had shown enough genetic variation among all ACP populations, under both genes. Our sequence data for both genes proved the invasion of the Chinese ACP population (Dcit-2) into Pakistan, through all phylogenetic relationship, which proved a similar genetic makeup among all ACP populations from both countries. Therefore, these results can be helpful to utilize any novel designed control measure equally for both countries.

Evaluation of the Xpert HCV Viral Load Finger-Stick Point-of-Care Assay.

Point-of-care hepatitis C virus (HCV) RNA testing is advantageous, enabling diagnosis of active infection in a single visit. This study evaluated the sensitivity and specificity of the Xpert HCV Viral Load Finger-Stick assay (Xpert HCV VL FS) for HCV RNA detection (finger-stick) and the Xpert HCV Viral Load assay (plasma) compared with the Abbott RealTime HCV Viral Load assay by venepuncture. Plasma and finger-stick capillary whole-blood samples were collected from participants in an observational cohort in Australia. Of 223 participants enrolled, HCV RNA was detected in 40% of participants (85 of 210) with available Xpert HCV Viral Load testing. Participants receiving HCV therapy were excluded from subsequent analyses (n = 16). Sensitivity of the Xpert HCV Viral Load assay for HCV RNA quantification in plasma collected by venepuncture was 100.0% (95% confidence interval [CI] 96.9%-100.0%) and specificity was 100.0% (95% CI, 94.4%-100.0%). Sensitivity of the Xpert HCV VL FS assay for HCV RNA quantification in samples collected by finger-stick was 100.0% (95% CI, 93.9%-100.0%) and specificity was 100.0% (95% CI, 96.6%-100.0%). The Xpert HCV VL FS test can accurately detect active infection from a finger-stick sample in 1 hour allowing single-visit HCV diagnosis.

Mitochondrial Genetic Diversity and Phylogeography ofMus musculus castaneusin Northern Punjab, Pakistan

Regions of Iran, Afghanistan, Pakistan and northwestern India have been proposed as the place of origin of Mus musculus castaneus. But despite the fact that Pakistan encompasses an important part of its range, M. m. castaneus populations in Pakistan have not been the subject of intensive genetic and biogeographic studies, except for a very small number of samples included in past studies. We studied genetic variation in M. m. castaneus (CAS) from northern Punjab Province, Pakistan, by using cytochrome b (Cytb) analysis in a sample of 98 individuals. Median-joining network revealed four well differentiated CAS sub-lineages coexisting within a small geographical region; these had previously been thought to have largely non-overlapping geographic distributions. Moreover, haplotypes from Pakistan occupied a central position in the network and all identified global haplotypes were also present in Pakistan. All identified CAS sub-lineages proved to be highly diverse on the basis of haplotype and nucleotide diversity indices. Tajima's D test and Fu's Fs tests of neutrality suggest recent population expansions in all sub-lineages. Expansion times were estimated as 21,760-134,930, 10,800-64,400 and 4950-30,665 ybp using substitution rates of 2.5%, 5% and 11%, respectively. Our results support the hypothesis that northern Punjab Province in Pakistan is the most likely source area for M. m. castaneus, and that the CAS sub-lineages in this region have undergone rapid population expansion events at different time periods, which appear to have benefitted from human-mediated transport, although one of them clearly predates the establishment of human settlements in this region.

Molecular discrimination of Opisthorchis-like eggs from residents in a rural community of central Thailand.

BackgroundOpisthorchis viverrini infection is a major public health problem in northern and northeastern Thailand. The chronic infection of O. viverrini is related to cholangiocarcinoma which causes high mortality in endemic areas. Therefore, the diagnosis, treatment, control and prevention of O. viverrini infection are necessary. The morphology of the egg is very similar to that of other species of human liver flukes (Opisthorchis felineus and Clonorchis sinensis) as well as that of small intestinal flukes in the family Heterophyidae. Thus, molecular characterization is crucially required to discriminate species of Opisthorchis-like eggs in fecal examination.Methodology/Principal findingsWe aimed to determine the prevalence of O. viverrini infection among villagers living in Sanamchaikate District, Chachoengsao Province, in central Thailand, where O. viverrini infection has previously been reported. A total of 2,609 fecal samples were examined for Opisthorchis-like eggs using microscopic examination. PCR-RFLP analysis of the ITS2 region was used to discriminate Opisthorchis-like eggs. The genetic structure of O. viverrini infection was demonstrated using nucleotide sequencing of cytochrome c oxidase subunit I (cox1) and NADH dehydrogenase subunit 1 (nad1). Testing of evolutionary neutrality of the cox1 and nad1 sequences of O. viverrini was performed using Tajima's D tests and Fu's Fs tests. Moreover, the haplotype networks and phylogenetic trees were constructed to study the relationships of O. viverrini isolated from different endemic areas. A high prevalence of O. viverrini infection is still observed in a rural community of Chachoengsao Province, central Thailand. The overall prevalence of Opisthorchis-like eggs using microscopic examination was 16.8%. PCR-RFLP profiles showed the predominant infection of O. viverrini (9.6%) including very low infections of other small intestinal flukes, Haplorchis taichui (0.08%) and Euparyphium albuferensis (0.08%). The genetic structure of O. viverrini populations in central Thailand was also described and revealed a non-significant difference in genetic diversity. In addition, the genetic background of the O. viverrini populations was closely related to the isolate from Lao PDR.Conclusions/SignificanceOur study highlighted the prevalence of O. viverrini infection in central Thailand indicating that control programs and health education regarding opisthorchiasis is still required in this endemic area. Additionally, the study demonstrated the genetic structure of O. viverrini, in central Thailand which could provide information on the molecular epidemiology of this parasite.

Genetic structure and demographic history of Lymantria dispar (Linnaeus, 1758) (Lepidoptera: Erebidae) in its area of origin and adjacent areas.

We analyzed the population genetic structure and demographic history of 20 Lymantria dispar populations from Far East Asia using microsatellite loci and mitochondrial genes. In the microsatellite analysis, the genetic distances based on pairwise F ST values ranged from 0.0087 to 0.1171. A NeighborNet network based on pairwise F ST genetic distances showed that the 20 regional populations were divided into five groups. Bayesian clustering analysis (K = 3) demonstrated the same groupings. The populations in the Korean Peninsula and adjacent regions, in particular, showed a mixed genetic pattern. In the mitochondrial genetic analysis based on 98 haplotypes, the median‐joining network exhibited a star shape that was focused on three high‐frequency haplotypes (Haplotype 1: central Korea and adjacent regions, Group 1; Haplotype 37: southern Korea, Group 2; and Haplotype 90: Hokkaido area, Group 3) connected by low‐frequency haplotypes. The mismatch distribution dividing the three groups was unimodal. In the neutral test, Tajima's D and Fu's FS tests were negative. We can thus infer that the Far East Asian populations of L. dispar underwent a sudden population expansion. Based on the age expansion parameter, the expansion time was inferred to be approximately 53,652 years before present (ybp) for Group 1, approximately 65,043 ybp for Group 2, and approximately 76,086 ybp for Group 3. We propose that the mixed genetic pattern of the inland populations of Far East Asia is due to these expansions and that the inland populations of the region should be treated as valid subspecies that are distinguishable from other subspecies by genetic traits.