Failure to genotype Human Cytomegalovirus by PCR-RFLP method due to sequence variation within the primer binding site

Rapid and sensitive point-of-care diagnosis of human cytomegalovirus infection using RPA-CRISPR technology

Background

Human cytomegalovirus (HCMV) is a common herpesvirus that can cause a range of symptoms, from mild conditions such as fevers to severe illnesses like pneumonia. Early and accurate diagnosis of HCMV infection is crucial, particularly for vulnerable populations with limited medical care. However, current diagnostic methods are often expensive, time-consuming, and require skilled technicians.

Materials and methods

We developed an HCMV-RPA-CRISPR diagnosis platform for the rapid and cost-effective detection of HCMV infection. This method utilizes recombinase polymerase amplification (RPA) to amplify the HCMV target gene isothermally without the need for thermal cycling equipment. The platform integrates the CRISPR/Cas12a system, significantly enhancing specificity and sensitivity. A total of 13 clinical blood samples were tested to evaluate the platform's effectiveness and accuracy. Additionally, a lateral flow assay (LFA) and fluorescence detection were incorporated for straightforward and rapid visual interpretation of the results.

Results

The assay effectively detected concentrations as low as a single copy of the positive control plasmid per microliter in under 1 h, without requiring specialized equipment or training. In clinical sample evaluations, both the fluorescence readout and LFA exhibited 100% sensitivity and specificity, identifying four HCMV-positive and nine HCMV-negative samples.

Conclusion

The HCMV-RPA-CRISPR diagnosis platform is comparably effective to qPCR for HCMV diagnosis. Its applicability in common clinical laboratories, clinics, and point-of-care settings, particularly in resource-limited environments, makes it a valuable tool for widespread HCMV screening and diagnosis.

Human cytomegalovirus glycoprotein B genotypes in Chinese hematopoietic stem cell transplant recipients

OBJECTIVES

To investigate the distribution of human cytomegalovirus (HCMV) glycoprotein B (gB) genotypes and to explore the possible relationship between gB genotypes and clinical characteristics in Chinese hematopoietic stem cell transplant (HSCT) recipients.

METHODS

A prospective analysis of gB genotypes was conducted on HCMV clinical isolates obtained from 102 HSCT recipients. Real-time quantitative PCR and PCR-based restriction fragment length polymorphism analysis were applied for the determination of viral loads and gB genotypes, respectively.

RESULTS

The distribution of gB genotypes was as follows: gB1, 54/102 (52.9%); gB3, 21/102 (20.6%); and mixtures, 27/102 (26.5%). The rate of viral clearance at day 21 was higher in patients infected with the gB1 genotype than in those infected with the gB3 genotype (56 and 29%, respectively; p = 0.036). In contrast, the rate of HCMV reactivation/reinfection was higher in patients infected with the gB3 genotype than in those infected with the gB1 genotype (81 and 56%, respectively; p = 0.041).

CONCLUSIONS

The HCMV gB1 genotype is the most prevalent among Chinese HSCT recipients; patients infected with the gB3 genotype have more difficulty eradicating the virus and have a higher risk of reactivation/reinfection than those infected with the gB1 genotype.

Cytomegalovirus gB genotype distribution in Mexican children undergoing allogeneic bone marrow transplantation

We used nested multiplex polymerase chain reaction to determine the distribution of cytomegalovirus gB genotype in 30 Mexican children undergoing bone marrow transplantation. The genotypes were: gB1, 9/30 (30%); gB2, 8/30 (27%); gB3, 4/30 (13%), and gB4, 1/30 (3%); mixed genotypes were identified in 8/30 patients (27%). We conclude that the predominant genotypes identified were gB2 and gB1. The gB5 genotype was not detected, and a high proportion of mixed genotype was found.

A cautionary note on the use of nested PCR for parasite screening--an example from avian blood parasites

The use of new powerful nested polymerase chain reaction (PCR) techniques to identify and screen for prevalence of parasites has a huge potential. It allows for the detection and identification of low-intensity infections, but its high sensitivity and technical setup may also induce problems. Here, we report a cautionary note regarding misleading amplification of avian malaria species (Haemoproteus and Plasmodium) during Leucocytozoon spp. detection. We used a previously described nested PCR method for the molecular detection of avian malaria and Leucocytozoon spp. In the first step of the PCR protocol, these parasites are detected simultaneously; in the second PCR, Haemoproteus and Plasmodium spp. are separated from Leucocytozoon spp. However, in certain cases when a bird was infected with avian malaria, we obtained a slightly longer PCR product during the detection of Leucocytozoon spp. Our data imply that these "false" Leucocytozoon fragments are the consequences of strong amplification of certain malaria lineages in the first PCR, which can also be detected after the second PCR amplification that is specific to Leucocytozoon spp. parasites. Because these "false" Leucocytozoon fragments are slightly longer than the normal Leucocytozoon fragments, we suggest the use of well-separating agarose gels, several positive controls, and molecular standards to facilitate their separation. If one obtains a fragment that differs in length from the one expected for Leucocytozoon spp., sequencing is essential. More generally, in order to limit this type of problem with nested PCR protocols, we suggest that the first and the second primer pair be chosen so that they have different annealing temperatures.

Identification of a highly conserved region in the human cytomegalovirus glycoprotein H gene and design of molecular diagnostic methods targeting the region

Genomic polymorphism of human cytomegalovirus (HCMV) leads to difficulties in the design of molecular diagnostic systems; therefore, a suitable target region was determined in the glycoprotein H (gH) gene, which has been reported to be the most conserved gene. A highly conserved region was identified from codon 1,282 to 1,988 of the gH gene by alignment of 23 nucleotide sequences (14 registered in the DNA Data Bank of Japan and 9 sequenced in this laboratory). Diagnostic methods based on nested PCR, real-time PCR and loop-mediated isothermal temperature amplification (LAMP) were designed for this region. Primers and a probe for nested and real-time PCR were designed for the completely conserved sequences in all HCMV strains. However, a few mismatched nucleotides could not be excluded from the LAMP primers due to the need for eight primer-binding sites in a 200bp-region. The sensitivities of the nested PCR, real-time PCR and LAMP reactions were 5, 10 and 100 copies/tube, respectively. An analysis of clinical specimens showed that both nested and real-time PCR detected HCMV with greater sensitivity than did a pp65 antigenemia assay and were expected to minimize the incidence of false-negative results, whereas the sensitivity of the LAMP reaction was comparable with that of the antigenemia assay.