Rapid PCR Research Articles

Detection and Quantification of Klebsiella pneumoniae in Fecal Samples Using Digital Droplet PCR in Comparison with Real-Time PCR.

This study aimed to develop a rapid and sensitive droplet digital PCR (ddPCR) assay for the specific detection of Klebsiella pneumoniae in fecal samples, and to evaluate its application in the clinic by comparison with real-time PCR assay and conventional microbial culture. Specific primers and a probe targeting the K. pneumoniae hemolysin (khe) gene were designed. Thirteen other pathogens were used to evaluate the specificity of the primers and probe. A recombinant plasmid containing the khe gene was constructed and used to assess the sensitivity, repeatability, and reproducibility of the ddPCR. Clinical fecal samples (n = 103) were collected and tested by the ddPCR, real-time PCR, and conventional microbial culture methods. The detection limit of ddPCR for K. pneumoniae was 1.1 copies/μL, about a 10-fold increase in sensitivity compared with real-time PCR. The ddPCR was negative for the 13 pathogens other than K. pneumoniae, confirming its high specificity. Clinical fecal samples gave a higher rate of positivity in the K. pneumoniae ddPCR assay than in analysis by real-time PCR or conventional culture. ddPCR also showed less inhibition by the inhibitor in fecal sample than real-time PCR. Thus, we established a sensitive and effective ddPCR-based assay method for K. pneumoniae. It could be a useful tool for K. pneumoniae detection in feces and may serve as a reliable method to identify causal pathogens and help guide treatment decisions. IMPORTANCE Klebsiella pneumoniae can cause a range of illnesses and has a high colonization rate in the human gut, making it crucial to develop an efficient method for detecting K. pneumoniae in fecal samples.

Development of rapid and cost-effective multiplex PCR assays to differentiate catfish of the genus Brachyplatystoma (Pimelodidae-Siluriformes) sold in Brazil.

The catfishes Brachyplatystoma filamentosum (Kumakuma), Brachyplatystoma vaillantii (Laulao catfish), and Brachyplatystoma rousseauxii (gilded catfish) are important fishery resources in Brazil, where they are sold both fresh and in the form of fillets or steaks. These species have morphological similarities, thus, they can be easily misidentified or substituted, especially after processed. Therefore, accurate, sensitive, and reliable methods are needed for the identification of these species to avoid commercial fraud. In the present study, we develop two multiplex PCR assays for the identification of the three catfish species. Each multiplex protocol combined three species-specific forward primers and a universal reverse primer to produce banding patterns able to discriminate the target species unequivocally. The length of the cytochrome C oxidase subunit I (COI) fragments was approximately 254 bp for B. rousseauxii, 405 bp for B. vaillantii, and 466 bp for B. filamentosum, while the control region (CR) assay produced fragments of approximately 290 bp for B. filamentosum, 451 bp for B. vaillantii, and 580 bp for B. rousseauxii. The protocols were sensitive enough to detect the target species at a DNA concentration of 1 ng/µL, with the exception of the CR of B. vaillantii, in which the fragment was only detectable at 10 ng/µL. Therefore, the multiplex assays developed in the present study were sensitive, accurate, efficient, rapid, and cost-effective for the unequivocal identification of the target species of Brachyplatystoma. They can be utilized by fish processing industries to certify their products, or by government agencies to authenticate products and prevent fraudulent commercial substitutions.

Impact of the FilmArray Rapid Multiplex PCR Assay on Clinical Outcomes of Patients with Bacteremia.

Bacteremia is a serious disease with a reported mortality of 30%. Appropriate antibiotic use with a prompt blood culture can improve patient survival. However, when bacterial identification tests based on conventional biochemical properties are used, it takes 2 to 3 days from positive blood culture conversion to reporting the results, which makes early intervention difficult. Recently, FilmArray (FA) multiplex PCR panel for blood culture identification was introduced to the clinical setting. In this study, we investigated the clinical impact of the FA system on decision making for treating septic diseases and its association with patients' survival. Our hospital introduced the FA multiplex PCR panel in July 2018. In this study, blood-culture-positive cases submitted between January and October 2018 were unbiasedly included, and clinical outcomes before and after the introduction of FA were compared. The outcomes included (i) the duration of use of broad-spectrum antibiotics, (ii) the time until the start of anti-MRSA therapy to MRSA bacteremia, and (iii) sixty-day overall survival. In addition, multivariate analysis was used to identify prognostic factors. In the FA group, overall, 122 (87.8%) microorganisms were concordantly retrieved with the FA identification panel. The duration of ABPC/SBT use and the start-up time of anti-MRSA therapy to MRSA bacteremia were significantly shorter in the FA group. Sixty-day overall survival was significantly improved by utilizing FA compared with the control group. In addition, multivariate analysis identified Pitt score, Charlson score, and utilization of FA as prognostic factors. In conclusion, FA can lead to the prompt bacterial identification of bacteremia and its effective treatment, thus significantly improving survival in patients with bacteremia.

Highly Sensitive Detection of PIK3CA Mutations by Looping-Out Probes-Based Melting Curve Analysis.

PIK3CA mutations have important therapeutic and prognostic implications in various cancer types. However, highly sensitive detection of PIK3CA hotspot mutations in heterogeneous tumor samples remains a challenge in clinical settings. To establish a rapid PCR assay for highly sensitive detection of multiple PIK3CA hotspot mutations. We described a novel melting curve analysis-based assay using looping-out probes that can enrich target mutations in the background of excess wild-type and concurrently reveal the presence of mutations. The analytical and clinical performance of the assay were evaluated. The developed assay could detect 10 PIK3CA hotspot mutations at a mutant allele fraction of 0.05-0.5% within 2h in a single step. Analysis of 82 breast cancer tissue samples revealed 43 samples with PIK3CA mutations, 28 of which were confirmed by Sanger sequencing. Further testing of 175 colorectal cancer tissue samples showed that 24 samples contained PIK3CA mutations and 19 samples were confirmed by Sanger sequencing. Droplet digital PCR supported that all mutation-containing samples undetected by sequencing contained mutations with a low allele fraction. The rapidity, ease of use, high sensitivity and accuracy make the new assay a potential screening tool for PIK3CA mutations in clinical laboratories.

Development and clinical validation of a one-step pentaplex real-time reverse transcription PCR assay for detection of hepatitis virus B, C, E, Treponema pallidum, and a human housekeeping gene

BackgroundWith the safety of blood transfusion being a major public health concern, the development of a rapid, sensitive, specific, and cost-effective multiplex PCR assay for simultaneous detection of hepatitis B virus(HBV), hepatitis C virus (HCV), hepatitis E virus (HEV), and Treponema pallidum(T. pallidum) in blood is crucial.MethodsFive primer pairs and probes were designed towards conserved regions of target genes and used to establish a one-step pentaplex real-time reverse transcription PCR(qRT-PCR) assay for simultaneous detection of HBV, HCV, HEV, T. pallidum, and RNase P(housekeeping gene), providing sample quality check. The clinical performance of the assay was further determined with 2400 blood samples from blood donors and patients in Zhejiang province, and compared the results with commercial singleplex qPCR and serological assays.ResultsThe 95% limit of detection(LOD) of HBV, HCV, HEV, and T. pallidum were 7.11 copies/µL, 7.65 copies/µL, 8.45 copies/µL, and 9.06 copies/µL, respectively. Moreover, the assay has good specificity and precision. Compared to the singleplex qPCR assay, the novel assay for detecting HBV, HCV, HEV, and T. pallidum presented 100% clinical sensitivity, specificity, and consistency. Several discrepant results between serological and pentaplex qRT-PCR assays were found. Of 2400 blood samples, there were 2(0.08%) HBsAg positive samples, 3(0.13%) anti-HCV positive samples, 29(1.21%) IgM anti-HEV positive samples and 6(0.25%) anti-T. pallidum positive samples proven negative in nucleic acid detection. 1(0.04%) HBV DNA positive sample and 1(0.04%) HEV RNA positive sample were detected negative by serological testing.ConclusionsThe developed pentaplex qRT-PCR is the first assay on simultaneous, sensitive, specific, and reproducible detection of HBV, HCV, HEV, T. pallidum, and RNase P in a single tube. It could detect pathogens in blood during the window period of infection and is a good tool for effectively screening blood donors and early clinical diagnosis.

Adequacy of using a single nasal swab for rapid influenza diagnostic testing, PCR, and whole genome sequencing.

Rapid influenza diagnostic tests (RIDT) demonstrate varying sensitivities, often necessitating reverse transcriptase polymerase chain reaction (RT-PCR) to confirm results. The two methods generally require separate specimens. Using the same anterior nasal swab for both RIDT and molecular confirmation would reduce cost and waste and increase patient comfort. The aim of this study was to determine if RIDT residual nasal swab (rNS) specimens are adequate for RT-PCR and whole genome sequencing (WGS). We performed RT-PCR and WGS on paired rNS and nasopharyngeal or oropharyngeal (NP/OP) swab specimens that were collected from primary care patients across all ages. We randomly selected 199 and 40 paired specimens for RT-PCR and WGS, respectively, from the 962 paired surveillance specimens collected during the 2014-2015 influenza season. Sensitivity and specificity for rNS specimens were 81.3% and 96.7%, respectively, as compared to NP/OP specimens. The mean cycle threshold (Ct) value for the NP/OP specimen was significantly lower when the paired specimens were both positive than when the NP/OP swab was positive and the nasal swab was negative (25.5 vs 29.5; p<0.001). Genomic information was extracted from all 40 rNS specimens and 37 of the 40 NP/OP specimens. Complete WGS reads were available for 67.5% (14 influenza A; 13 influenza B) of the rNS specimens and 59.5% (14 influenza A; 8 influenza B) of the NP/OP specimens. It is feasible to use a single anterior nasal swab for RIDT followed by RT-PCR and/or WGS. This approach may be appropriate in situations where training and supplies are limited. Additional studies are needed to determine if residual nasal swabs from other rapid diagnostic tests produce similar results.

An Overview of 10 Years of Activity of a Molecular Laboratory for Buruli Ulcer Diagnosis at a Field Hospital in Benin.

Buruli ulcer (BU) is a neglected tropical disease caused by Mycobacterium ulcerans. Early diagnosis is crucial to prevent morbidity. In November 2012, a field laboratory fully equipped for the rapid on-site quantitative PCR (qPCR) diagnosis of M. ulcerans was established at the Buruli ulcer treatment center (CDTLUB) center in Pobè Benin, a region where BU is endemic. We describe its first 10 years of activity and its gradual evolution into an expert laboratory for BU diagnosis. From 2012 to 2022, the laboratory analyzed 3,018 samples from patients attending consultations for suspected BU at the CDTLUB in Pobè. Ziehl-Neelsen staining and qPCR targeting the IS2404 sequence were performed. Since 2019, the laboratory has also received and analyzed 570 samples from other centers. The laboratory confirmed the diagnosis of BU by qPCR for 39.7% samples: M. ulcerans DNA was detected in 34.7% of swabs, 47.2% of all fine needle aspiration samples (FNA) and 44.6% of all skin biopsy specimens. Positive Ziehl-Neelsen staining results were obtained for 19.0% samples. Bacterial load, estimated by qPCR, was significantly greater for the Ziehl-Neelsen-positive samples than for Ziehl-Neelsen-negative samples, and detection rates were highest for FNA samples. Overall, 26.3% of the samples received from other centers were positive for BU. Most of these samples were sent by the CDTLUBs of Lalo, Allada, and Zagnanado, Benin. The establishment of the laboratory in the CDTLUB of Pobè has been a huge success. Optimal patient care depends on the close proximity of a molecular biology structure to BU treatment centers. Finally, FNA should be promoted among caregivers. IMPORTANCE Here, we describe the first 10 years of activity at a field laboratory established at the Buruli ulcer treatment center (CDTLUB) in Pobè, Benin, a country in which Mycobacterium ulcerans is endemic. Between 2012 and 2022, the laboratory analyzed 3,018 samples from patients consulting the CDTLUB of Pobè with a suspected clinical BU. Ziehl-Neelsen staining and qPCR targeting the IS2404 sequence were performed. In total, 39.7% of samples tested positive by qPCR and 19.0% tested positive by Ziehl-Neelsen staining. Detection rates were highest for FNA samples, and the bacterial loads estimated by qPCR were significantly higher for Ziehl-Neelsen-positive samples than for Ziehl-Neelsen-negative samples. Since 2019, the laboratory has also analyzed 570 samples received from outside the CDTLUB of Pobè, 26.3% of which were positive for BU. Most of these samples were sent by the CDTLUBs of Lalo, Allada, and Zagnanado in Benin. The establishment of the laboratory in the CDTLUB of Pobè has been a huge success, with major benefits for both the medical staff and patients. Our findings illustrate that the usefulness and feasibility of having a diagnostic center in rural Africa, where the disease is endemic, is a key part of optimal patient care, and that FNA should be promoted to increase detection rates.

Detection and prevalence of HBsAg and HBV DNA among visiting patients attending health facilities in Nigeria

Hyper-endemicity of the Hepatitis B virus (HBV) has for long been retained in parts of Sub-Saharan Africa, including Nigeria with a prevalence rate above 8%. Despite the implementation of vaccination programs, factors such as inadequate diagnostic protocols, the prevalence of occult infections, and population group-specific susceptibility to infection remain overlooked in control strategies. This study, therefore, aims at investigating the prevalence of hepatitis B viral infection, the presence of mutant strains, and establishing a link between age, blood parameters and susceptibility to infection. A total of 451 blood samples from participants aged 1–50 years were tested for the presence of hepatitis B surface antigen (HBsAg) and HBV DNA using rapid diagnostic testing and PCR molecular-based assay. Age, blood group and hemoglobin (Hb) genotype were used to evaluate associated risk of infection. Statistical analysis was done using Python3. A prevalence of 5.8% and 18.2% were recorded using rapid diagnostic testing and PCR molecular-based assay respectively. Correlation between age and, HBV DNA and HBsAg positivity gave a p-value of 1.672. Error rates of 4.4% and 16.9% were recorded for false positives and false negatives respectively, with a rapid test kit sensitivity of 7.32% and specificity of 94.58%. Blood group O rhesus D positive (O⁺) showed a statistically significant higher risk of infection (P < 0.001, odd ratio (OR) = 0.38, 95% CI = 0.23–0.63) compared to non-O blood types. Age groups 21- 30 years and 31–40 years, both showed high relative risk and odd ratios. The low sensitivity found for the available RDT kits negatively influenced the ability to screen for Hepatitis B strains, hence, the high rate of false negatives. The Hb genotype may also play some role or have some association with the viral infection. This study highlights areas to specifically look into in implementing HBV eradication strategies.

Rapid and scalable DNA extraction and real-time PCR assay from boxwood tissue for the detection of Calonectria pseudonaviculata, causal agent of boxwood blight.

Boxwood blight can be challenging to detect in the field, especially when symptoms are mild, thus requiring large numbers of plants to be screened. Therefore, a rapid diagnostic assay that can detect the pathogen from large amounts of plant tissue would be useful. Here, we present a crude DNA extraction protocol that is rapid and scalable. The DNA extraction protocol can process large volumes of tough boxwood tissue rapidly without using cetyltrimethylammonium bromide (CTAB) or phenol-chloroform to remove inhibitors. Additionally, to detect the boxwood blight pathogen, Calonectria pseudonaviculata, we developed a TaqMan probe to use with previously described PCR primers for a real-time PCR assay. The assay's limit of detection was determined by diluting symptomatic boxwood leaves in non-diseased leaves and by adding spores to non-diseased leaves to simulate diagnostic scenarios. The assay was able to detect the pathogen in symptomatic leaves diluted up to 1×104 to 1×105 fold in non-diseased leaves, and from as low as 1,000 to 10,000 spores added to 1.2 g of non-diseased leaves. The ability to extract DNA from large volumes of plant tissue facilitates screening more plant tissue using the real-time PCR assay without increasing the number of samples to process in the lab.

Hemihydranencephaly of Premature Infant - Case Report

Abstract Hydranencephaly represents a rare anomaly of the central nervous system and is characterized by the parenchymal absence which is replaced with a membranous sac filled with cerebrospinal liquid, glial tissue and ependyma. When it is manifested as hemihydranencephaly, the patient’s prognosis is better. We presented a case of a premature infant with hemihydranencephaly in twin pregnancy that had a fatal outcome. A premature infant in a controlled pregnancy was delivered at 31 weeks of gestational age. The mother of the newborn was hospitalized in the Clinic for Infective Diseases since she had tested positive for SARS-Covid- 19. Following an urgent Caesarean section, the newborn was tested for Covid 19 using the rapid antigen and PCR test and the results were negative. In the delivery room, the tactile stimulation, aspiration, positive pressure ventilation of the infant were applied, after which it was intubated. After the intubation, a manual heart massage was performed, after which the cardiac activity and agonal breathing movements were detected.” Three hours later, cardiorespiratory arrest happened, following unsuccessful resuscitation. The other twin was born with no anomalies, but showed signs of respiratory distress syndrome. Autopsy revealed that there was a thin-walled cavity filled with clear, yellowish liquid in the right hemisphere. Documenting cases of newborns with hydranencephaly is of a great importance for counseling parents regarding length of survival, successful management of pregnancy, and performance of prenatal diagnostic procedures.

Mild COVID-19 outcomes in adults with inborn errors of immunity: a single-center experience

Currently, 640 million cases of coronavirus disease 2019 (COVID-19) and 6.6 million deaths have been reported world-wide. Risk factors for severe COVID-19 are known, including those with compromised immunity. Among patients with inborn errors of immunity (IEI), early reports of severe outcomes lead to strict masking and social distancing measures. While this resulted in relatively low infection rates among those with IEI, real-world data describing the clinical course of COVID-19 in this patient population have remained limited. We performed a retrospective study of adult IEI patients followed by our center in which a positive test (rapid antigen or PCR) for COVID-19 was determined between November 2021-November 2022. Medical charts were reviewed, and patient interviews conducted. All patients provided informed consent. Twenty-nine patients were enrolled (22 females, 7 males), aged between 18–69 years (median: 20–29 years). The cohort included those with antibody deficiencies (41.37%), combined immunodeficiencies (34.48%; HIES, CARD11, STAT1-GOF), immune dysregulation disorders (20.69%; LRBA deficiency, AIRE deficiency) and phagocyte defect (3.45%; CGD). The duration of symptoms ranged between 3 days-4 weeks (median: < 1 week). Upper respiratory symptoms (including sore throat, congestion) were reported in 97% while fever was present in 41% of patients. Prior to infection, 14 (48%) patients had underlying asthma or bronchiectasis - 2 subsequently experienced shortness of breath and were treated with inhalers or Sotrovimab, respectively. No treatment was required in 65.5% of cases. The remaining received Paxlovid (10.3%), Sotrovimab (13.79%), or antibiotics (10.3%). Of the 2 patients with STAT1-GOF, one tested positive during a repeat episode of febrile neutropenia which required hospitalization. No other patients were hospitalized or needed ICU admission. No deaths were recorded. In light of these favourable outcomes, patients with IEI can gradually and safely return to normal activities.

Development of Shortened Enrichment Methods for Detection of Salmonella Typhimurium Spiked in Milk.

Rapid and accurate testing of pathogenic Salmonella enterica in dairy products could reduce the risk of exposure to the bacterial pathogens for consumers. This study aimed to reduce the assessment time needed for enteric bacteria recovery and quantification in food using the natural growth properties of Salmonella enterica Typhimurium (S. Typhimurium) in cow's milk and efficiently using rapid PCR methods. Over 5 h of 37 °C enrichment, culture and PCR methods measured increases in the non-heat-treated S. Typhimurium concentration at similar rates, with an average increase of 2.7 log10 CFU/mL between the start of enrichment and 5 h. In contrast, no bacteria were recovered by culture after S. Typhimurium in milk received heat treatment, and the number of gene copies of heat-treated Salmonella detected by PCR did not increase with the enrichment time. Thus, comparing culture and PCR data over just 5 h of enrichment time can detect and differentiate between replicating bacteria and dead bacteria.

Retrospective and Comparative Study of Three Molecular Assays for the Macrolide Resistance Detection in Mycoplasma genitalium Positive Urogenital Specimens.

The capacity of Mycoplasma genitalium to develop resistance to macrolides makes detection of macrolide resistance genes by rapid real-time PCR assays increasingly necessary in clinical diagnostic laboratories so as to initiate appropriate treatment as rapidly as possible. The aim of this retrospective and comparative study was to conduct the clinical evaluation of three commercially available kits for macrolide resistance detection. A total of 111 M. genitalium positive samples analyzed in the Clinical Microbiology Laboratory of the Miguel Servet University Hospital, Zaragoza (Spain) were used. After M. genitalium molecular confirmation, the three assays under study were evaluated and discrepant results were resolved via sequencing. The clinical sensitivity for resistance detection was 83% (95% confidence interval, 69% to 93%) for the ResistancePlus® MG panel kit (SpeeDx Pty Ltd., Sydney, Australia), 95% (84% to 99%) for AllplexTM MG & AziR Assay (Seegene®, Seoul, Korea), and 97% (88% to 99%) for the VIASURE macrolide resistance-associated mutations (23SrRNA) Real time PCR detection kit (Certest Biotec, Zaragoza, Spain). The clinical specificity was 100% (94% to 100%) for Allplex and VIASURE assays and 95% (86% to 99%) for SpeeDx assay. The results arising from this study are cause for strong consideration for the implementation of rapid real-time PCR assays in clinical diagnosis laboratories to eliminate treatment failure and transmission as soon as possible.

Analysis of EGFR Mutation by Rapid PCR Methods Can Yield Better Quality Results Using Intra-Operative Frozen Section Tissue in Early Stage, Non-Small Cell Lung Cancer Patients

Analysis of EGFR Mutation by Rapid PCR Methods Can Yield Better Quality Results Using Intra-Operative Frozen Section Tissue in Early Stage, Non-Small Cell Lung Cancer Patients

Identification of sex-linked codominant markers and development of a rapid LAMP-based genetic sex identification method in channel catfish (Ictalurus punctatus)

Channel catfish (Ictalurus punctatus), a commercially important aquaculture species, is native to North America and has spread worldwide. Channel catfish exhibit sexual size dimorphism, with males growing faster than females. Therefore, the creation of an all-male population is promising for growth improvement in channel catfish. In the process of monosex fish breeding, the development of sex-specific genetic markers is the most critical step. Although sex-linked SSRs and SNPs have been developed in channel catfish, they are polymorphic, unstable, and difficult to use for rapid sex genotyping. In this study, three codominant markers with large size differences between their two alleles were identified by performing a detailed comparison of the region on X and Y chromosomes that enriched male-specific SNPs using preexisting RAD-seq data and genome data. After examination by one wild and three artificially bred populations using electrophoresis on agarose gel, the accuracy rate reached 100%, suggesting that all three codominant markers could be effectively used for genetic sex identification in channel catfish. To achieve genetic sex identification performed in the field without complex equipment, a rapid LAMP-based method was established for the identification of genetic sex in channel catfish based on the codominant markers we identified. Overall, this study established rapid and effective PCR- and LAMP-based methods to identify the genetic sex of channel catfish in the laboratory and in the field.

Malaria parasite prevalence in Sub-Saharan African migrants screened in Sweden: a cross-sectional study

Asymptomatic infections with malaria parasites are common in populations in endemic areas. These infections may persist in migrants after arrival in a non-endemic area. Screening to find and clear these infections is generally not implemented in non-endemic countries, despite a potential negative health impact. We performed a study to evaluate the Plasmodium parasite prevalence in migrants living in Sweden. Adults and children born in Sub-Saharan Africa (SSA) were invited in the study between April 2019 and June 2022at 10 different sites, mainly as part of the national Migrant Health Assessment Program in Stockholm and Västerås, Sweden. Rapid diagnostic tests (RDT) and real-time PCR were used to detect malaria parasites. Prevalence and test sensitivity were calculated with 95% confidence intervals (CI). Univariate and multivariable logistic regression were used to evaluate associations with PCR positivity. In total, 789 individuals were screened for Plasmodium spp. of which 71 (9.0%) were positive by PCR and 18 (2.3%) also by RDT. When performed during the national screening program, 10.4% was PCR positive. A high prevalence was detected in migrants with Uganda as the country of last residence, 53/187 (28.3%), and in this group the prevalence was highest in children, 29/81 (35.8%). Among the PCR positive, 47/71 (66.2%) belonged to families with at least one other member testing positive (odds ratio [OR] 43.4 (95% CI 19.0-98.9), and the time lived in Sweden ranged between 6 and 386 days. A high malaria parasite prevalence was found in migrants from SSA, particularly in children offered screening in Stockholm, Sweden during the study period. Awareness of asymptomatic malaria infection is needed and screening for malaria in migrants arriving from high endemic countries should be considered. The Swedish Research Council, Stockholm County Council and Centre for Clinical Research, Västmanland, Sweden.

Some clinical and epidemiological aspects of HIV/ hepatitis C coinfection

Aim . To study some clinical and epidemiological aspects of HIV/hepatitis C coinfection in the Republic of Tajikistan. Materials and methods . The material for the study was the data from clinical, epidemiological and virological examinations of 70 patients with HIV/hepatitis C coinfection. In all observed patients, the diagnosis was confirmed based on clinical and epidemiological data and confirmed by rapid testing, ELISA, and PCR. Results discussion . The disease in patients with HIV/hepatitis C coinfection clinically proceeds with weakness and general malaise (92.8%), loss of appetite (67.1%), heaviness in the liver (45%), heartburn (25%), bitterness in the mouth (19%), nausea and anorexia (32.8%), bleeding from the gums (13%), yellowness of the sclera (11.4%), weight loss (41.4%), hepatomegaly (83%). Opportunistic pathology is represented by candidiasis (32.8%), herpes infection (22.8%), CMV (7.1%), pneumocystis pneumonia (4.2%), Kaposi’s sarcoma (4.2%), cerebral toxoplasmosis (1.4%). People who practice intravenous drug administration, as well as their sexual partners, are more likely to be infected. It has been established that males under the age of 45 predominate among coinfected patients. As for secondary and opportunistic infections, they are associated with a decrease in the immune status in the face of CD4+ - lymphocytes in patients with coinfection. Conclusion . The studies carried out make it possible to identify the category of people most at risk of infection with HIV and hepatitis C, which must be taken into account when screening the population. Early diagnosis of HIV/ hepatitis C coinfection will help reduce the number of complications and mortality in this category of patients.

Recurrence hospitalization due to SARS-CoV-2 infection on human immunodeficiency virus patients

COVID-19 is a global health concern with varying severity. Moderate to severe cases require isolation for 10-20 days, and those with weakened immune systems (like HIV) should isolate for 20 days. Indonesia has a rising number of HIV cases. HIV-positive individuals have a higher risk of COVID-19 and may have lower antibody levels after vaccination. Two case studies of HIV-positive patients who contracted SARS-CoV-2 are presented. In case 1, a 29-year-old patient who received the COVID-19 vaccine and was on antiretroviral therapy was hospitalized three times with worsening symptoms, and unfortunately did not survive. In case 2, a 46-year-old patient with a history of tuberculosis and also on antiretroviral therapy was hospitalized twice, reporting mild symptoms, and did not experience any further symptoms related to COVID-19 after being discharged. Both patients tested positive for COVID-19 using rapid antigen tests and PCR tests and did not report any history of contact with COVID-positive individuals. These case studies highlight the challenges faced by HIV-positive individuals in managing COVID-19, and the need for continued research in this area. Immunocompromised COVID-19 patients need special isolation, even with mild symptoms. Longer isolation periods may be necessary, as studies show positive tests can still mean infectiousness. Viral culture tests can help identify contagious individuals who test positive on PCR tests. People with HIV may need a COVID-19 booster vaccine due to lower antibody levels after the initial vaccine. Further research is needed to develop antiviral treatments for COVID-19 infection in individuals with immunocompromised.

SARS-CoV-2 specific T-cell humoral response assessment after COVID-19 vaccination using a rapid direct real-time PCR amplification.

The SARS-CoV-2 immune response is mediated by both humoral and cellular immunity. In this study, SARS-CoV-2 specific cellular immunity was tested by a novel direct real-time PCR (dRT-PCR) assay, targeting mRNA of CXCL10, and compared with respect to an ELISA measuring interferon gamma (IFN-γ) release. Whole blood (Li-He) and serum samples were collected from 92 healthcare workers (HCW), with three doses of homologous (Pfizer/BioNTech, n=74) or heterologous (Pfizer/BioNTech and Vaxzevria or Moderna, n=18) vaccinations. Li-He samples were incubated with SCV2 PANEL-1-T-ACTIVATION (Hyris srl, Lodi, Italy), or CoV-2 IGRA TUBE ELISA (Euroimmune, Lubeck, Germany). CXCL10 mRNA expression was analyzed by bCube/bApp (Hyris), while IFN-γ was evaluated by quant-T-Cell SARS-CoV-2 ELISA (Euroimmune). Anti-SARS-CoV-2 S-RBD IgG levels were measured in sera using a CLIA assay (Snibe, Shenzen, China). Imprecision of dRT-PCR assay was found to be satisfactory, and the two methods for measuring Tcell immunity to SARS-CoV-2 peptides agreed in 82/87 (94.2%) of results. At qualitative dRT-PCR analyses, 81 subjects (93.2%) resulted as reactive to SARS-CoV-2 peptides, 3 (3.4%) were borderline and 3 were negative (3.4%). At univariate and multivariate analyses of quantitative dRT-PCR mRNA of CXCL10 and IFN-γ release results showed no difference between HCW with previous infection, homologous/heterologous vaccination, or demographical features. Anti-SARS-CoV-2 S-RBD IgG was associated with the previous infection and thetime between the last vaccination or positivity. Direct RT-PCR appeared accurate for determining the presence or absence of immunoreactivity of SARS-CoV-2 specific Tcells, especially when rapid analyses are required, such as for organ transplantation.

‘CoviSwiftTM’: A point-of-care RT-PCR device for SARS-CoV-2 and its variant detection

We present the point-of-care (POC) molecular diagnostic solution, evaluated during COVID-19 pandemic caused by SARS-CoV-2 (Dec 2021). The POC comprised of a complete platform from self-sampling to RT-PCR testing of SARS-CoV-2 and its variants on portable Compact Q Real time polymerase chain reaction system. The multiplex assay was designed to target S, ORF1, and N genes of SARS-CoV-2 genome in a single tube with RNaseP as endogenous internal control. The present POC enables high accuracy (>95%) and high-throughput testing with a turnaround time of 45 min. It provides a unique platform from self-sample collection to report generation with rapid protocol, pipette and expert-free operation, long shelf-life stability and room temperature storage which enable to increase the efficiency of molecular testing. This novel test named “CoviSwift™ COVID-19 S PLUS RAPID PCR KIT” has been approved by CDSCO, Indian National Regulatory Authority, India, and is in use for clinical settings in India.