Viral Load Determination Research Articles

Association of cycle threshold values of CBNAAT with severity and outcome in COVID-19

Determination of viral load through cycle threshold (Ct) values may act as a predictor of severity and outcomes in patients with corona virus disease 2019 (COVID-19). However, variable literature is available regarding this relationship. Our study attempted to explore this association and the effect of various socio-demographic and clinical parameters on severity and outcome of COVID-19. Retrospective analysis of records of 731 patients whose nasopharyngeal/ oropharyngeal swabs were subjected to cartridge based nucleic acid amplification (CBNAAT) on Cepheid Xpert Xpress SARS-Cov-2 was done. Cycle threshold (Ct) values of N2 and E genes were studied in relation to severity and outcome of COVID-19. The viral load as determined by Ct values was classified as high (<25), medium (25.1-32) and low (>32). Association of socio-demographic and clinical parameters with respect to severity and outcome was also studied. Severity and mortality were significantly more in elder individuals, those belonging to the rural background, those with symptoms >7 days in duration before presentation and those with increasing number of co-morbidities (Severity: p<0.001, mortality: p <0.001, 0.005, 0.006 and <0.001 respectively). The Ct values of gene N2 and E inversely correlated with severity and mortality from the disease (N2 gene: p=0.001 for both severity and mortality, E gene: severity: p<0.001, mortality: p=0.016 respectively). The severity of the illness and chances of mortality were significantly lesser when the CT value of N2 gene was >32, in comparison when it was upto 25, and when between 25.1 and 32 (severity: p=0.032 and 0.003 respectively, mortality: p=0.018 and <0.001 respectively). Almost similar trends were seen with respect to E gene (severity: p<0.001 and 0.067 respectively, mortality p=0.175 and 0.005 respectively). Viral load as determined by Ct values of N2 and E genes can act as surrogate markers for prediction of severity and disease outcomes in COVID-19.

Brief Report: Impact of the COVID-19 Pandemic on Virological Suppression in People Living With HIV Attending a Large Italian HIV Clinic.

Background:We assessed the impact of the coronavirus disease 2019 (COVID-19) pandemic on HIV suppression rates in people living with HIV (PLWH) attending a large Italian HIV clinic.Setting:The HIV outpatient clinic of the Infectious Diseases Department of Luigi Sacco Hospital, Milan, Italy, which serves more than 5000 PLWH per year.Methods:A before and after quasi-experimental study design was used to make a retrospective assessment of the monthly trend of HIV-RNA determinations of ≥50 among the PLWH attending our clinic, with “before” being the period from January 1, 2016 to February 20, 2020, and “after” being the period from February 21, 2020 to December 31, 2020 (the COVID-19 period). Interrupted time series analysis was used to evaluate any changes in the trend.Results:During the study period, 70,349 HIV-RNA viral load determinations were made, and the percentage of HIV-RNA viral load determinations of <50 copies/mL increased from 88.4% in 2016 to 93.2% in 2020 (P < 0.0001). There was a significant monthly trend toward a decrease in the number of HIV-RNA determinations of ≥50 copies/mL before the pandemic (β −0.084; standard error 0.015; P < 0.001), and this did not significantly change after it started (β −0.039, standard error 0.161; P = 0.811).Conclusions:A high prevalence of viral suppression was maintained among the PLWH referring to our clinic, despite the structural barriers raised by the COVID-19 pandemic. The use of simplified methods of delivering care (such as teleconsultations and multiple antiretroviral treatment prescriptions) may have contributed to preserving this continuum.

Diagnostic Accuracy of SARS-CoV-2 Rapid Antigen Detection Testing in Symptomatic and Asymptomatic Children in the Clinical Setting.

ABSTRACTAntigen-based rapid diagnostic tests (RDTs) are used in children despite the lack of data. We evaluated the diagnostic performance of the Panbio-COVID-19 Ag Rapid Test Device (P-RDT) in children. Symptomatic and asymptomatic participants 0 to 16 years old had two nasopharyngeal swabs (NPS) for both reverse transcription-PCR (RT-PCR) and P-RDT. A total of 822 participants completed the study, of which 533 (64.9%) were symptomatic. Among the 119 (14.5%) RT-PCR-positive patients, the P-RDT sensitivity was 0.66 (95% confidence interval [CI] 0.57 to 0.74). Mean viral load (VL) was higher among P-RDT-positive patients than negative ones (P < 0.001). Sensitivity was 0.91 in specimens with VL of >1.0E6 IU/ml (95% CI 0.83 to 0.99) and decreased to 0.75 (95% CI 0.66 to 0.83) for specimens >1.0E3 IU/ml. Among symptomatic participants, the P-RDT displayed a sensitivity of 0.73 (95% CI 0.64 to 0.82), which peaked at 1.00 at 2 days post-onset of symptoms (DPOS) (95% CI 1.00 to 1.00), then decreased to 0.56 (95% CI 0.23 to 0.88) at 5 DPOS. There was a trend toward lower P-RDT sensitivity in symptomatic children <12 years (0.62 [95% CI 0.45 to 0.78]) versus ≥12 years (0.80 [95% CI 0.69 to 0.91]; P = 0.09). In asymptomatic participants, the P-RDT displayed a sensitivity of 0.43 (95% CI 0.26 to 0.61). Specificity was 1.00 in symptomatic and asymptomatic children (95% CI 0.99 to 1.00). The overall 73% and 43% sensitivities of P-RDT in symptomatic and asymptomatic children, respectively, was below the 80% cutoff recommended by the World Health Organization. We observed a correlation between VL and P-RDT sensitivity, as well as variation of sensitivity according to DPOS, a major determinant of VL. These data highlight the limitations of RDTs in children, with the potential exception in early symptomatic children ≥12yrs.

MaxRatio improves the detection of samples with abnormal amplification profiles on QIAgen’s artus HIV-1 qPCR assay

Background: Accurate viral load (VL) determination is paramount to determine the efficacy of anti-HIV-1 therapy. The conventional method used, fit-point (FP), assumes an equal efficiency in the polymerase chain reaction (PCR) among samples that might not hold for low-input templates. An alternative approach, maxRatio, was introduced to compensate for inhibition in PCR. Methods: Herein, we assessed whether maxRatio could improve VL quantification using 2,544 QIAgen artus HI virus-1 RT-PCR reactions. The assay’s standard dilutions were used to build external standard curves with either FP or maxRatio that re-calculated the VLs. Results: FP and maxRatio were highly comparable (Pearson’s ρ=0.994, Cohen’s κ=0.885), and the combination of the two methods identified samples (n=41) with aberrant amplification profiles. Conclusions: The combination of maxRatio and FP could improve the predictive value of the assay.

MaxRatio improves the detection of samples with abnormal amplification profiles on QIAgen’s artus HIV-1 qPCR assay

Background: Accurate viral load (VL) determination is paramount to determine the efficacy of anti-HIV-1 therapy. The conventional method used, fit-point (FP), assumes an equal efficiency in the polymerase chain reaction (PCR) among samples that might not hold for low-input templates. An alternative approach, maxRatio, was introduced to compensate for inhibition in PCR.Methods: Herein, we assessed whether maxRatio could improve VL quantification using 2,544 QIAgen artus HI virus-1 RT-PCR reactions. The assay’s standard dilutions were used to build external standard curves with either FP or maxRatio that re-calculated the VLs.Results: FP and maxRatio were highly comparable (Pearson’s ρ=0.994, Cohen’s κ=0.885), and the combination of the two methods identified samples (n=41) with aberrant amplification profiles.Conclusions: The combination of maxRatio and FP could improve the predictive value of the assay.

Prevalence and viral load determination of BK polyomavirus among Iranian patients with brain tumors.

Background:Due to persistent infections of human central nervous system (CNS), polyomaviruses have been identified as one of the risk factors for brain tumor development. Human BK virus is of significant interest due to its experimental neuro-oncogenic potential and the possible association with CNS neoplasms. However, the results of different studies are discrepant. In the present study, we aimed to investigate the prevalence of BK virus genome and quantify BK viral load in Iranian patients with primary and metastatic brain malignancies.Methods:To assess the prevalence of BK virus sequences, a total of 58 fresh brain tumors were examined by quantitative real-time PCR. The BK viral load was determined as viral copy number per cell. Results:Of the 58 brain tumor samples BK tumor antigen (TAg) sequences were detected in 26 (44.8%) of cases. In primary brain tumors, BK virus sequences were recognized more frequently in schwannomas (15.5%) and meningiomas (12.1%). The mean BK virus TAg copy number in positive cases was 0.20×10-3±0.27×10-3 (range 0.01×10-3- 0.8×10-3) copies per cell.Conclusion:Taken together, in the present study low copy numbers of BK virus TAg gene was detected in brain tumor cells, which can indicate that BK virus may contribute to tumor induction by indirect mechanisms or neuro-persistence of this virus without any pathological consequences.

SARS-CoV-2 RNA in plasma samples of COVID-19 affected individuals: a cross-sectional proof-of-concept study

BackgroundRecent studies showed that plasma SARS-CoV-2 RNA seems to be associated with worse COVID-19 outcome. However, whether specific population can be at higher risk of viremia are to date unexplored.MethodsThis cross-sectional proof-of-concept study included 41 SARS-CoV-2-positive adult individuals (six affected by haematological malignancies) hospitalized at two major hospital in Milan, for those demographic, clinical and laboratory data were available. SARS-CoV-2 load was quantified by ddPCR in paired plasma and respiratory samples. To assess significant differences between patients with and patients without viremia, Fisher exact test and Wilcoxon test were used for categorical and continuous variables, respectively.ResultsPlasma SARS-CoV-2 RNA was found in 8 patients (19.5%), with a median (IQR) value of 694 (209–1023) copies/mL. Viremic patients were characterized by an higher mortality rate (50.0% vs 9.1%; p = 0.018) respect to patients without viremia. Viremic patients were more frequently affected by haematological malignancies (62.5% vs. 3.0%; p < 0.001), and had higher viral load in respiratory samples (9,404,000 [586,060-10,000,000] vs 1560 [312–25,160] copies/mL; p = 0.002).ConclusionsEven if based on a small sample population, this proof-of-concept study poses the basis for an early identification of patients at higher risk of SARS-CoV-2 viremia, and therefore likely to develop severe COVID-19, and supports the need of a quantitative viral load determination in blood and respiratory samples of haematologic patients with COVID-19 in order to predict prognosis and consequently to help their further management.

Estimating HIV incidence in the Akwa Ibom AIDS indicator survey (AKAIS), Nigeria using the limiting antigen avidity recency assay.

IntroductionHIV incidence estimates are important to characterize the status of an epidemic, identify locations and populations at high risk and to guide and evaluate HIV prevention interventions. We used the limiting antigen avidity assay (LAg) as part of a recent infection testing algorithm to estimate HIV incidence in the Akwa Ibom AIDS Indicator Survey (AKAIS), Nigeria.MethodsIn 2017, AKAIS, a cross‐sectional population‐based study was conducted at the household (HH) level in 31 local government areas (LGAs) of Akwa Ibom state. Of the 8963 participants aged ≥15 years who were administered questionnaires for demographic and behavioural data, 8306 consented to HIV rapid testing. Whole‐blood specimens were collected from 394 preliminary HIV‐seropositive individuals for CD4+ cell count determination and plasma storage. Samples were shipped to a central quality laboratory for HIV confirmatory testing and viral load determination. A total of 370 HIV‐positive specimens were tested for the recent HIV infection using the LAg assay.ResultsOf the 8306 consenting adults, the HIV prevalence was 4.8%. Of the 370 HIV‐positive samples tested for HIV recency, the median age was 35 years, 48.8% had CD4+ cell count >500/mm3 and 81.3% was not virally suppressed. Viral suppression was greater among females (21%) than for males (13%). A total of 11 specimens were classified as recent based on the LAg assay and HIV viral load ≥1000 copies/mL. The weighted, adjusted HIV‐1 incidence was 0.41/100 person‐years (95% CI 0.16 to 0.66); translating to 13,000 new cases of HIV infections annually in Akwa Ibom, a state with a population of 5.5 million. The HIV incidence rate was similar in females and males (0.41% and 0.42% respectively). The incidence rate was the highest among participants aged 15 to 49 years (0.44%, 95% CI 0.15 to 0.74) translating to 11,000 new infections annually, about 85% of all new infections in the state.ConclusionsThe finding of the high HIV incidence among the 15 to 49‐year age group calls for renewed and innovative efforts to prevent HIV infection among young adults in Akwa Ibom state.

Real-time loop-mediated isothermal amplification assay for rapid detection of human papillomavirus 16 in oral squamous cell carcinoma

ObjectiveThe present study established a real-time loop-mediated isothermal amplification (qLAMP) for rapid detection of human papillomavirus subtype 16 (HPV-16) in oral squamous cell carcinoma (OSCC). MethodsThe qLAMP assay was optimized targeting the HPV-16 E7 gene. The analytical sensitivity and specificity of the assay were determined using HPV-18 (ATCC® 45152D™), HPV-35 (ATCC® 40330™), HPV-43 (ATCC® 40338™) and HPV-56 (ATCC® 40549™) viral strains and oral bacteria. HPV-16 standard curve was constructed for determination of HPV-16 viral load. The diagnostic performance of the assay was evaluated from 63 OSCC patients comprising 63 tissue, 13 saliva and 49 blood samples, in comparison with p16 immunohistochemistry (IHC), in-house PCR and nested PCR assays. ResultsThe detection limit of developed LAMP and PCR assays was 4.68 × 101 and 4.68 × 103 copies/μl, respectively. qLAMP assay enabled detection of positive results as early as 23 min at 67 °C. This assay can detect HPV-16 positivity in 23 % (3/13) saliva and 4.8 % (3/63) tissue samples with the viral load ranging from 4.68 × 101 to 4.68 × 104 copies/μl. HPV-16 positivity was not detected in all the blood samples. The sensitivity and specificity of qLAMP were 100 % in comparison with that of p16 IHC and nested PCR. ConclusionThis study reports for the first time on the use of qLAMP assay for detection of HPV-16 in OSCC in both tissue and saliva as the sample matrix which holds promise in improving the diagnostic application owing to its rapidity, simplicity, high sensitivity and specificity.

Role and effects of zinc supplementation in HIV-infected patients with immunovirological discordance: A randomized, double blind, case control study.

It has been estimated that between 15% and 18% of patients who start antiretroviral therapy (ART) do not achieve a successful immune recovery despite complete virological suppression. In the literature this phenomenom is known as poor immune recovery or immunovirological discordance (IVD). Zinc has an immunomodulatory role associated with T lymphocytes and its supplementation could enhance immune recovery. To determine if zinc supplementation on IVD patients prevents immune failure after 12 months of supplementation. Secondary objectives were to determine serum zinc levels in HIV patients with and without IVD and the frequency of hypozincemia in discordant patients. We reviewed the historical record of patients under care at Arriarán Foundation. Following inclusion criteria were defined: 1) age ≥ 18 years, 2) standard ART (three effective drugs) for at least 18 months, 3) virologically suppressed for 12 months, 3) persistence of CD4 count ≤200 cells/mm3 and/or increase ≤ 80 cells/mm3 after one year of viral undetectability. A control group was assigned paired 1:1 by sex, age (± 2 years) that did achieved an increase of CD4> 350 cells/ mm3. In both groups plasma zinc levels were determined. In a later phase, patients with IVD were randomized to receive zinc (15 mg daily) versus placebo. Patients were followed for 12 months with CD4 count, viral load and zinc levels determinations every 4-6 months. A total of 80 patients, 40 patients with IVD criteria and 40 controls were included. 92.5% were men, and age average was 47.5 years. The median baseline CD4 was 189 cells/mm3 (71-258) in the cases vs. 552.5 cells/ mm3 (317-400) in the control group with a median increase at the end of the study of 39 cell/mm3 and 19 cell/mm3 respectively. There was no difference in baseline plasma zinc levels between both groups (81.7 + 18.1 in cases versus 86.2 + 11.0 in controls). In the 40 patients with IVD, the median absolute increase in CD4 after annual zinc supplementation was 31.5 cells/mm3 in the treated group versus 50 cells/mm3 in the placebo group, this difference being statistically not significant (p = 0.382). Patients with IVD have plasma zinc levels similar to those who achieve adequate immune recovery. Zinc supplementation in IVD patients showed a statistically non-significant difference in in CD4 levels between cases and controls. The results warrant a comparative study with a larger number of patients.

Molecular characteristics of HBV infection among blood donors tested HBsAg reactive in a single ELISA test in southern China

BackgroundHepatitis B virus (HBV) infection is a major concern for blood safety in high-prevalence HBV countries such as China. In Shenzhen, dual hepatitis B surface antigen (HBsAg) enzyme-linked immunosorbent assays (ELISAs) have been adopted in parallel with nucleic acid testing (NAT) for donors for over a decade. A small proportion of blood donors test reactive (R) for HBsAg but negative through routine NAT, which can lead to HBV infection with an extremely low viral load.ObjectivesWe aimed to investigate and analyze the molecular characteristics of HBV among blood donors that tested HBsAg R in a single ELISA test.MethodsBlood donations were evaluated in this study if confirmed HBsAg R through one of two ELISA kits. Samples with non-reactive (NR) results by NAT were collected and tested for HBsAg by chemiluminescent microparticle immunoassay (CLIA) with a neutralization test. The level of HBsAg was further assessed by electrochemiluminescence immunoassay (ECLIA). The viral basic core promoter (BCP) and pre-core (PC) and S regions were amplified by nested PCR. Quantitative real-time PCR (qPCR) for viral load determination and individual donation (ID)-NAT were adopted simultaneously. HBsAg was confirmed with CLIA, ECLIA, nested PCR, qPCR, and ID-NAT.ResultsOf the 100,252 donations, 38 and 41 were identified as HBsAg R with Wantai and DiaSorin ELISA kits, respectively. Seventy-nine (0.077%, 79/100,252) blood samples with ELISA R-NR and NAT NR results were enrolled in the study. Of these, 17 (21.5%,17/79) were confirmed as HBsAg-positive. Of the 14 genotyped cases, 78.6% (11/14) were genotype B, and C and D were observed in two and one sample, respectively. Mutations were found in the S gene, including Y100C, Y103I, G145R, and L175S, which can affect the detection of HBsAg. A high-frequency mutation, T1719G (93.3%), was detected in the BCP/PC region, which reduced the viral replication.ConclusionA small number of blood samples with HBsAg ELISA R-NR and NAT NR results were confirmed as HBV infection, viral nucleic acids were found in most of the samples through routine NAT methods. It is necessary to employ more sensitive and specific assays for the detection of HBV infection among blood donors.

Virological and Immunologic Outcome of HIV Infected Drug Experienced Adults in North Central Nigeria

Background: Antiretroviral therapy (ART) has decreased the mortality and morbidity among people living with HIV and AIDS (PLWH). Viral load (VL) has been used by clinicians as primary tool recommended by WHO to monitor patients progress on High Antiretroviral active therapy (HAART). There is a paucity of information on Virological and immunological outcomes of HIV infected drug experience adults’ patients in north central Nigeria. We conducted a tertiary hospital based cross-sectional study at federal medical centre in Nasarawa state between December 2019 to march 2020. Method: A total of 474 HIV positive adult were enrolled using a Systematic random technique. Blood specimen for CD+4 T cells count and viral load determination were obtained and PCR-Real time and Flow-cytometry were used to estimate plasma viral load and CD4+ T cell count respectively. Frequency was used to determine percentage and logistic regression was used to determine the associated factors with Virological suppression and immunology outcome in patients on HAART 95% CI and odd ratio (OR) was used to measure strength of association. Results: From the 474 cohort that were enrolled 34.6% were on WHO baseline clinical stage IIV and 57.8% of cohort were on HAART, started treatment regimen in less than a year with 42.2% diagnosed and confirmed with HIV infection between 1-5years. 57.8% were transferred into the centre as a major reason for enrolment. 57.8% has history of TB treatment in the past while 42.2% of the study participants who were eligible for treatment initiation were determine by CD4+ counts with a median interquartile range of 180 (92-300) cells/mm3. virological suppression (VL level < 1000 copies/ml) was found in 85% (95% CI 77.7, 86.1) of study participants, and it has been associated with CD4 cell count between 250 and 400 cells/mm3 (adjusted odds ratio (AOR) = 2.56; 95% CI 1.14, 5.75) and > 499 cells/mm3 (AOR = 7.71; 95% CI 3.48, 17.09) at VL testing and current age > 40 years old (AOR = 5.40; 95% CI 2.3, 10.01). Similarly, favourable immunological status (≥250 cells/mm3 for male and ≥ 600 cells/mm3 for female) was observed in 52.9% (95% CI 47.4, 58.8) of the study participants. Baseline CD4 cell count of > 200 cells/mm3, age at enrolment of 26 through 40 years old, and urban residency were significantly associated with favourable immunological outcome. Conclusion: Low Immunological recovery among study cohort was observed although viral suppression was shown in majority of the HIV infected adult who are on HAART. Early initiation on HAART should be encouraged in other to achieve immunological recovery and viral suppression in order to achieve the USAIDS- 90-90-90 to end HIV pandemic by 2030.

Sexually transmitted infections among women living with HIV in a Brazilian city

BackgroundClinical improvements following highly active antiretroviral therapy (HAART) may increase high-risk behaviors resulting in sexually transmitted infections (STI). Optimism related to the success of HAART in slowing disease progression, reducing viral load, and improving health status might be important factors for increasing sexual risk behaviors such as less use of condoms. ObjectiveTo determine the prevalence of Chlamydia trachomatis, Neisseria gonorrhoeae, syphilis, hepatitis B and C, high-risk HPV, and cervical cytological abnormalities among women living with HIV (WLHIV) who attended a Reference Center for STI/AIDS in Brazil. MethodsA cross-sectional study was conducted among 151 WLHIV attending an STI Clinic in Vitória city, Brazil. A structured questionnaire, including demographic, behavioral, and clinical information, was used for data collection. Serological tests for HIV, syphilis, hepatitis C and B, CD4 counts, and viral load determination were performed. Cervical samples were collected for cytology and real-time PCR for HPV,Chlamydia, and Neisseria gonorrhoeae. ResultsIn this study, 59% of women had at least one diagnosed STI at the time of the first clinic visit; 31% had clinical forms of anogenital HPV, 10% syphilis, 8%Neisseria gonorrhoeae, 5.0% trichomoniasis, 3% Chlamydia trachomatis, 1% hepatitis B, and 1% hepatitis C; 6.7% of the women presented with cervical cytological abnormalities. Furthermore, 46.3% of women had HR-HPV, and 17.6% had HPV 16/18. Only 5% of the women had a CD4 count <200 cells/mm3, 61.6% had undetectable HIV viral load, and 81.3% were currently on HAART. ConclusionA high prevalence of STI and HR-HPV infections were observed among HIV-infected women in this investigation. Prevention programs need to focus on counseling WLHIV and their regular partners with focused interventions such as couples counseling and education programs.

Human Papillomavirus Infection Among HIV-positive Women in Lubumbashi, Democratic Republic of the Congo

<i>Background</i>: Human Papillomavirus (HPV) infection is the most common sexually transmitted infection in the world, particularly affecting people living with human immunodeficiency virus (HIV). A synergy between the two viruses is however described by several authors but very little is known in women living with HIV-HPV co-infection in Lubumbashi in the South of the Democratic Republic of Congo (DRC). <i>Objective</i>: The purpose of this study was to determine the prevalence of HPV infection in women living with HIV, to define the socio-demographic profile of HPV infection and to analyze certain clinical and paraclinical parameters. <i>Methodology</i>: A total of 77 women, including 58 HIV-infected women (group 1) and 19 HIV-free women (group 2), were included in a cross-sectional descriptive study that was conducted from November 01 to 30, 2019 at the HIV-AIDS Mother-Child Transmission Prevention Unit (MCTPU) of the Lubumbashi University Clinics (LUC). HPV was tested on cervical-vaginal secretions obtained either by self-sampling or by a sample taken by a previously trained examiner. HPV was investigated by the INNO-LIPA (PCR) method at the Microbiology, Bioorganic Chemistry and Macromolecular Unit laboratory of the Free University of Brussels in Belgium (FUB) while the diagnosis of HIV infection (PCR), viral load determination and CD4 level assay was performed in the LUC laboratory. <i>Results</i>: The overall frequency of HPV infection was 74.03%. It was significantly higher in HIV-infected women than in non-HIV-infected women (81.08% vs. 52.63%). The socio-demographic profile of the HPV-infected patient was made up of predominantly married, multi-parented women, aged on average 35, with a secondary education level and an average socio-economic level. Low monthly incomes and HIV infection were almost 4 times at risk for HPV infection (OR 4.2 [1,439-12,262] and OR 3.75 [1,269-11,080] respectively). Finally, HIV-positive patients infected with HPV had overall low levels of Lymphocyte T CD4 compared to those not infected with HPV. <i>Conclusion</i>: Our study shows that in Lubumbashi, HPV infection is present in both HIV-positive and negative women but its prevalence is distinctly higher in HIV-positive patients than those without HIV infection. It is interesting to determine in subsequent studies the different genotypes of HPV circulating in Lubumbashi and to define the proportion of genotypes at high carcinogenic risk.

Prevalence of Intestinal Parasitic Infection and Associated Factors Among HAART Initiated Children Attending at University of Gondar Comprehensive Specialized Hospital, Northwest Ethiopia.

BackgroundHuman immunodeficiency virus (HIV) and intestinal parasites co-infections are the most common causes of clinical illness and death, especially for children living in resource constrained setting. Therefore, the aim of this study was to determine the prevalence and associated factors of intestinal parasites among highly active anti-retroviral therapy (HAART) initiated children.MethodsCross-sectional study was conducted among 255 HAART initiated HIV-infected children at the University of Gondar Comprehensive Specialized Hospital from January to April 2020. Socio-demographic characteristics were collected using a structured questionnaire via a face-to-face interview. Clinical data of the children were collected by reviewing the medical records. Venous blood was collected for complete blood counts, viral load determination, and blood film examination. Flotation concentration technique was done in addition to direct wet mount for parasitological examination. Bi-variable and multi-variable logistic regression analysis were used to check the presence of significant association, and P-value<0.05 was considered as statistically significant.ResultsThe overall prevalence of intestinal parasite infection (IPI) among the study participants was 22.4% (95% CI=17–28%). The presence of opportunistic infection (AOR=2.09 95% CI=1.81–5.43), no eating under-cooked animal products (AOR=0.38 95% CI=0.16–0.94), male sex (AOR=0.45 95% CI=0.22–0.90), viral load rate >1,000 copies/mL (AOR=1.80 95% CI=1.67–4.19), and cytopenia (AOR=2.71 95% CI=1.59–12.25) showed significant association with the prevalence of IPI.ConclusionEntamoeba histolytica and Ascaris lumbricoides were the most prevalent intestinal parasites among HAART initiated children. Among HAART initiated children, IPI were associated with gender, cytopenia, viral load, undercooked animal products, and the presence of opportunistic infections. Therefore, health education, prompt treatment, and regular deworming should be implemented to alleviate the burden of intestinal parasites in HIV-infected children.

Surface enhanced Raman spectroscopy of RNA samples extracted from blood of hepatitis C patients for quantification of viral loads.

Raman spectroscopy is a promising technique to analyze the body fluids for the purpose of non-invasive disease diagnosis. To develop a surface-enhanced Raman spectroscopy (SERS) based method for qualitative and quantitative analysis of HCV from blood samples. SERS was employed to characterize the Hepatitis C viral RNA extracted from different blood samples of hepatitis C virus (HCV) infected patients with predetermined viral loads in comparison with total RNA of healthy individuals. The SERS measurements were performed on 27 extracted RNA samples including low viral loads, medium viral loads, high viral loads and healthy/negative viral load samples. For this purpose, silver nanoparticles (Ag NPs) were used as SERS substrates. Furthermore, multivariate data analysis technique, Principal Component Analysis (PCA) and Partial Least Square Regression (PLSR) were also performed on SERS spectral data. The SERS spectral features due to biochemical changes in the extracted RNA samples associated with the increasing viral loads were established which could be employed for HCV diagnostic purpose. PCA was found helpful for the differentiation between Raman spectral data of RNA extracted from hepatitis infected and healthy blood samples. PLSR model is established for the determination of viral loads in HCV positive RNA samples with 99 % accuracy. SERS can be employed for qualitative and quantitative analysis of HCV from blood samples.

Second line anti-retroviral therapy failure in a pediatric cohort of an Ethiopian tertiary hospital: A retrospective observational study

Background: Sub-Saharan Africa carries the largest burden of pediatric HIV infection. The extent and factors affecting the success of second line anti-retroviral treatment in the region have not been well-studied. This study aimed to determine the rate and determinants of failure of second line anti-retroviral treatment among children and adolescents on follow-up at an Ethiopian tertiary teaching hospital. Methods and materials: A retrospective observational cohort study was conducted at Tikur Anbessa Specialized Hospital, Addis Ababa, Ethiopia. Structured data abstraction forms were used to collect socio-demographic, clinical and diagnostic data. Descriptive statistics and bivariate analysis were used to describe the magnitude of the problem and its associations. Results: A total of 76 children and adolescents who were taking second line anti-retroviral treatment and had at least a single viral load determination while under care were analyzed. Their mean age was 16.1 years. Failure of second line anti-retroviral drugs was seen in 14 of the 76 while 4 of them fulfilled eligibility criteria for a switch to third line anti-retroviral treatment. The mean duration till virologic failure was 17.6 months. The mean CD4 and viral load upon requirement of a third line regimen was 612.2/mm3 and 82,131.3 copies/ml. Second line antiretroviral treatment virologic failure was significantly associated with the age of the child or adolescent. Conclusion: There was a high rate of virologic failure among children and adolescents under second line anti-retroviral drugs in our hospital. Our findings also highlight the need for provision of third line second line anti-retroviral drugs. Challenges for delivering a standard care were infrequent viral load testing and delayed initiation of second line treatment after confirming failure of first line regimens.

A Comprehensive Prospective Study to Understand Chikungunya Infection in Delhi Region during 2010-2011

INTRODUCTION: Chikungunya is an arbovirus causing febrile illness with high strike rate and is known for outbreaks in more than 60 countries globally. During 2010-2011 unusual high number of suspected Chikungunya infection patients attended AIIMS OPD, Delhi, India. The NCR region with its semiarid geography restricts arbovirus outbreaks to monsoon months and is previously known for Dengue outbreaks although Chikungunya outbreaks were previously unknown to the region. The surge in suspected Chikungunya infection cases indicates a possible outbreak in the NCR region. This comprehensive prospective and follow-up study was designed to understand the Chikungunya infection among patients attending AIIMS OPD during 2010-11. METHOD: During June 2010 to Dec 2011, 2346 blood samples were collected from outpatients and inpatients attending AIIMS OPD, New Delhi. Samples were grouped in acute and chronic cases. Some patients were also enrolled for year-long follow-up study. Serum samples were tested for CHIKV using PCR and for IgM antibodies to chikungunya virus by IgM-capture ELISA. Real-time PCR was performed targeting the E1 gene for viral load determination in patient sera. RESULT: CHIKV positivity of 35% (746/2112) in acute and 67% (156/234) in chronic suspected cases were found by ELISA. most affected patients belonged to the age group >30-45 yrs. and above in both genders. Acute confirmed cases included 383 (51.3%) females and 363 (48.7%) males and chronic includes 92 (58.9%) females and 64 (41.1%) males. Clinical symptoms include polyarthralgia, fever, and rashes. Maximum positivity was seen in Oct-Nov of both years. During follow-up study, 118 patients enrolled, persisting polyarthralgia and anti-CHIKV IgM was detected up to 2 years while circulating CHIKV was detected by PCR up to 3 months in few patients. CONCLUSION: Chikungunya virus has emerged in Delhi during 2010 and contributed to about 30-40% of fever and arthralgia. CHIKV prevalence is highest in post monsoon month of October. The virus can remain in blood circulation for weeks, while anti-CHIKV IgM can persist for more than a year with complaints of periodic polyarthralgia.

Prevalence of chronic obstructive pulmonary disease in patients diagnosed with HIV without prior antiretroviral treatment

Introduction Chronic obstructive pulmonary disease (COPD) is the most prevalent respiratory problem in the world. Patients with human immunodeficiency virus (HIV) infection have a higher prevalence of smoking and recurrent lung infections and are at higher risk of COPD. Objective To determine the prevalence of COPD in HIV-diagnosed patients referred to an infectious diseases hospital. Method Individuals with HIV infection without previous or ongoing antiretroviral treatment, with chronic respiratory symptoms, with or without a history of exposure for the development of COPD were included. Pre- and post-bronchodilation spirometry, high-resolution computed tomography, viral load determination and CD4 count were carried out. Spirometry measurements were compared with Wilcoxon's test. Results Sixty-six HIV-diagnosed patients, with a mean age of 31.5 years were included; 64 were males and two females. The prevalence of COPD was 7.6 %. The group with obstruction had a lower CD4 count (27.3 versus 225.9) and higher viral load (165,000 versus 57,722), in comparison with the group without obstruction. A positive correlation was observed between lower viral load and higher forced expiratory volume in 1 second/forced vital capacity ratio. Conclusion HIV-positive patients with a lower CD4 count and a higher viral load show a decrease in spirometry values.

MaxRatio improves the detection of samples with abnormal amplification profiles on QIAgen's artus HIV-1 qPCR assay.

Background: Accurate viral load (VL) determination is paramount to determine the efficacy of anti-HIV-1 therapy. The conventional method used, fit-point (FP), assumes an equal efficiency in the polymerase chain reaction (PCR) among samples that might not hold for low-input templates. An alternative approach, maxRatio, was introduced to compensate for inhibition in PCR. Methods: Herein, we assessed whether maxRatio could improve VL quantification using 2,544 QIAgen artus HI virus-1 RT-PCR reactions. The assay's standard dilutions were used to build external standard curves with either FP or maxRatio that re-calculated the VLs. Results: FP and maxRatio were highly comparable (Pearson's ρ=0.994, Cohen's κ=0.885), and the combination of the two methods identified samples (n=41) with aberrant amplification profiles. Conclusions: The combination of maxRatio and FP could improve the predictive value of the assay.