Molecular Genotyping and a Novel MicroRNA of BK Polyomavirus Associated with Renal Failure Patients

Background:

The family Polyomaviridae includes the human polyomavirus BKV. The virus infects humans in a broad population without the affected individuals exhibiting any apparent symptoms. Viral pathogenicity and replication are regulated by two microRNAs (miRNAs) encoded by BKV, bkv-miR-B1-3p, and bkv-miR-B1-5p, which target host genes as well as viral early genes.

Objectives:

To quantify the BKV deoxyribonucleic acid (DNA) and viral DNA (VP1) sequence variation in renal failure patients with an assessment of viral miRNA expression.

Materials and Methods:

Of the 323 patients admitted to the Dialysis Unit at Al-Hussein Medical City in Karbala with renal failure, 114 chose to participate in the study. The included individuals were 73 males and 41 females. Urine and blood samples (41, 73, respectively) were collected, extracted, purified, and assayed by a real-time PCR-based Taq Man target VPI gene to determine genotype. The assessment of the miRNA assay was done by real-time PCR-based SYBR green.

Results:

The samples revealed that 21 (18%) samples with BK virus DNA. The positive result was male 12 out of 73 (16.4%) with a mean age ± SD of 40.92 ± 13.47 and female 9 out of 41 (22%) with a mean age of 57 ± 18.72, and a statistically significant P value of 0.025. The rate of BKV DNA in males aged 40 was higher than in females aged 57. The BKV genotype 1 was detected in positive results without other genotypes. The BKV DNA viral load median is 2361 (range 17 to 30.002.143) copies/mL.

Nested PCR was down to the amplification result after sequencing, alignment, and phylogenetic tree analysis. BKV PP355797 isolate was shown as new genetic variants related to gene bank BKV in different countries at total genetic changes (0.02%–0.01%). positive BKV DNA sample, urine, and blood were analyzed. The results showed the expression of both miRNAs in all positive BKV DNA. The fold change of miRNA compares with a reference gene, bkv-miR-B1-5p, with a median of 3.03 (range 0.32 to 41.77), and bkv-miR-B1-3p with a median of 3.65 (range 0.05 to 12.10). There are no statistical differences between bkv-miR-B1-3p and bkv-miR-B1-5p in expression ( P -value > 0.5 = 0.678).

Conclusions:

BKV early VP1 sequencing in plasma and urine samples at the beginning of the infection helps identify the strain that is more likely to cause viral nephropathy. BKV miRNAs and BKV DNA levels were found to be correlated in both urine and plasma, suggesting that viral miRNAs may represent the amount of virus and serve as a stable biomarker for miRNA in both clinical and in vitro experiment samples.