Mixture Of Genotypes Research Articles

High prevalence of the B2+C2 subgenotype mixture in patients with chronic hepatitis B in Eastern China

To investigate the prevalence of hepatitis B virus (HBV) genotype mixtures among patients with chronic hepatitis B (CHB) in Eastern China. A total of 4908 chronic HBV patients from Eastern China were enrolled. HBV genotypes and subgenotypes were determined using a multiplex PCR technique. Serum viral loads and hepatitis B e antigen (HBeAg) levels detected using real-time fluorescent quantitative PCR and ELISA assay, respectively. The presence of precore/basic core promoter (PC/BCP) mutations was examined with PCR and direct sequencing of the amplified products. HBV genotypes B, C, D, B+C, and B+D were found in 19.21%, 64.75%, 1.49%, 13.63%, and 0.92% of the patients, respectively. In 669 patients with the genotype mixture B+C, the subgenotypes B2+C2 and B2+C1 accounted for 68.13% and 31.87%, respectively, no other subgenotypes were identified. HBV B+C was more frequent in the patients with moderate CHB than in patients with mild CHB. In patients with moderate CHB, the subgenotype mixture B2+C2 was lower than B2+C1 (51.97% vs 63.38%), while the opposite situation was found in patients with severe CHB (22.15% vs 15.49%). The highest average viral load was found in patients with the genotype B+C mixture. The prevalence of HBV B2+C2 increased in patients from 50 to 59 years of age and was significantly different from the proportion of patients in the same age group with genotype B (23.2% vs 15.2%). A double mutation (G1896A) in the PC was significantly more common in subgenotype B2+C2 than in subgenotype B2+C1. The HBV B2+C2 subgenotype was prevalent in CH patients with a high HBV replication status and correlated with a more severe course of the disease.

Experimental mixtures of Phthorimaea operculella granulovirus isolates provide high biological efficacy on both Phthorimaea operculella and Tecia solanivora (Lepidoptera: Gelechiidae)

The Guatemalan potato moth Tecia solanivora (Povolny) recently invaded part of South America, colonizing zones where Phthorimaea operculella (Zeller), another potato moth species belonging to the same group, was previously established. T. solanivora is now the major insect pest of potato in this area encompassing Venezuela, Colombia and Ecuador. P. operculella granulovirus (PhopGV) (Betabaculovirus) is a biocontrol agent to be considered for the simultaneous management of these two potato pests, instead of classical chemical insecticides. In a previous work, five PhopGV isolates were isolated in Colombia from T. solanivora and were tested against larvae of the same species showing variable efficacies. Infections with mixtures of different genotypes of Baculoviruses had been carried out in a wide range of species and several showed interesting results. In the present study, the effect of sequential passages of PhopGV in P. operculella and T. solanivora larvae was analyzed through biological assays. Three different mixtures containing a Peruvian PhopGV isolate (Peru) adapted to P. operculella and a Colombian PhopGV isolate (VG003) adapted to T. solanivora were tested. A preliminary analysis of the correlation between the genotypic marker egt gene and the level of pathogenicity after a variable number of replication cycles was made. Mixtures of virus isolates showed a higher efficacy in both hosts compared to individual PhopGV isolates. This higher pathogenicity was maintained through passages. In P. operculella the mixtures were between 2.8 and 23.6-fold (from 7.15OB/mm2 to 0.10OB/mm2) more pathogenic than isolate Peru applied alone. In T. solanivora they were between 2.3 and 4.9-fold (from 12.29OB/mm2 to 1.25OB/mm2) more pathogenic than isolate VG003 alone. Viral biopesticide containing a mixture of selected genotypes active against each hosts seemed suitable for the development of a biopesticide aimed to simultaneously control P. operculella and T. solanivora.

Bacterial biofilms in a ‘genes‐to‐ecosystems’ context

In ecology, there is an increasing amount of research dedicated to understanding how intraspecific genetic diversity can extend beyond the population level to influence the assembly of communities and the functioning of ecosystems. In this issue of Molecular Ecology, Koh etal. (2012) take this exploration to a new level using bacterial biofilms and protozoan grazers. They show that there is heritable variation in the phenotypes of different variants of biofilms of Serratia marcescens and that these strains display complementarity when combined in a diverse assemblage. Mixtures of variants were significantly more resistant to protozoan grazing than either wild-type or variant biofilms grown in monocultures. While similar biodiversity effects of genotype mixtures have been observed in other systems, Koh etal. (2012) link phenotype variation of the biofilms to a single nucleotide polymorphism in one regulatory gene. Importantly, the authors demonstrate that minimal changes in a genotype can result in substantial shifts in interspecific ecological interactions.

Late blight resistance gene from Solanum ruiz-ceballosii is located on potato chromosome X and linked to violet flower colour

BackgroundPhytophthora infestans (Mont.) de Bary, the causal organism of late blight, is economically the most important pathogen of potato and resistance against it has been one of the primary goals of potato breeding. Some potentially durable, broad-spectrum resistance genes against this disease have been described recently. However, to obtain durable resistance in potato cultivars more genes are needed to be identified to realize strategies such as gene pyramiding or use of genotype mixtures based on diverse genes.ResultsA major resistance gene, Rpi-rzc1, against P. infestans originating from Solanum ruiz-ceballosii was mapped to potato chromosome X using Diversity Array Technology (DArT) and sequence-specific PCR markers. The gene provided high level of resistance in both detached leaflet and tuber slice tests. It was linked, at a distance of 3.4 cM, to violet flower colour most likely controlled by the previously described F locus. The marker-trait association with the closest marker, violet flower colour, explained 87.1% and 85.7% of variance, respectively, for mean detached leaflet and tuber slice resistance. A genetic linkage map that consisted of 1,603 DArT markers and 48 reference sequence-specific PCR markers of known chromosomal localization with a total map length of 1204.8 cM was constructed.ConclusionsThe Rpi-rzc1 gene described here can be used for breeding potatoes resistant to P. infestans and the breeding process can be expedited using the molecular markers and the phenotypic marker, violet flower colour, identified in this study. Knowledge of the chromosomal localization of Rpi-rzc1 can be useful for design of gene pyramids. The genetic linkage map constructed in this study contained 1,149 newly mapped DArT markers and will be a valuable resource for future mapping projects using this technology in the Solanum genus.

Point mutations in the West Nile virus (Flaviviridae; Flavivirus) RNA-dependent RNA polymerase alter viral fitness in a host-dependent manner in vitro and in vivo

The West Nile virus (WNV) genome contains a single RNA-dependent RNA polymerase (RdRp) gene, which is responsible for replication of the viral genome and, as such, is an important target for antiviral therapy. Viral RdRps are known to lack proofreading capabilities and as a result viruses such as WNV exist as a mixture of viral genotypes within an infection, enabling the virus to readily emerge and adapt to new host environments. To test the consequences of subtle structural alterations remote from the RdRp active-site, the following single point mutations were engineered in the WNV NS5 RdRp coding region: T363N, A365N, and T537I; these mutations were selected in an effort to stabilize the secondary structural elements near the rNTP binding pocket of the RdRp. Mutant viruses were tested in vitro on Vero, C6/36, Culex tarsalis and DF-1 cell types and in vivo in one day old chickens and Culex pipiens mosquitoes. Plaque morphology was affected by each mutation and growth and RNA replication kinetics were altered as well. Our results demonstrate that subtle alteration of the RdRp protein away from the active site can have a significant overall biological effect on WNV fitness, and that this effect can be host-dependent.

Study of the prevalence of human Papillomavirus infection in Chinese women with cervical cancer

Human papillomavirus (HPV) have been recognized as oncogenic factor in cervical carcinoma. There was an increased incidence of cervical cancer in Chinese women. However, little is known about the prevalence of HPV genotypes in Chinese women with cervical cancer and risk factors of cervical cancer. Cervical exfoliated cells were prospectively collected from 792 women with cervical cancer referred for colposcopic examination. The individual HPV genotypes in these specimens were identified (HPV GenoArray test kit; Hybribio Ltd., Hong Kong). Meanwhile, the clinical data and laboratory result of these patients were gathered. HPV-positive was found in 588/792 (74.2%). The prevalence of the HR-HPV were 516/792 (65.2%). and 51.0% of these patients were infected with mixtures of HR genotypes. HPV positive rate in various clinical stages and differentiation degree of uterine cervical cancer had no statistical differences (P>0.05). HPV positive rate in squamous cancer and adeno-carcinoma had statistical differences respectively with other pathological types (P<0.05).The logistic regression analysis showed that HPV16 infection or HPV58 infection or age over 40 might increase the risk of carcinogennesis of the cervix. The infection rate and superinfection rate of HPV from Chinese women with disease of uterine cervix were high. The patients with HPV16 or HPV58 infection or age over 40 years were associated with increased risk of cervical cancer. Key words: Human papillomavirus, Chinese women, cervical cancer.

Assessment of the impact of resistant and susceptible canola on Plasmodiophora brassicae inoculum potential

The impact on clubroot severity of growing susceptible canola or mixtures of resistant and susceptible canola genotypes was examined. Bioassays revealed greater clubroot severity and incidence, and reduced plant height, where 100% of a susceptible cultivar had been grown. A higher proportion of susceptible plants within a resistant canola crop increased root hair and secondary infections. Regression analysis of root hair infection and the amount of Plasmodiophora brassicae DNA (as determined by quantitative PCR) revealed strong linear relationships between the two parameters. The linear relationships between root hair infection and P. brassicae DNA were stronger for the resistant cultivar than for the susceptible cultivar when regression analysis was conducted by cultivar over the sampling dates. In conclusion, the cropping of a resistant cultivar reduced clubroot severity, while the presence of susceptible volunteer canola increased inoculum potential. Quantitative PCR was a reliable tool for the quantification of root hair infection.

DNA fingerprinting and new tools for fine‐scale discrimination of Arabidopsis thaliana accessions

One of the main strengths of Arabidopsis thaliana as a model species is the impressive number of public resources available to the scientific community. Exploring species genetic diversity--and therefore adaptation--relies on collections of individuals from natural populations taken from diverse environments. Nevertheless, due to a few mislabeling events or genotype mixtures, some variants available in stock centers have been misidentified, causing inconsistencies and limiting the potential of genetic analyses. To improve the identification of natural accessions, we genotyped 1311 seed stocks from our Versailles Arabidopsis Stock Center and from other collections to determine their molecular profiles at 341 single nucleotide polymorphism markers. These profiles were used to compare genotypes at both the intra- and inter-accession levels. We confirmed previously described inconsistencies and revealed new ones, and suggest likely identities for accessions whose lineage had been lost. We also developed two new tools: a minimal fingerprint computation to quickly verify the identity of an accession, and an optimized marker set to assist in the identification of unknown or mixed accessions. These tools are available on a dedicated web interface called ANATool (https://www.versailles.inra.fr/ijpb/crb/anatool) that provides a simple and efficient means to verify or determine the identity of A. thaliana accessions in any laboratory, without the need for any specific or expensive technology.

Relationships between arthropod richness, evenness, and diversity are altered by complementarity among plant genotypes

Biodiversity is quantified via richness (e.g., the number of species), evenness (the relative abundance distribution of those species), or proportional diversity (a combination of richness and evenness, such as the Shannon index, H'). While empirical studies show no consistent relationship between these aspects of biodiversity within communities, the mechanisms leading to inconsistent relationships have received little attention. Here, using common evening primrose (Oenothera biennis) and its associated arthropod community, we show that relationships between arthropod richness, evenness, and proportional diversity are altered by plant genotypic richness. Arthropod richness increased with O. biennis genotypic richness due to an abundance-driven accumulation of species in response to greater plant biomass. Arthropod evenness and proportional diversity decreased with plant genotypic richness due to a nonadditive increase in abundance of a dominant arthropod, the generalist florivore/omnivore Plagiognathas politus (Miridae). The greater quantity of flowers and buds produced in polycultures-which resulted from positive complementarity among O. biennis genotypes-increased the abundance of this dominant insect. Using choice bioassays, we show that floral quality did not change in plant genotypic mixtures. These results elucidate mechanisms for how plant genotypic richness can modify relationships between arthropod richness, evenness, and proportional diversity. More broadly, our results suggest that trophic interactions may be a previously underappreciated factor controlling relationships between these different aspects of biodiversity.

Genotypic richness and phenotypic dissimilarity enhance population performance

Increases in biodiversity can result from an increase in species richness, as well as from a higher genetic diversity within species. Intraspecific genetic diversity, measured as the number of genotypes, can enhance plant primary productivity and have cascading effects at higher trophic levels, such as an increase in herbivore and predator richness. The positive effects of genotypic mixtures are not only determined by additive effects, but also by interactions among genotypes, such as facilitation or inhibition. However, so far there has been no effort to predict the extent of such effects. In this study, we address the question of whether the magnitude of the effect of genotype number on population performance can be explained by the extent of dissimilarity in key traits among genotypes in a mixture. We examine the relative contribution of genotype number and phenotypic dissimilarity among genotypes to population performance of the soil arthropod, Orchesella cincta. Nearly homogeneous genotypes were created from inbred isofemale lines. Phenotypic dissimilarity among genotypes was assessed in terms of three life-history traits that are associated with population growth rate, i.e., egg size, egg development time, and juvenile growth rate. A microcosm experiment with genotype mixtures consisting of one, two, four, and eight genotypes, showed that genotypic richness strongly increased population size and biomass production and was associated with greater net diversity effects. Most importantly, there was a positive log-linear relationship between phenotypic dissimilarity in a mixture and the net diversity effects for juvenile population size and total biomass. In other words, the degree of phenotypic dissimilarity among genotypes determined the magnitude of the genotypic richness effect, although this relationship leveled off at higher values of phenotypic dissimilarity. Although the exact mechanisms responsible for these effects are currently unknown, similar advantages of trait dissimilarity have been found among species. Hence, to better understand population performance, genotype number and phenotypic dissimilarity should be considered collectively.

Practical use of GenoType® HelicoDR, a molecular test for Helicobacter pylori detection and susceptibility testing

Compared to culture-based method, the sensitivity, specificity, positive, and negative predictive values of the GenoType® HelicoDR for detecting Helicobacter pylori resistance were, respectively, 100, 86.2, 89.7%, and 100% to clarithromycin as well as 82.6, 95.1, 90.5%, and 90.7% to fluoroquinolones. This molecular assay detected a mixture of genotypes and could successfully analyze biopsies without transport/storage limitations.

Synchronous attack is advantageous: mixed genotype infections lead to higher infection success in trematode parasites

Co-infecting parasite genotypes typically compete for host resources limiting their fitness. The intensity of such competition depends on whether parasites are reproducing in a host, or using it primarily as a transmission vehicle while not multiplying in host tissues (referred to as 'competition hypothesis'). Alternatively, simultaneous attack and co-infection by several parasite genotypes might facilitate parasite infection because such a diverse attack could present an additional challenge to host immune defence (referred to as 'facilitation hypothesis'). We tested the competition hypothesis by comparing the production of transmission stages (cercariae) from snails infected with one or two genotypes of the trematode Diplostomum pseudospathaceum. We found that cercarial production did not differ between the two groups of snails, suggesting lower per genotype production in double infections, and competition for host resources. Second, we tested the facilitation hypothesis by comparing parasite infection success on fishes (proportion of parasites establishing in the host) using cercariae originating from single-infected snails, double-infected snails and artificial mixtures of the single genotypes. In both cases, we found higher infection success when fishes were challenged with two parasite genotypes instead of one, supporting the facilitation hypothesis. Our results suggest that constraints defining the success of multiple genotype infections in parasites with multiple host life cycles include both between-genotype resource competition in the host and performance of host immune defences against a diverse parasite challenge.

Detection and Resolution of Cryptosporidium Species and Species Mixtures by Genus-Specific Nested PCR-Restriction Fragment Length Polymorphism Analysis, Direct Sequencing, and Cloning

Molecular methods incorporating nested PCR-restriction fragment length polymorphism (RFLP) analysis of the 18S rRNA gene of Cryptosporidium species were validated to assess performance based on limit of detection (LoD) and for detecting and resolving mixtures of species and genotypes within a single sample. The 95% LoD was determined for seven species (Cryptosporidium hominis, C. parvum, C. felis, C. meleagridis, C. ubiquitum, C. muris, and C. andersoni) and ranged from 7 to 11 plasmid template copies with overlapping 95% confidence limits. The LoD values for genomic DNA from oocysts on microscope slides were 7 and 10 template copies for C. andersoni and C. parvum, respectively. The repetitive nested PCR-RFLP slide protocol had an LoD of 4 oocysts per slide. When templates of two species were mixed in equal ratios in the nested PCR-RFLP reaction mixture, there was no amplification bias toward one species over another. At high ratios of template mixtures (>1:10), there was a reduction or loss of detection of the less abundant species by RFLP analysis, most likely due to heteroduplex formation in the later cycles of the PCR. Replicate nested PCR was successful at resolving many mixtures of Cryptosporidium at template concentrations near or below the LoD. The cloning of nested PCR products resulted in 17% of the cloned sequences being recombinants of the two original templates. Limiting-dilution nested PCR followed by the sequencing of PCR products resulted in no sequence anomalies, suggesting that this method is an effective and accurate way to study the species diversity of Cryptosporidium, particularly for environmental water samples, in which mixtures of parasites are common.

Rapid formation of distinct hybrid lineages after secondary contact of two fish species (Cottus sp.)

Homoploid hybridization after secondary contact between related species can lead to mixtures of genotypes which have the potential for rapid adaptation to new environmental conditions. Here, we focus on a case where anthropogenic changes within the past 200 years have allowed the hybridization between two fish species (Cottus rhenanus and Cottus perifretum) in the Netherlands. Specifically, we address the question of the dynamics of the emergence of these hybrids and invasion of the river systems. Using a set of 81 mostly ancestry-informative SNP markers, as well as broad sample coverage in and around the area of the initial contact, we find a structured hybrid swarm with at least three distinct hybrid lineages that have emerged out of this secondary contact situation. We show that genetically coherent groups can occur at geographically distant locations, while geographically adjacent groups can be genetically different, indicating that some form of reproductive isolation between the lineages is already effective. Using a newly developed modelling approach, we test the relative influence of founding admixture, drift and migration on the allele compositions of the sampling sites. We find that the allele frequency distributions can best be explained if continued gene flow between the parental species and the hybrid lineages is invoked. Genome mapping of the invasive lineage in the Rhine shows that major chromosomal rearrangements were not involved in creating this distinct lineage. Our results show that hybridization after secondary contact can quickly lead to multiple independent new lineages that have the capacity to form hybrid species.

High resolution genotyping of clinical Aspergillus flavus isolates from India using microsatellites.

BackgroundWorldwide, Aspergillus flavus is the second leading cause of allergic, invasive and colonizing fungal diseases in humans. However, it is the most common species causing fungal rhinosinusitis and eye infections in tropical countries. Despite the growing challenges due to A. flavus, the molecular epidemiology of this fungus has not been well studied. We evaluated the use of microsatellites for high resolution genotyping of A. flavus from India and a possible connection between clinical presentation and genotype of the involved isolate.Methodology/Principal FindingsA panel of nine microsatellite markers were selected from the genome of A. flavus NRRL 3357. These markers were used to type 162 clinical isolates of A. flavus. All nine markers proved to be polymorphic displaying up to 33 alleles per marker. Thirteen isolates proved to be a mixture of different genotypes. Among the 149 pure isolates, 124 different genotypes could be recognized. The discriminatory power (D) for the individual markers ranged from 0.657 to 0.954. The D value of the panel of nine markers combined was 0.997. The multiplex multicolor approach was instrumental in rapid typing of a large number of isolates. There was no correlation between genotype and the clinical presentation of the infection.Conclusions/SignificanceThere is a large genotypic diversity in clinical A. flavus isolates from India. The presence of more than one genotype in clinical samples illustrates the possibility that persons may be colonized by multiple genotypes and that any isolate from a clinical specimen is not necessarily the one actually causing infection. Microsatellites are excellent typing targets for discriminating between A. flavus isolates from various origins.

DNA sampling from eggshell swabbing is widely applicable in wild bird populations as demonstrated in 23 species

There is increasing interest in noninvasive DNA sampling techniques. In birds, there are several methods proposed for sampling DNA, and of these, the use of eggshell swabbing is potentially applicable to a wide range of species. We estimated the effectiveness of this method in the wild by sampling the eggs of 23 bird species. Sampling of eggs was performed twice per nest, soon after the clutch was laid and again at the end of egg incubation. We genotyped DNA samples using a set of five conserved microsatellite markers, which included a Z-linked locus and a sex-typing marker. We successfully collected avian DNA from the eggs of all species tested and from 88.48% of the samples. In most of the cases, the DNA concentration was low (ca. 10 ng/μL). The number of microsatellite loci amplified per sample (0-5) was used as a measure of the genotyping success of the sample. On average, we genotyped 3.01 ± 0.12 loci per sample (mean ± SE), and time of sampling did not seem to have an effect; however, genotyping success differed among species and was greater in those species that used feather material for lining their nest cups. We also checked for the occurrence of possible genotyping errors derived from using samples with very low DNA quantities (i.e. allelic dropout or false alleles) and for DNA contamination from individuals other than the mother, which appeared at a moderate rate (in 44% of the PCR replicates and in 17.36% of samples, respectively). Additionally, we investigated whether the DNA on eggshells corresponded to maternal DNA by comparing the genotypes obtained from the eggshells to those obtained from blood samples of all the nestlings for six nests of magpies. In five of the six magpie nests, we found evidence that the swab genotypes were a mixture of genotypes from both parents and this finding was independent of the time of incubation. Thus, our results broadly confirm that the swabbing of eggshells can be used as a noninvasive method for obtaining DNA and is applicable across a wide range of bird species. Nonetheless, genotyping errors should be properly estimated for each species by using a suite of highly polymorphic loci. These errors may be resolved by sampling only recently laid eggs (to avoid non-maternal DNA contamination) or by performing several PCR replicates per sample (to avoid allelic dropout and false alleles) and/or by increasing the amount of DNA used in the PCR through increasing the volume of the PCR or increasing the concentration of template DNA.

Molecular characterization of G and P-types bovine rotavirus strains from Goiás, Brazil: high frequency of mixed P-type infections

In this study, 331 samples from calves less than one month old from a dairy herd in the district of Piracanjuba, state of Goiás, Brazil were tested for rotavirus. Thirty-three samples (9.9%) tested positive for rotavirus. Out of those, 31 were submitted to G and P characterization by reverse transcription followed by semi-nested polymerase chain reaction. Two samples were characterized as G6P[1], three as G10P[11] and five as G6P[11]. The majority of the samples (51.6%) displayed multiple P genotypes (P-genotype mixtures), including typical human genotypes P[4] and P[6M], suggesting the occurrence of co-infections and genetic reassortment. Also, the detection of human genotypes in bovine samples may be considered evidence of the zoonotic potential of rotaviruses. To our knowledge, this is the first report of such a high frequency of P genotype mixtures in bovine rotavirus samples. It also increases data on G and P rotavirus genotypes circulating in dairy herds in Brazil and can help in the development of more efficient immunization approaches, thereby controlling infection and reducing economical losses.

Genetic and Biological Analysis of ColombianPhthorimaea operculellaGranulovirus Isolated fromTecia solanivora(Lepidoptera: Gelechiidae)

Tecia solanivora (Lepidoptera: Gelechiidae) is an invasive potato pest of the north of South America that recently colonized zones where Phthorimaea operculella (Lepidoptera: Gelechiidae), a taxonomically related insect, was established. Nowadays, both species can be found in most areas in different proportions. The Phthorimaea operculella granulovirus (PhopGV) was found to efficiently control P. operculella and was used as a biopesticide in storage conditions. However, no appropriate biological control methods exist for T. solanivora, and the use of granulovirus isolates would provide a solution. The Colombian Corporation for Agricultural Research (CORPOICA) carried out several T. solanivora larva samplings in Colombia with the aim of finding potential isolates. Five geographical granulovirus isolates from T. solanivora (VG001, VG002, VG003, VG004, and VG005) were found, and molecular analysis by REN profiles shows three different genotypic variants in Colombia. Analysis of their genomes revealed their relatedness to PhopGV. Two isolates exhibited submolar bands in their REN patterns, suggesting a mixture of viral genotypes. These data were confirmed by PCR amplification and sequencing of particular regions of the viral genomes. Their biological activity was assayed on both hosts, T. solanivora and P. operculella. A significantly higher pathogenicity in both hosts was observed with isolates VG001 and VG005 than with isolate VG003 or a Peruvian isolate (from P. operculella) used as a reference in the bioassay. Based on their molecular and biological activity characteristics, VG001 and VG005 isolates should be selected for further analysis in order to establish their potential as biological control agents.

Diagnostic accuracy of an allele-specific reverse transcriptase-PCR assay targeting the H275Y oseltamivir resistant mutation in 2009 pandemic influenza A/H1N1 virus

Oseltamivir resistant 2009 pandemic influenza A/H1N1 viruses (pH1N1) are emerging and rapid molecular assays identifying these strains are needed for clinical management. Development and evaluation of an allele-specific, real-time reverse transcriptase-PCR assay (ASPCR) targeting the H275Y oseltamivir resistant mutation in pH1N1 virus. ASPCR uses two allele-specific forward primers (wild-type and mutant) and a common reverse primer and probe. Wild-type and mutant genotypes were defined by the difference in PCR Ct values (DeltaCt(mut-wt)) between the mutant primer and wild-type primer amplification curves for the same sample. Mixtures of wild-type and mutant genotypes were analyzed to evaluate sensitivity and determine assay cut-off values. ASPCR results were confirmed using an allelic discrimination assay (AD) and pyrosequencing. Mixtures containing 5-95% mutant genotype could be detected. A DeltaCt(mut-wt)>or=3.5 identified wild-type genotype (<10% mutant); between 3.5 and -3.5 identified mixed genotypes (10-90% mutant); and <or=-3.5 identified fully mutant genotype (>90% mutant). Among 264 clinical samples, 171 were wild-type, 10 were mixed, and 29 were fully mutant. The 39 samples with mixed or mutant results were from 11 patients. Of 107 samples with sufficient volume tested by ASPCR and AD, 12 were indeterminate by AD due to low viral load, 86 were wild-type by both assays, and 9 were mutant by both assays. Thirteen samples were confirmed by pyrosequencing and one discrepant sample was mixed by ASPCR and fully mutant by pyrosequencing. ASPCR is sensitive, quantitative and specific for H275Y mutation analysis and provides an accurate approach for detecting pH1N1 oseltamivir resistance in clinical samples.

Genotypic variation and mixtures of Lyme Borrelia in Ixodes ticks from North America and Europe.

BackgroundLyme disease, caused by various species of Borrelia, is transmitted by Ixodes ticks in North America and Europe. Studies have shown the genotype of Borrelia burgdorferi sensu stricto (s.s.) or the species of B. burgdorferi sensu lato (s.l.) affects the ability of the bacteria to cause local or disseminated infection in humans.Methodology/Principal FindingsWe used a multilocus PCR electrospray mass spectrometry assay to determine the species and genotype Borrelia from ticks collected in New York, Connecticut, Indiana, Southern Germany, and California and characterized isolates from parts of the United States and Europe. These analyses identified 53 distinct genotypes of B. burgdorferi sensu stricto with higher resolution than ospC typing. Genotypes of other members of the B. burgdorferi sensu lato complex were also identified and genotyped including B. afzelii, B. garinii, B. lusitaniae, B. spielmanii, and B. valaisiana. While each site in North America had genotypes unique to that location, we found genotypes shared between individual regions and two genotypes found across the United States. Significant B. burgdorferi s.s. genotypic diversity was observed between North America and Europe: only 6.6% of US genotypes (3 of 45) were found in Europe and 27% of the European genotypes (3 of 11) were observed in the US. Interestingly, 39% of adult Ixodes scapularis ticks from North America were infected with more than one genotype of B. burgdorferi s.s. and 22.2% of Ixodes ricinus ticks from Germany were infected with more than one genotype of B. burgdorferi s.l.Conclusions/SignificanceThe presence of multiple Borrelia genotypes in ticks increases the probability that a person will be infected with more than one genotype of B. burgdorferi, potentially increasing the risks of disseminated Lyme disease. Our study indicates that the genotypic diversity of Borrelia in ticks in both North America and Europe is higher then previously reported and can have potential clinical consequences.