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Lim YZ, Teoh BT, Sam SS, Azizan NS, Khor CS, Nor'e SS, Abd-Jamil J, AbuBakar S. A TaqMan minor groove binder probe-based quantitative reverse transcription polymerase chain reaction for detection and quantification of chikungunya virus. Trop Biomed 2023; 40:313-319. [PMID: 37897164 DOI: 10.47665/tb.40.3.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023]
Abstract
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus with widespread distribution across the globe. Since 2016, CHIKV re-emerged in several countries including Indian subcontinent and Southeast Asia. A proper diagnostic tool for early diagnosis of CHIKV infection is crucial to facilitate patient management and control virus transmission at the earliest stage of outbreak. Therefore, a TaqMan minor groove binder (MGB) probe-based quantitative reverse transcription polymerase chain reaction (qRT-PCR) assay was developed to detect and quantify the CHIKV. The primers and probe were designed based on a conserved genomic region of 730 global CHIKV sequences that is located between nsP1 and nsP2 genes. The nucleotide mismatches of primers and probe with 730 global CHIKV sequences and 13 alphaviruses were then analysed in silico. In this study, the last 5 nucleotides at 3' end of primers and 5' end of probe were considered to be the critical regions for priming. In silico analysis revealed that the critical regions of primers and probe were at least 99.6% matched with the 730 global CHIKV sequences. Besides, the primers and probe showed at least 5/20 (25.0%) and 4/17 (23.5%) nucleotide mismatches with 13 alphaviruses respectively. The amplification efficiency of qRT-PCR assay was 100.59% (95% CI= 93.06, 109.33) with a R2 score of 0.957. Its limit of detection (LOD) at 95% probability level was 16.6 CHIKV RNA copies (95% CI= 12.9, 28.9). The qRT-PCR assay was specific to CHIKV without cross-reacting with all dengue virus serotypes, Getah virus, Tembusu virus and Zika virus. The diagnostic results of qRT-PCR assay were perfectly agreed (k=1.000, p=0.003) with a commercial trioplex assay, with sensitivity of 100% (95% CI= 61, 100) and specificity of 100% (95% CI= 44, 100). Overall, the developed qRT-PCR assay is ideal for rapid, sensitive and specific detection as well as quantification of CHIKV.
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Affiliation(s)
- Y Z Lim
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HICoE), Universiti Malaya, 50603 Kuala Lumpur, Malaysia
- Institute for Advanced Studies, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - B T Teoh
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HICoE), Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - S S Sam
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HICoE), Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - N S Azizan
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HICoE), Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - C S Khor
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HICoE), Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - S S Nor'e
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HICoE), Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - J Abd-Jamil
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HICoE), Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - S AbuBakar
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HICoE), Universiti Malaya, 50603 Kuala Lumpur, Malaysia
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Kalichman SC, Eaton LA, Kalichman MO, Sam SS, Caliendo AM. Prepandemic Predictors of Medication Adherence and HIV Viral Load During the First Year of COVID-19. J Acquir Immune Defic Syndr 2023; 92:242-249. [PMID: 36730771 PMCID: PMC9911104 DOI: 10.1097/qai.0000000000003129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 10/24/2022] [Indexed: 02/04/2023]
Abstract
ABSTRACT Studies have reported significant immediate impacts of the COVID-19 pandemic on the social relationships and health care of people living with HIV. This study followed a closed cohort of young people living with HIV over the first year of the COVID-19 pandemic. Participants were men and women (N = 140) age 36 years and younger who were living with HIV and had demonstrated suboptimal adherence to antiretroviral therapy, unsuppressed HIV viral load, or active substance use in a run-in study. The results confirmed that participants continued to experience significant disruptions to their social relationships and health care over the course of the first year of the COVID-19 pandemic. There was evidence for sustained impacts on transportation, housing stability, and food security during the first year of COVID-19. Multivariable models showed that greater pre-COVID-19 social support predicted greater antiretroviral therapy adherence and greater HIV suppression (lower viral load) over the first year of the COVID-19 pandemic. Efforts to plan and prepare people living with HIV for future social crises, including future pandemics, should emphasize building and sustaining social support.
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Affiliation(s)
- Seth C. Kalichman
- Institute for Collaborative Health Intervention and Policy, University of Connecticut, Storrs, CT
| | - Lisa A. Eaton
- Institute for Collaborative Health Intervention and Policy, University of Connecticut, Storrs, CT
| | - Moira O. Kalichman
- Institute for Collaborative Health Intervention and Policy, University of Connecticut, Storrs, CT
| | - Soya S. Sam
- Division of Infectious Diseases, The Miriam Hospital, Providence, RI; and
- Department of Medicine, Warren Alpert Medical School of Brown University, Providence, RI
| | - Angela M. Caliendo
- Department of Medicine, Warren Alpert Medical School of Brown University, Providence, RI
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Orang’o EO, Bocage AE, Liu TD, Itsura PM, Tonui PK, Muthoka K, Stephen K, Caliendo AM, Sam SS, Cu-Uvin S. Human Immunodeficiency Virus Type 1 RNA Genital Tract Shedding After Cryotherapy for Cervical Intraepithelial Neoplasia in Western Kenya. Open Forum Infect Dis 2022; 10:ofac662. [PMID: 36632424 PMCID: PMC9830484 DOI: 10.1093/ofid/ofac662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
This prospective study of 39 women living with human immunodeficiency virus (HIV) on antiretroviral therapy in Western Kenya aimed to quantify genital tract HIV-1 RNA (GT-HIV RNA) shedding before and after cryotherapy for cervical intraepithelial neoplasia. Most GT-HIV RNA shedding was detected precryotherapy, suggesting that cryotherapy was not the primary cause of shedding.
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Affiliation(s)
| | - Anne E Bocage
- Correspondence: Anne Bocage, BA, Warren Alpert Medical School, Brown University, 222 Richmond St, Box G-M117, Providence RI 02912, USA ()
| | - Tao D Liu
- Department of Biostatistics, Brown University, Providence, Rhode Island, USA
| | - Peter M Itsura
- Department of Reproductive Health, Moi University, Eldoret, Kenya
| | - Philip K Tonui
- Department of Reproductive Health, Moi University, Eldoret, Kenya
| | - Kapten Muthoka
- Academic Model Providing Access to Healthcare Partnership, Eldoret, Kenya
| | - Kiptoo Stephen
- Department of Reproductive Health, Moi University, Eldoret, Kenya
| | - Angela M Caliendo
- Division of Infectious Disease, The Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Soya S Sam
- Division of Infectious Disease, The Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA,Division of Infectious Diseases, Miriam Hospital, Providence, Rhode Island, USA
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Chin KL, Teoh BT, Sam SS, Loong SK, Tan KK, Azizan NS, Lim YK, Khor CS, Nor'e SS, Abd-Jamil J, AbuBakar S. Development of a TaqMan minor groove binding probe-based quantitative reverse transcription polymerase chain reaction for the detection and quantification of Zika virus. Trop Biomed 2022; 39:518-523. [PMID: 36602210 DOI: 10.47665/tb.39.4.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Zika virus (ZIKV) infection has emerged as a global health concern following epidemic outbreaks of severe neurological disorders reported in Pacific and Americas since 2016. Therefore, a rapid, sensitive and specific diagnostic test for ZIKV infection is critical for the appropriate patient management and the control of disease spread. A TaqMan minor groove binding (MGB) probe-based quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assay was developed based on the conserved sequence regions of 463 ZIKV NS2B genes. The designed ZIKV qRT-PCR assay was evaluated for its detection limit, strain coverage and cross-reactivity. We further assessed the clinical applicability of qRT-PCR assay for ZIKV RNA detection using a total 18 simulated clinical specimens. The detection limit of the qRT-PCR assay was 11.276 ZIKV RNA copies at the 95% probability level (probit analysis, p<= 0.05). Both Asian and African ZIKV strains were detected by the qRT-PCR assay without cross-reacting with DENV-1, DENV-2, DENV-3, DENV-4, CHIKV, JEV, LGTV, GETV and SINV. The qRT-PCR assay demonstrated a perfect agreement (k = 1.000, P < 0.001) with the reference assay; the sensitivity and specificity of the qRT-PCR assay were 100% (95% CI= 79.6-100) and 100% (95% CI= 43.9-100) respectively. The qRT-PCR assay developed in this study is a useful diagnostic tool for the broad coverage detection and quantification of both the Asian and African ZIKV strains.
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Affiliation(s)
- K L Chin
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Center of Excellence (HICoE), Universiti Malaya, 50603 Kuala Lumpur, Malaysia.,Institute for Advanced Studies, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - B T Teoh
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Center of Excellence (HICoE), Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - S S Sam
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Center of Excellence (HICoE), Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - S K Loong
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Center of Excellence (HICoE), Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - K K Tan
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Center of Excellence (HICoE), Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - N S Azizan
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Center of Excellence (HICoE), Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Y K Lim
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Center of Excellence (HICoE), Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - C S Khor
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Center of Excellence (HICoE), Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - S S Nor'e
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Center of Excellence (HICoE), Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - J Abd-Jamil
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Center of Excellence (HICoE), Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - S AbuBakar
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Center of Excellence (HICoE), Universiti Malaya, 50603 Kuala Lumpur, Malaysia.,Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
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Nyandiko W, Holland S, Vreeman R, DeLong AK, Manne A, Novitsky V, Ngeresa A, Chory A, Aluoch J, Orido M, Jepkemboi E, Sam SS, Caliendo AM, Ayaya S, Hogan JW, Kantor R. HIV-1 Treatment Failure, Drug Resistance, and Clinical Outcomes in Perinatally Infected Children and Adolescents Failing First-Line Antiretroviral Therapy in Western Kenya. J Acquir Immune Defic Syndr 2022; 89:231-239. [PMID: 34723922 PMCID: PMC8752470 DOI: 10.1097/qai.0000000000002850] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 10/19/2021] [Indexed: 02/03/2023]
Abstract
BACKGROUND Long-term impact of drug resistance in perinatally infected children and adolescents living with HIV (CALWH) is poorly understood. We determined drug resistance and examined its long-term impact on failure and mortality in Kenyan CALWH failing first-line non-nucleoside reverse transcriptase inhibitor-based antiretroviral therapy (ART). SETTING Academic Model Providing Access to Healthcare, western Kenya. METHODS Participants were enrolled in 2010-2013 (timepoint 1) and a subsample re-enrolled after 4-7 years (timepoint 2). Viral load (VL) was performed on timepoint 1 samples, with genotyping of those with detectable VL. Primary endpoints were treatment failure (VL >1000 copies/mL) at and death before timepoint 2. Multinomial regression analysis was used to characterize resistance effect on death, failure, and loss-to-follow-up, adjusting for key variables. RESULTS The initial cohort (n = 480) was 52% (n = 251) female, median age 8 years, median CD4% 31%, 79% (n = 379) on zidovudine/abacavir + lamivudine + efavirenz/nevirapine for median 2 years. Of these, 31% (n = 149) failed at timepoint 1. Genotypes at timepoint 1, available on n = 128, demonstrated 93% (n = 119) extensive resistance, affecting second line. Of 128, 22 failed at timepoint 2, 17 died, and 32 were lost to follow-up before timepoint 2. Having >5 resistance mutations at timepoint 1 was associated with higher mortality [relative risk ratio (RRR) = 8.7, confidence interval (CI) 2.1 to 36.3] and loss to follow-up (RRR = 3.2, CI 1.1 to 9.2). Switching to second line was associated with lower mortality (RRR <0.05, CI <0.05 to 0.1) and loss to follow-up (RRR = 0.1, CI <0.05 to 0.3). CONCLUSION Extensive resistance and limited switch to second line in perinatally infected Kenyan CALWH failing first-line ART were associated with long-term failure and mortality. Findings emphasize urgency for interventions to sustain effective, life-long ART in this vulnerable population.
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Affiliation(s)
- Winstone Nyandiko
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
- Moi University College of Health Sciences, Eldoret, Kenya
| | | | - Rachel Vreeman
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | | | - Anthony Ngeresa
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - Ashley Chory
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Josephine Aluoch
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - Millicent Orido
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - Eslyne Jepkemboi
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | | | | | - Samuel Ayaya
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
- Moi University College of Health Sciences, Eldoret, Kenya
| | - Joseph W Hogan
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
- Brown University, Providence, RI, USA
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Bocage A, Orang'o O, Liu T, Itsura P, Tonui P, Muthoka K, Stephen K, Sam SS, Caliendo A, Cu-Uvin S. HIV-1 RNA Genital Tract Shedding After Cryotherapy for Visual Inspection with Acetic Acid-Positive Cervical Lesions in Western Kenya. Am J Obstet Gynecol 2022. [DOI: 10.1016/j.ajog.2021.11.1278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Sam SS, Rogers R, Gillani FS, Tsongalis GJ, Kraft CS, Caliendo AM. Evaluation of a Next-Generation Sequencing Metagenomics Assay to Detect and Quantify DNA Viruses in Plasma from Transplant Recipients. J Mol Diagn 2021; 23:719-731. [PMID: 33706010 PMCID: PMC8279015 DOI: 10.1016/j.jmoldx.2021.02.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 01/08/2021] [Accepted: 02/25/2021] [Indexed: 11/24/2022] Open
Abstract
Viral infections are major causes of morbidity and mortality in solid-organ and hematopoietic stem cell transplant recipients. This study evaluated the performance of the Galileo Pathogen Solution metagenomics Next-Generation sequencing assay to detect and quantify 11 DNA viruses (cytomegalovirus, Epstein-Barr virus, BK virus, human adenovirus, JC virus, herpes simplex virus 1 and 2, varicella zoster virus, human herpesvirus 6A and 6B, and parvovirus B19) and to qualitatively detect torque teno virus. DNA extracted from 47 plasma samples of viremic transplant recipients were subjected to DNA library preparation with pathogen enrichment/human background depletion, sequencing, and automated data analysis. The viral loads were determined with the Galileo assay using a standard curve generated from a calibration panel. All of the samples tested had a 100% agreement with the real-time quantitative PCR (qPCR) assays in detecting the primary virus targets and the majority of the quantified samples had a viral load difference within 0.46 log10 IU/mL or copies/mL. The mean difference for cytomegalovirus between the Galileo and qPCR assays was 0.21 log10 IU/mL (SD, ±0.43 log10 IU/mL). The mean difference for BK virus between the Galileo and qPCR assays was 0.17 log10 cp/mL (SD, ±0.67 log10 cp/mL). Additionally, 75 co-infections were detected in 31 samples by the Galileo assay. The study findings show that the Galileo assay can simultaneously detect and quantify multiple viruses in transplant recipients with results that are comparable with standard-of-care qPCR assays.
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Affiliation(s)
- Soya S Sam
- Division of Infectious Diseases, The Miriam Hospital, Providence, Rhode Island; Division of Infectious Diseases, Warren Alpert School of Medicine, Brown University, Providence, Rhode Island.
| | - Ralph Rogers
- Division of Infectious Diseases, Warren Alpert School of Medicine, Brown University, Providence, Rhode Island
| | - Fizza S Gillani
- Division of Infectious Diseases, The Miriam Hospital, Providence, Rhode Island; Division of Infectious Diseases, Warren Alpert School of Medicine, Brown University, Providence, Rhode Island
| | - Gregory J Tsongalis
- Department of Pathology, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
| | - Colleen S Kraft
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Angela M Caliendo
- Division of Infectious Diseases, Warren Alpert School of Medicine, Brown University, Providence, Rhode Island
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Abstract
BACKGROUND AND OBJECTIVE HIV viral load measurements play a critical role in monitoring disease progression in those who are on antiretroviral treatment. In order to obtain an accurate measurement, rapid sample preparation techniques are required. There is an unmet need for HIV extraction instruments in resource-limited settings, where HIV prevalence is high. Therefore, the objective of our study was to develop a three-dimensional (3D) microfluidic system to extract HIV-1 RNA with minimal electricity and without complex laboratory instruments. METHODS A 3D microfluidic system was designed in which magnetic beads bound with nucleic acids move through immiscible oil-water interfaces to separate HIV-1 RNA from the sample. Polymerase chain reaction (PCR) amplification was used to quantify the total amount of HIV-1 RNA extracted as we optimized the system through chip design, bead type, carry-over volume, carrier RNA concentration, and elution buffer temperature. Additionally, the extraction efficiency of the 3D microfluidic system was evaluated by comparing with a Qiagen EZ1 Advanced XL instrument using 20 HIV-1-positive plasma samples. RESULTS Our method has near-perfect (100%) extraction efficiency in spiked serum samples with as little as 50 copies/mL starting sample. Furthermore, we report carry-over volumes of 0.31% ± 0.006% of total sample volume. Using the EZ1 Advanced XL as a gold standard, the average percentage HIV-1 RNA extracted using the microchip was observed to be 65.4% ± 24.6%. CONCLUSIONS From a clinical perspective, the success of our method opens up its possible use in diagnostic tests for HIV in the remote areas where access to vortexes and centrifuges is not available. Here we present a proof-of-concept device which, with further development, could be used for sample preparation at the point of care.
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Affiliation(s)
- Rachel N Deraney
- Center for Biomedical Engineering, School of Engineering, Brown University, 182 Hope Street, Providence, RI, 02912, USA
| | - Derek Troiano
- Center for Biomedical Engineering, School of Engineering, Brown University, 182 Hope Street, Providence, RI, 02912, USA
| | | | - Soya S Sam
- Division of Infectious Diseases, The Miriam Hospital, Providence, RI, USA
| | - Angela M Caliendo
- Department of Medicine, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University, 182 Hope Street, Providence, RI, 02912, USA.
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Sam SS, Ingersoll J, Racsa LD, Caliendo AM, Racsa PN, Igwe D, Abdul-Ali D, Josephson C, Kraft CS. Long-term stability of CMV DNA in human breast milk. J Clin Virol 2018; 102:39-41. [PMID: 29486386 DOI: 10.1016/j.jcv.2018.02.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/16/2018] [Accepted: 02/19/2018] [Indexed: 10/18/2022]
Abstract
BACKGROUND Human cytomegalovirus (CMV) is the leading cause of intrauterine and perinatal viral infection. The most common route of CMV transmission in newborns is through breastmilk and this can lead to infant morbidity and mortality. Breast milk that has been frozen for an extended period may need to be tested for CMV DNA to determine the source of infection. It has been a challenge for clinical laboratories to ensure the stability of CMV DNA in frozen breast milk for accurate viral load measurement. OBJECTIVES To evaluate the stability of CMV DNA in breast milk by testing quantitative viral loads over a 28-day period for breast milk stored at 4 °C and a 90-day period for breast milk stored at -20 °C. STUDY DESIGN Baseline viral loads were determined on day 0 and the samples stored at 4 °C underwent extraction and amplification at four time points, up to 28 days. The samples stored at -20 °C underwent extraction and amplification at five time points up to 90 days. Log10 values were calculated and t-test, Pearson's coefficient, and concordance correlation coefficient were calculated. RESULTS There was no statistically significant difference between the time points by t-test, and correlation coefficients showed greater than 90% concordance for days 0 and 28 as well as days 0 and 90 at both storage temperatures tested. CONCLUSIONS The concentration of CMV DNA in breast milk was stable for 28 days at 4 °C and 90 days at -20 °C as the concentrations did not differ significantly from the baseline viral loads.
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Affiliation(s)
- Soya S Sam
- Division of Infectious Diseases, The Miriam Hospital, Providence, RI, United States.
| | - Jessica Ingersoll
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Lori D Racsa
- Peoria-Tazewell Pathology Group, Peoria, IL, United States
| | - Angela M Caliendo
- Department of Medicine, Alpert Medical School of Brown University, Providence, RI, United States
| | | | - Doris Igwe
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Deborah Abdul-Ali
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Cassandra Josephson
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Colleen S Kraft
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
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Sam SS, Caliendo AM, Ingersoll J, Abdul-Ali D, Kraft CS. Performance evaluation of the Aptima HSV-1 and 2 assay for the detection of HSV in cutaneous and mucocutaneous lesion specimens. J Clin Virol 2017; 99-100:1-4. [PMID: 29253834 DOI: 10.1016/j.jcv.2017.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 12/04/2017] [Accepted: 12/12/2017] [Indexed: 10/18/2022]
Abstract
BACKGROUND Timely and precise laboratory diagnosis of Herpes simplex viruses (HSV) is required to guide clinical management. OBJECTIVES The study evaluated limit of detection (LOD) and performance characteristics of the Aptima HSV 1 & 2 assay in comparison to four assays. STUDY DESIGN The multi-center study compared qualitative detection of HSV-1 and 2 by the Aptima HSV-1 and 2 assay (Hologic) to ELVIS culture, Lyra Direct (Quidel), AmpliVue (Quidel) and a laboratory developed test (LDT). LOD was performed using VTM and STM diluted viral concentrations and clinical performance was evaluated using 505 swab specimens. RESULTS The Aptima LOD studies performed showed a lower detection limit for STM specimens as 1450 copies/mL and 430 copies/mL for HSV1 and HSV-2 respectively; the LOD for VTM specimens was 9370 copies/mL and 8045 copies/mL for HSV-1 and HSV-2 respectively. When the assays were analyzed based on the positive consensus result established the Aptima had 95% of percent positive agreement (PPA) and 100% negative percent agreement (NPA) for the HSV-1. For the HSV-2, the PPA and NPA for Aptima were 96% and 100% respectively. AmpliVue had 1.8% invalid rate, while Lyra had no invalid results but an inhibition rate of 0.8%. Aptima and LDT did not have any invalid or inhibited results. CONCLUSION The results indicate that the Aptima HSV-1 & 2 assay is sensitive and the performance characteristics of the Aptima assay is comparable to the assays analyzed for the detection and differentiation of HSV-1 and 2 from cutaneous and mucocutaneous lesions.
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Affiliation(s)
- Soya S Sam
- Division of Infectious Diseases, The Miriam Hospital, Providence, RI, United States.
| | - Angela M Caliendo
- Department of Medicine, Warren Alpert School of Medicine, Brown University, Providence, RI, United States
| | - Jessica Ingersoll
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Deborah Abdul-Ali
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Colleen S Kraft
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
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Abstract
Inheritance of polymorphisms in the interleukin (IL)-10 promoter and IL-12B genes, which influence cytokine production and activities, may define the balance in T helper response in infection and autoimmune diseases. In the present study, we investigated the distribution of the IL-10 promoter and IL-12B gene polymorphisms in a multiethnic Malaysian population. Overall, our findings suggest that the IL-12B and IL-10 -592 genotypes were distributed homogenously across all major ethnic groups, including Malays, Chinese, and Indians, except for polymorphisms at IL-10 -1082. At this gene locus, the ethnic Chinese showed a significantly lower allele frequency of -1082G (2.1%) compared to the Malay (12.2%) and Indian (15.3%) populations. Results for the IL-12B and IL-10 gene polymorphisms were consistent with those reported for the Asian population, but markedly different from those of the African and Caucasian populations. Our findings suggest that there are specific genetic variations between different ethnic groups, which should be examined in all gene population-based association studies.
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Affiliation(s)
- S S Sam
- Tropical Infectious Diseases Research and Education Center, Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - B T Teoh
- Tropical Infectious Diseases Research and Education Center, Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - S AbuBakar
- Tropical Infectious Diseases Research and Education Center, Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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Cervinski MA, Sam SS, Steinmetz HB, Wood B, Tsongalis GJ. Validation of interleukin 28B genotyping assay for clinical use. Clin Biochem 2014; 47:478-80. [PMID: 24462832 DOI: 10.1016/j.clinbiochem.2014.01.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 01/10/2014] [Accepted: 01/13/2014] [Indexed: 12/11/2022]
Abstract
OBJECTIVES The favorable CC genotype at rs12979860 upstream of the interleukin (IL)-28B gene is correlated with a greater post-treatment sustained virologic response rate in chronic hepatitis C infected patients. We report on our validation of a clinical genotyping assay for rs12979860 polymorphisms in the IL28B locus. DESIGN AND METHODS The rs12979860 genotype was determined using a TaqMan® Real-Time PCR allelic discrimination assay with primers and probes specific for the C and T alleles on the Applied Biosystems 7500 Fast Real-Time PCR System. RESULTS The rs12979860 genotype determined by our assay was concordant with the genotypes obtained from a reference laboratory. The allelic frequency was similar to that reported in the HapMap project (rs12979860 C=0.65, T=0.35) and did not deviate from Hardy-Weinberg equilibrium. CONCLUSION Clinical availability of this assay in conjunction with other factors will allow the prediction of the individual patient's response to therapy.
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Affiliation(s)
- Mark A Cervinski
- Department of Pathology, The Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States.
| | - Soya S Sam
- Department of Pathology, The Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States
| | - Heather B Steinmetz
- Department of Pathology, The Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States
| | - Brendan Wood
- Department of Pathology, The Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States
| | - Gregory J Tsongalis
- Department of Pathology, The Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States
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Hoh BP, Sam SS, Umi SH, Mahiran M, Nik Khairudin NY, Rafidah Hanim S, Abubakar S. A novel rare copy number variant of the ABCF1 gene identified among dengue fever patients from Peninsular Malaysia. Genet Mol Res 2014; 13:980-5. [PMID: 24634119 DOI: 10.4238/2014.february.19.9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Copy number variation (CNV) is a form of genetic variation in addition to single nucleotide polymorphisms. The significance of CNV in the manifestation of a number of diseases is only recently receiving considerable attention. We genotyped 163 dengue patients from Peninsular Malaysia for genes possibly linked to dengue infection using quantitative real-time PCR. Here, we report a serendipitous discovery of a novel rare CNV of the ABCF1 gene among the dengue patients. Among these patients, two had a gain of 1 copy (CN = 3) and one had lost 1 copy (CN = 1), indicating that a rare CNV of the ABCF1 gene was detected among dengue patients from Peninsular Malaysia. Although the gene is suspected to regulate inflammatory responses and pathogen-induced cytokine storm, its relevance to dengue requires further investigation.
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Affiliation(s)
- B P Hoh
- Institute of Medical Molecular Biotechnology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Jalan Hospital, Sungai Buloh, Selangor, Malaysia
| | - S S Sam
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - S H Umi
- Institute of Medical Molecular Biotechnology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Jalan Hospital, Sungai Buloh, Selangor, Malaysia
| | - M Mahiran
- Department of Medicine, Hospital Kota Bharu, Kelantan, Malaysia
| | | | - S Rafidah Hanim
- Department of Microbiology and Parasitology, School of Medical Science, Health Campus, Universiti Sains Malaysia, Kota Bharu, Kelantan, Malaysia
| | - S Abubakar
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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Sam SS, Steinmetz HB, Tsongalis GJ, Tafe LJ, Lefferts JA. Validation of a solid-phase electrochemical array for genotyping hepatitis C virus. Exp Mol Pathol 2013; 95:18-22. [PMID: 23583628 DOI: 10.1016/j.yexmp.2013.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 04/03/2013] [Indexed: 12/14/2022]
Abstract
Hepatitis C viral infection is a major cause of progressive liver disease. HCV genotype is one of the most significant baseline predictors of response to HCV antiviral therapy. The objective was to evaluate an HCV genotyping method that targets the 5'-untranslated region (UTR) to detect genotypes/subtypes using the GenMark eSensor® XT-8 system. The HCV amplicon of major genotypes/subtypes from the Roche TaqMan® HCV assay served as a template for the nested PCR followed by a direct analysis on the XT-8 detection system. The assay was validated for limit of detection (LOD), specificity, accuracy and precision. The LOD determined was below 175 IU/ml for all the subtypes except 6ab. The genotypes detected using this assay were in concordance with the LiPA assay. The high performance characteristics (LOD, specificity, intra- and inter-assay precision, and accuracy), make this assay particularly well suited for clinical HCV genotyping in order to guide antiviral therapy.
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Affiliation(s)
- Soya S Sam
- Department of Pathology, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756, USA.
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