Single-tube Multiplex Polymerase Chain Reaction Research Articles

Analysis of the epidemiological situation of influenza in Guangzhou under the prevention and control of COVID-19 in June 2022.

Under the prevention and control measures of COVID-19, the epidemiological situation of respiratory pathogens is not well known. Understanding the patterns of respiratory pathogens epidemiology under the prevention and control measures of COVID-19 is important to guide resource allocation for existing and future treatment and prevention strategies. In total, 659 fever outpatients nasopharyngeal swabs were collected at fever illness onset during June in 2022 at the First Hospital of Guangzhou Medical University. Swabs were tested by real-time fluorescent single-tube multiplex polymerase chain reaction (PCR) for 12 respiratory pathogens. Moreover, 108 of the 659 swabs were tested for influenza virus antigen. At least one pathogen was detected in 477 (72.38%) of 659 fever outpatients with multiple pathogens identified in 25 (3.79%). The highest multiple infectious pattern is parainfluenza virus in combination with influenza (five cases). Influenza A virus (IFA), human rhinovirus (HRV), and parainfluenza virus are the three leading virus pathogens with proportions of 64.64%, 5.01%, and 2.88%. School-age children and adult groups have the highest pathogens positivity rate of 81.28% and 83.87%. A high proportion of adolescents and adults has respiratory pathogens detected during fever illnesses during June in 2022 under the prevention and control of COVID-19. These data indicate that diagnosis, prevention, and control of respiratory tract infection should be paid attention under the prevention and control of COVID-19.

A study of the composition of the Obsoletus complex and genetic diversity of Culicoides obsoletus populations in Spain

BackgroundThe Culicoides obsoletus species complex (henceforth ‘Obsoletus complex’) is implicated in the transmission of several arboviruses that can cause severe disease in livestock, such as bluetongue, African horse sickness, epizootic hemorrhagic disease and Schmallenberg disease. Thus, this study aimed to increase our knowledge of the composition and genetic diversity of the Obsoletus complex by partial sequencing of the cytochrome c oxidase I (cox1) gene in poorly studied areas of Spain.MethodsA study of C. obsoletus populations was carried out using a single-tube multiplex polymerase chain reaction (PCR) assay that was designed to differentiate the Obsoletus complex sibling species Culicoides obsoletus and Culicoides scoticus, based on the partial amplification of the cox1 gene, as well as cox1 georeferenced sequences from Spain available at GenBank. We sampled 117 insects of the Obsoletus complex from six locations and used a total of 238 sequences of C. obsoletus (ss) individuals (sampled here, and from GenBank) from 14 sites in mainland Spain, the Balearic Islands and the Canary Islands for genetic diversity and phylogenetic analyses.ResultsWe identified 90 C. obsoletus (ss), 19 Culicoides scoticus and five Culicoides montanus midges from the six collection sites sampled, and found that the genetic diversity of C. obsoletus (ss) were higher in mainland Spain than in the Canary Islands. The multiplex PCR had limitations in terms of specificity, and no cryptic species within the Obsoletus complex were identified.ConclusionsWithin the Obsoletus complex, C. obsoletus (ss) was the predominant species in the analyzed sites of mainland Spain. Information about the species composition of the Obsoletus complex could be of relevance for future epidemiological studies when specific aspects of the vector competence and capacity of each species have been identified. Our results indicate that the intraspecific divergence is higher in C. obsoletus (ss) northern populations, and demonstrate the isolation of C. obsoletus (ss) populations of the Canary Islands.Graphical abstract

Molecular Detection of Alpha Thalassemia: A Review of Prevalent Techniques.

Alpha thalassemia (α-thalassemia) is an autosomal recessive disorder due to the reduction or absence of α globin chain production. Laboratory diagnosis of α-thalassemia requires molecular analysis for the confirmatory diagnosis. A screening test, comprising complete blood count, blood smear and hemoglobin quantification by high performance liquid chromatography and capillary electrophoresis, may not possibly detect all the thalassemia diseases. This review focused on the molecular techniques used to detect α-thalassemia, and the advantages and disadvantages of each technique were highlighted. Multiplex gap-polymerase chain reaction, single-tube multiplex polymerase chain reaction, multiplex ligation-dependent probe amplification, and loop-mediated isothermal amplification were used to detect common deletion of α-thalassemia. Furthermore, the reverse dot blot analysis and a single tube multiplex polymerase chain reaction could detect non-deletion mutation of the α-globin gene. Sanger sequencing is widely used to detect non-deletion mutations of α-thalassemia. Recently, next-generation sequencing was introduced in the diagnosis of both deletion and point mutations of α-thalassemia. Despite the advantages and disadvantages of different techniques, the routine method employed in the laboratory should be based on the facility, expertise, available equipment, and economic conditions.

Molecular analysis and association with clinical and laboratory manifestations in children with sickle cell anemia.

ObjectivesTo analyze the frequency of βS-globin haplotypes and alpha-thalassemia, and their influence on clinical manifestations and the hematological profile of children with sickle cell anemia.MethodThe frequency of βS-globin haplotypes and alpha-thalassemia and any association with clinical and laboratorial manifestations were determined in 117 sickle cell anemia children aged 3–71 months. The confirmation of hemoglobin SS and determination of the haplotypes were achieved by polymerase chain reaction-restriction fragment length polymorphism, and alpha-thalassemia genotyping was by multiplex polymerase chain reaction (single-tube multiplex-polymerase chain reaction).ResultsThe genotype distribution of haplotypes was 43 (36.7%) Central African Republic/Benin, 41 (35.0%) Central African Republic/Central African Republic, 20 (17.0%) Rare/atypical, and 13 (11.1%) Benin/Benin. The frequency of the α3.7 deletion was 1.71% as homozygous (−α3.7/−α3.7) and 11.9% as heterozygous (−α3.7/αα). The only significant association in respect to haplotypes was related to the mean corpuscular volume. The presence of alpha-thalassemia was significantly associated to decreases in mean corpuscular volume, mean corpuscular hemoglobin and reticulocyte count and to an increase in the red blood cell count. There were no significant associations of βS-globin haplotypes and alpha-thalassemia with clinical manifestations.ConclusionsIn the study population, the frequency of alpha-thalassemia was similar to published data in Brazil with the Central African Republic haplotype being the most common, followed by the Benin haplotype. βS-globin haplotypes and interaction between alpha-thalassemia and sickle cell anemia did not influence fetal hemoglobin concentrations or the number of clinical manifestations.

A comprehensive survey of both RHD and RHCE allele frequencies in sub‐Saharan Africa

The RH system is one of the most polymorphic blood group systems with numerous allele variants affecting Rh polypeptides expression. This complexity is at the origin of difficulties for transfusion of African patients especially sickle cell disease patients requiring chronic transfusion therapy with high risk of immunization. As a complete survey of RH variants is lacking in African populations, we performed red blood cell genotyping to determine the type and frequency of RHD and RHCE alleles in sub-Saharan African populations. A total of 347 blood samples were collected from individuals of six nonpygmoid and three pygmoid populations. RH typing was performed using two single-tube multiplex polymerase chain reaction amplifications (BioArray Solutions, Immucor). All six sub-Saharan nonpygmoid populations exhibited constant variety in both type and frequency of aberrant RHD and RHCE alleles. Predicted partial RH1 (1.8%) and RH5 (0.9%) phenotypes were less than expected. Conversely, predicted partial phenotype RH2 (5.5%) was frequent. Data confirmed the high frequency of samples positive for the non-clinically significant RH10/RH20 antigens (39.5%) and revealed a high frequency of RH54 (DAK, 8.1%). The pygmoid groups showed higher percentages of predicted partial RH antigens and greater heterogeneity reflecting wide genetic differentiation. Our data show that frequencies of aberrant RHD and RHCE alleles were similar, irrespective of location and ethnicity. In view of the predicted frequencies and relative clinical significance of both private antigens and high-prevalence antigens absent, the most relevant assays for individuals of African descent in a transfusion setting are for 1) partial RH2 in the patient and 2) RH54 (DAK) in the donor.


 Diagnosis of α-Thalassemia-1 Southeast Asian Type Deletion and Fetal Gender by Single-Tube Multiplex Real-Time PCR

The combination of an x-linked hematologic disorder with a heterozygous alpha-thalassemia-1 Southeast Asian (SEA) type deletion might lead to severe anemia in male infants. This study is to develop a simple and cost-effective single tube multiplex real-time PCR for the diagnosis of alpha-thalassemia-1 SEA type deletion and detect fetal gender. Multiplex real-time polymerase chain reaction (PCR) for the detection of alpha-thalassemia-1 SEA type deletion gene, wild type alpha-globin gene, and sex-determining region Y (SRY) gene was validated by analysis of 95 cord blood samples (60 normal individuals, 28 heterozygous of alpha-thalassemia-1 SEA type deletion and 7 Bart's hydrops fetalis). The change in threshold cycle (deltaC(T)) was analyzed by subtracting the C(T-mutant) from C(T-wild) type. Mean deltaC(T) values were significantly different among these three groups, and a SRY gene determination was 100% in concordance with fetal genders. Furthermore, analysis of fetal gender did not affect the deltaC(T) of alpha-thalassemia-1 SEA detection. Combined alpha-thalassemia-1 SEA type detection and fetal gender determination in a single-tube multiplex real-time PCR is an alternative assay for a conventional method for the diagnosis of alpha-thalassemia-1 SEA deletion and fetal gender.

One single-tube PCR assay to detect both CD17 (A>T) and IVS-II nt-654 (C>T) homozygous mutations of β-thalassemia

Several methods can be used to detect gene mutations associated with b-thalassemia, but it is difficult to achieve reliable and reproducible results. In this study, we introduce a new method, a single-tube multiplex polymerase chain reaction (PCR) assay, to detect both CD17 (A>T) and IVS-II nt-654 (C>T) homozygous mutations. Materials and methods: This new method designs specific primers to diagnose homozygous mutations and normal controls. Results: After PCR amplification, homozygous mutations produce different fragments from normal controls. Conclusion: This study represents an important step towards the development of a novel protocol to diagnose b-thalassemia and other diseases that target numerous mutations.

Establishment of a medium‐throughput approach for the genotyping of RHD variants and report of nine novel rare alleles

The routinely used serologic methods are robust in accurately typing standard D- or D+ blood. However, they result in discrepancy in weak or partial D blood, which requires genetic analysis. We have previously used denaturing high-performance liquid chromatography (DHPLC) to screen the entire RHD-coding sequence. However, DHPLC is technically challenging, labor-intensive, and time-consuming. To overcome these inconveniences, we sought to develop a new two-step approach. A total of 430 blood samples with D phenotype ambiguity were recruited for this study. The three most frequent weak D alleles (i.e., weak D, Type 1; weak D, Type 2; and weak D, Type 3), which altogether account for 60% to 90% of the atypical RHD alleles in the Caucasian population, were first identified by Tm-shift genotyping. The remaining unidentified samples were then subjected to a single-tube multiplex polymerase chain reaction (PCR) amplification of all 10 RHD exons followed by direct sequencing. Optimal conditions for efficient and reliable identification of the three most common weak D variants by Tm-shift genotyping were established. All 10 RHD exons were successfully amplified in a single-multiplex PCR procedure. Employment of the two-step analysis identified RHD variants in 91.6% of the 430 studied samples. Two of the nine previously undescribed variants, c.335G>T and c.939G>A, were found to cause aberrant mRNA splicing by means of a splicing minigene assay. The new two-step analysis proved to be much easier and cheaper than the DHPLC method and therefore is convenient to be used as a routine, medium-throughput approach for RHD genotyping.

Rapid isolation of translocation breakpoints in chronic myeloid and acute promyelocytic leukaemia

Isolation and sequencing of the translocation breakpoint in chronic myeloid leukaemia-(CML) and acute promyelocytic leukaemia (APML) may help to elucidate the mechanism of translocation and provide a molecular marker for monitoring of minimal residual disease. Amplification across the translocation breakpoint was performed in samples from 91 patients with CML and 15 patients with APML using single-tube multiplex polymerase chain reaction (PCR) involving 308 primers for CML and 40 primers for APML. Nonspecific amplification was removed by a modification of PCR, termed sequential hybrid primer PCR (SHP-PCR), which involved two sequential rounds of PCR, each of which used a low concentration of a specially designed hybrid primer. The resultant amplified material was sequenced. The method as finally developed was simple quick and robust. The translocation breakpoint was successfully isolated and sequenced in all 106 samples. The strategy of highly multiplexed PCR followed by SHP-PCR is thus an effective method for isolating the translocation breakpoint in CML and APML. It may also be applicable to other haematological disorders characterised by translocation, deletion or inversion.

Combined Molecular Diagnosis of B-cell Lymphomas With t(11;14)(q13;q32) or t(14;18)(q32;q21) Using Multiplex- and Long Distance Inverse-Polymerase Chain Reaction

Translocations t(14;18)(q32;q21) and t(11;14)(q13;q32) are recurrent findings in follicular lymphoma (FL) and mantle cell lymphoma (MCL), respectively. However, the molecular counterparts of these translocations can only be detected in up to 75% of FL and 50% of MCL cases using routine techniques. To improve the efficiency of detection, we first devised a single-tube multiplex-polymerase chain reaction (PCR) assay with primers located within a conserved immunoglobulin heavy chain (IGH) sequence and 5' to the main breakpoint cluster regions of BCL2 and CCND1. Using this assay in 17 FL and 11 MCL diagnostic DNA samples, we readily identified a BCL2-IGH fusion in 65% of FL patients and a CCND1-IGH fusion in 55% of MCL patients. In the remaining cases, we used long distance inverse-PCR to detect BCL2-IGH and CCND1-IGH fusion genes with different BCL2 and CCND1 breakpoint locations. We found additional translocations in 3 patients (17%) with FL and in 4 patients (36%) with MCL. Taken together, we show that multiplex-PCR combined with long distance inverse-PCR detected a t(14;18) in 82% of FL patients and a t(11;14) in 91% of MCL patients, demonstrating that this 2-step protocol is an effective approach for molecular detection of t(11;14) and t(14;18) in B-cell lymphomas.

Single‐Tube Multiplex PCR for Rapid and Sensitive Diagnosis of Subgenus B and Other Subgenera Adenoviruses in Clinical Samples

We developed a new diagnostic method of subgenus (Sub) B adenovirus (Ad) in clinical samples using non-nested polymerase chain reaction (PCR). Sequences of the conserved hexon-coding region of representative strains of eight serotypes (3, 7, 11, 14, 16, 21, 34 and 35) of Sub B Ad were heterogeneous. In order to distinguish Ad serotype 3 (Ad 3) and Ad 7 from the other serotypes of Sub B Ad, and to differentiate Ad 3 and 7 from each other, 3 different downstream primers were designed based on the sequence heterogeneity. By a single-tube PCR method using a combination of 6 primers including the 3 new primers, Ads demonstrated to amplify 188, 206, 284, and 301 bp DNA fragments for Ad 3, Ad 7, other Sub B Ads, and non-Sub B Ads, respectively. A total of 114 clinical samples were selected to evaluate the direct applicability of our PCR. The results were compared with previous culture results. Sixty-seven out of 71 (94%) Sub B Ad culture-positive samples, and 15 out of 19 (79%) Sub C or E-positive samples amplified products of the expected size. Two of 20 (10%) culture-negative samples from pharyngoconjunctival fever patients were identified as Ad 3 by the PCR. Four samples, from which non-Ad viruses were isolated, were negative by the PCR. The present study might provide a rapid and sensitive diagnosis method for infections caused by Sub B Ads.

Single-tube multiplex-PCR screen for common deletional determinants of α-thalassemia

-Thalassemia is very common throughout all tropical and subtropical regions of the world. In Southeast Asia and the Mediterranean regions, compound heterozygotes and homozygotes may have anemia that is mild to severe (hemoglobin [Hb] H disease) or lethal (Hb Bart's hydrops fetalis). We have developed a reliable, single-tube multiplex–polymerase chain reaction (PCR) assay for the 6 most frequently observed determinants of -thalassemia. The assay allows simple, high throughput genetic screening for these common hematological disorders. (Blood. 2000;95:360-362)