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Detection of cytomegalovirus (CMV) by digital PCR in stool samples for the non-invasive diagnosis of CMV gastroenteritis | Virology Journal

sufferers and samples

This examine enrolled sufferers from 2017 to 2020 who have been receiving allo-HSCT or chimeric antigen receptor T cell (CAR-T) remedy and had gastrointestinal signs equivalent to belly ache and diarrhea lasting longer than two weeks. The examine was authorized by the Ethics Committee of Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (TJ-IRB20180809). Informed consent was obtained from the contributors. Watery stool samples have been positioned in sterile containers and instantly despatched to the laboratory after assortment, briefly saved at 4°C, after which processed inside 8 hours of assortment.

DNA extraction

We filtered the watery stool samples with a 300 mesh filter material and centrifuged the samples at 3000 rpm for 10 min, collected the supernatant and centrifuged once more for 10 min to take away the greedy elements. Both strategies have been began with 1 ml fecal supernatant. Cell-free DNA and whole DNA have been extracted utilizing a QIAamp Circulating Nucleic Acid Kit (catalog quantity 55114; Qiagen, Valencia, CA, USA) and QIAamp DNA Stool Mini Kit (catalog quantity 51504; Qiagen, Valencia, CA, USA), respectively, based on the directions from the producer and each elution volumes have been 25 µl. DNA focus was measured utilizing a Qubit Fluorometer 3.0 (Qubit dsDNA HS Assay Kit; Invitrogen, Carlsbad, CA, USA) or a NanoDrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) when the focus was out of vary Qubit Fluorometer (0-10 ng/µL). DNA samples have been used instantly in assay experiments or saved at −20 °C after extraction.

Design of primers and probes

Probes and primers concentrating on the conserved area for IE1 (innate early protein gene 1) of CMV and the reference gene human nuclear RNase P protein POP4 have been generated utilizing Primer Express software program model 3.0.1 (Thermo Fisher Scientific, Waltham , MA, USA) and designed synthesized by Sangon Biotech Company (Shanghai, China). The sequences of the CMV primers have been as follows: ahead 5′-GTGATCCATGTGCTTATGACTTTGT-3′, reverse 5′-GCCTTGGTCACGGGTGTCT-3′, and probe 5′-FAM-ATCATGTGTTTAGGCCC-MGB-3′. The sequences of the reference primers have been as follows: ahead 5′-GGCGGGTGGTCCTGGAGTACT-3′, reverse 5′-AGAGGCCTTTGGCTTTCTTCTT-3′, and probe 5′-VIC-ACCCGCCACAAGC-MGB-3′. The lengths of the CMV and POP4 amplicons have been 64 bp and 68 bp, respectively.

Digital PCR

The dPCR method was carried out as beforehand described [17]. Briefly, a response combine consisting of 10 µl 2× ddPCR Supermix (no dUTPs; Bio–Rad, Hercules, USA), primers (1 µl, 10 µmol/l), fluorescently labeled probes (2 µl, 2.5 µmol/l) , and a couple of µl of DNA template (vary 0.6-66 ng) have been loaded right into a Quantalife QX200 Droplet Digital PCR System (Bio-Rad, Hercules, USA), the whole quantity of the response combine was 20 µl. Water-in-oil droplets have been generated in eight-well cartridges utilizing the QX200 droplet generator and transferred to a 96-well polypropylene plate sealed with foil paper. The plate was then positioned in an ABI thermal cycler (Thermo Fisher Scientific, Waltham, MA, USA). Conditions have been as follows: 95°C for 5 min, adopted by 40 cycles of 95°C for 30 s, 60°C for 1 min (not more than 2.5°C/sec ramp price), with 10 min maintain at 98°C and a remaining maintain at 4°C. After PCR, the outcomes have been learn by a QX200 droplet reader and analyzed in QuantaSoft software program model 1.7.4 based on the producer’s directions. Each response was analyzed individually and the thresholds have been adjusted manually if wanted and adjusted individually for the fluorescence channels. The remaining copy quantity outcomes in the unique samples have been offered by default as copies/mL for the CMV DNA section and reference gene (extra recordsdata 1, 2, 3, 4, 5, 6, 7).

Plasmid development and verification

The CMV goal sequence was joined to the plasmid vector pUC57 to assemble a plasmid commonplace for testing quantitative capability, and the recombinant plasmid was reworked E. coli DH5α to finish proliferation. The recombinant plasmid was extracted and purified with the EndoFree Plasmid Maxi Kit (catalog quantity 12362; Qiagen, Valencia, CA, USA) and quantitated with a NanoDrop spectrophotometer, then the copy quantity was calculated with identified focus, molecular weight and Avogadro’s fixed. The recombinant plasmid was linearized by the restriction enzymes HindIII (catalog quantity R0104S; NEB, USA) and BamHI (catalog quantity R0136S; NEB, USA), leaving the intact CMV goal sequence on the linearized plasmid. Five-fold serial dilutions have been carried out at concentrations starting from roughly 10,000 copies/µl to three.2 copies/µl and subjected to dPCR. Each commonplace focus was repeated 3 times beneath the similar circumstances to find out quantitative linearity.

Plasma CMV DNA Analysis

3 ml of ethylenediaminetetraacetic acid (EDTA) anticoagulated entire blood samples have been collected after which centrifuged at 3000 rpm for 5 min to gather 100 µl of plasma for CMV DNA detection. The plasma samples have been processed and CMV DNA was examined based on the directions of the HCMV PCR Fluorescence Qualification Detection Kit (Daan-Gene, Guangzhou, China).

Statistical evaluation

All statistical analyzes have been carried out utilizing R v4.0.5 statistical software program. The paired-sample Wilcoxon signed rank check, Fisher’s actual check, and Pearson’s chi-square check have been used as acceptable in particular conditions.

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