Geographic characteristics of HTLV-1 molecular subgroups and genetic substitutions in East Asia: Insights from complete genome sequencing of HTLV-1 strains isolated in Taiwan and Japan.

BACKGROUND: Although Japan is a major endemic area for human T-lymphotropic virus type 1 (HTLV-1) and the virus has been well-studied in this region, there is limited research on HTLV-1 in surrounding regions. In this study, we determined the complete genome sequences of HTLV-1 strains isolated from Taiwan and Japan and investigated the geographic characteristics of molecular subgroups and substitution mutations to understand the spread of HTLV-1 and its correlation with human migration. METHODOLOGY/PRINCIPAL FINDINGS: The complete genome sequences of 26 HTLV-1 isolates from Taiwan were determined using next-generation sequencing and were compared with those of 211 isolates from Japan in terms of subgroup and genetic mutations. In total, 15/26 (58%) isolates from Taiwan belonged to the transcontinental subgroup and 11/26 (42%) isolates belonged to the Japanese subgroup. The transcontinental subgroup was significantly more prevalent among Taiwanese isolates than Japanese isolates (58% vs 18%, P < 0.0001). The mutation rate for the complete HTLV-1 sequence was as low as 0.2%. On examining individual base substitutions, the G-to-A mutation was predominant. Bayesian phylogenetic tree analysis estimated the time to the most recent common ancestor for the transcontinental and Japanese subgroups to be 28447 years. The transcontinental subgroups from Taiwan and Japan appeared to form clusters according to their respective regions. CONCLUSIONS/SIGNIFICANCE: The transcontinental subgroup of HTLV-1 is predominant in Taiwan, while the Japanese subgroup is common in Japan. The difference in subgroup distribution may be attributed to the initial spread of the transcontinental subgroup in East Asia, followed by the influx of the Japanese subgroup.

Genotyping and serotyping profiles showed weak Jka presentation for previously typed as Jknull donors.

BACKGROUND AND OBJECTIVES: Kidd blood group system consists of two major antigens: Jka and Jkb . Both the antigens are absent in individuals typed as Jknull and may develop clinically significant anti-Jk3 antibody. Screening donors for provision of Jknull blood is an ongoing task for blood centres with Jknull blood units kept frozen for specific requirements. In 2016, we discovered a previously typed Jknull donor to be Jka weak positive. Therefore, a study was conducted for our donors to verify Jknull status and to reinforce our typing protocol. MATERIALS AND METHODS: In this experiment, donors previously typed and screened as Jknull were tested with four antisera of Jka and Jkb , and each with gel card for serology testing. Sequence analysis was performed for SLC14A1 gene for the detection of JKnull and weak alleles for genetic testing. RESULTS: Among the 30 samples, four were serologically identified as Jk(a+w ) and genotypically identified as heterozygous for the JK*01W.01 allele. The other 26 were confirmed to be Jknull with JK*02N.01 as the most frequent allele. None of JK*B weak alleles were detected, but three were identified as false positives in the tube method. Gel card gave great accuracy for Jkb detection, but failed to give consistent results for weak Jka . CONCLUSION: By combining the tube method and gel card method in serology, along with complementary genetic testing, the possibility of misinterpreting weak Jka expression was eliminated, and we were able to provide Jknull blood for safe clinical transfusion.

ABO genotyping with next-generation sequencing to resolve heterogeneity in donors with serology discrepancies.

BACKGROUND: ABO subtypes are characterized by the alteration of antigens present and their expression levels on red blood cells and many are linked to genetic changes in the ABO gene. Weakened expression of antigens should be identified to prevent transfusion reactions or ABO-incompatible transplantations. Genotyping can be applied to identify subtypes to complement serologic testing. Next-generation sequencing (NGS) has shown to provide sensitive and accurate genotyping results as well as valuable cis/trans information. Here we took advantage of NGS and applied it to resolve serology discrepancies in ABO typing. STUDY DESIGN AND METHODS: In this study, we customized capture probes targeting the entire ABO gene and sequenced on MiSeq Illumina. The subtype-causing variants were identified, and cis/trans association to ABO alleles was determined. The results from NGS, serology, and Sanger sequencing were compared. RESULTS: Four control samples typed A, B, O, and AB were correctly genotyped. Of 24 serologically discrepant samples, subtype-causing variations were found in 20 cases, with two unresolved and two identified as weakening of ABO antibody in reverse. The types of variations include 17 known subtype alleles, one novel variant, one novel large deletion, and one microchimerism. Haplotypes encompassing Exons 6 and 7 of ABO were reconstructed in 17 of the 20 samples. CONCLUSION: This study demonstrated a full coverage of ABO by capture-based panel, phasing analysis with NGS in ABO genotyping resolved heterogeneity with novel allele and microchimerism findings. This approach provided a more precise method for subtyping and thereby leading to safer transfusion.

Sequence-Based Typing for Platelet alloantigens.

Human platelet antigen (HPA) typing is largely performed by use of DNA-based techniques in patients that require assessing the risk of HPA alloimmunization. In this chapter, HPA typing by sequencing-based typing (SBT) techniques is described.

Human platelet antigen alleles in 998 Taiwanese blood donors determined by sequence-specific primer polymerase chain reaction.

Polymorphism of human platelet antigens (HPAs) leads to alloimmunizations and immune-mediated platelet disorders including fetal-neonatal alloimmune thrombocytopenia (FNAIT), posttransfusion purpura (PTP), and platelet transfusion refractoriness (PTR). HPA typing and knowledge of antigen frequency in a population are important in particular for the provision of HPA-matched blood components for patients with PTR. We have performed allele genotyping for HPA-1 through -6 and -15 among 998 platelet donors from 6 blood centers in Taiwan using sequence-specific primer polymerase chain reaction. The HPA allele frequency was 99.55, and 0.45% for HPA-1a and -1b; 96.49, and 3.51% for HPA-2a and -2b; 55.81, and 44.19% for HPA-3a and -3b; 99.75, and 0.25% for HPA-4a and -4b; 98.50, and 1.50% for HPA-5a and -5b; 97.75 and 2.25% for HPA-6a and -6b; 53.71 and 46.29% for HPA-15a and -15b. HPA-15b and HPA-3a, may be considered the most important, followed by HPA-2, -6, -1, -5, and -4 systems, as a cause of FNAIT, PTP, and PTR based on allele frequency. HPA-4b and HPA-5b role cannot be excluded based on their immunogenicity. A larger-scale study will now be conducted to confirm these hypotheses and to establish an apheresis donor database for the procurement of HPA-matched apheresis platelets for patients with PTR.

Epitope-based matching for HLA-alloimmunized platelet refractoriness in patients with hematologic diseases.

BACKGROUND: For HLA-alloimmunized patients, platelet (PLT) concentrations are provided either at matched HLA-A and HLA-B loci or by serologic cross-reactivity groups (CREG) matching strategy. However, this method has some limitations. STUDY DESIGN AND METHODS: In this study, the epitope-based matching (EBM) method was evaluated for selecting proper HLA-typed PLTs for patients with PLT transfusion refractoriness. Bead-based single-antigen HLA antibody detection method and HLAMatchmaker software were used to define the epitopes recognized by HLA-specific antibodies and to select compatible PLTs for nine patients with alloimmunized refractoriness. Corrected count increments (CCIs) were prospectively determined to compare successful transfusion rates among different matching methods in 142 PLT transfusions. In addition, HLA antibodies were serially detected to see whether any emerging antibodies appeared after receiving the EBM-matched PLTs. RESULTS: The transfusion success rates evaluated with 1-hour CCIs for perfect matching or lacking any mismatching at HLA-A and -B locus (A/BU)-matched, CREG-matched, and EBM-matched PLTs were 85.2, 63.2, and 83.7%, respectively. Compared to CREG-matched PLTs, EBM-matched PLTs showed better transfusion results (p = 0.035). In the follow-up study (7 months; range, 3-13 months), no emerging HLA-specific antibodies were detected after receiving EBM-matched PLTs. CONCLUSIONS: EBM performed on the basis of bead-based single-antigen HLA antibody detection coupled with the HLAMatchmaker program is recommended in choosing proper PLTs for refractory patients when A/BU-matched PLTs were not available.

Purification and characterization of inducible cephalexin synthesizing enzyme in Gluconobacter oxydans.

Cephalexin synthesizing enzyme (CSE) of Gluconobacter oxydans ATCC 9324 was purified up to about 940-fold at a yield of 12%. CSE biosynthesis in G. oxydans was found inducible in the presence of D-phenylglycine but not its substrate phenylglycine methyl ester. The purified enzyme was shown homogeneous on SDS-PAGE and exhibited a specific activity of 440 U per mg protein. The apparent molecular mass of the native enzyme was estimated to be 70 kDa over a Superdex 200 gel filtration column and 68 kDa on SDS-PAGE, indicating that the native enzyme is a monomer. Its isoelectric focusing point is 7.1, indicating a neutral character. The enzyme had maximal activity around pH 6.0 to 6.5, and this activity was thermally stable up to 40 degrees C. Synthesis of cephalexin from D-phenylglycine methyl ester and 7-amino-3-deacetoxycephalosporanic acid (7-ADCA) by the purified CSE was demonstrated. Its L-enantiomer was not accepted by CSE. Apart from cephalexin, ampicillin was also synthesized by the purified CSE from its acyl precursors and 6-aminopenicillanic acid (6-APA). Substrate specificity studies indicated that the enzyme required a free alpha amino group and an activated carboxyl group as a methyl ester of D-form phenylglycine. Interestingly, the purified enzyme did not catalyze hydrolysis of its products, e.g., cephalexin, cephradine, and ampicillin, in contrast to enzymes from other strains of Pseudomonadaceae.