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Pauly MD, Ganova-Raeva L. Point-of-Care Testing for Hepatitis Viruses: A Growing Need. Life (Basel) 2023; 13:2271. [PMID: 38137872 PMCID: PMC10744957 DOI: 10.3390/life13122271] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/23/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Viral hepatitis, caused by hepatitis A virus (HAV), hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis D virus (HDV), or hepatitis E virus (HEV), is a major global public health problem. These viruses cause millions of infections each year, and chronic infections with HBV, HCV, or HDV can lead to severe liver complications; however, they are underdiagnosed. Achieving the World Health Organization's viral hepatitis elimination goals by 2030 will require access to simpler, faster, and less expensive diagnostics. The development and implementation of point-of-care (POC) testing methods that can be performed outside of a laboratory for the diagnosis of viral hepatitis infections is a promising approach to facilitate and expedite WHO's elimination targets. While a few markers of viral hepatitis are already available in POC formats, tests for additional markers or using novel technologies need to be developed and validated for clinical use. Potential methods and uses for the POC testing of antibodies, antigens, and nucleic acids that relate to the diagnosis, monitoring, or surveillance of viral hepatitis infections are discussed here. Unmet needs and areas where additional research is needed are also described.
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Affiliation(s)
| | - Lilia Ganova-Raeva
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd., NE, Atlanta, GA 30329, USA;
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Pauly MD, Weis-Torres S, Hayden TM, Ganova-Raeva LM, Kamili S. Development of simple, rapid, and sensitive methods for detection of hepatitis C virus RNA from whole blood using reverse transcription loop-mediated isothermal amplification. J Clin Microbiol 2023; 61:e0077123. [PMID: 37933990 PMCID: PMC10662345 DOI: 10.1128/jcm.00771-23] [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: 06/20/2023] [Accepted: 09/19/2023] [Indexed: 11/08/2023] Open
Abstract
Hepatitis C virus (HCV) infection is an underdiagnosed global health problem. Diagnosis of current HCV infections typically requires testing for HCV RNA using high-complexity laboratory tests. Methods for the detection of HCV RNA that are simple, inexpensive, rapid, and compatible with use outside of a laboratory setting are very important in order to improve access to hepatitis C diagnostic testing and facilitate accelerated linkage to care. We developed and evaluated three simple workflows for extracting HCV RNA from small volumes of whole blood for use in a sensitive, pan-genotypic RT-LAMP assay. The water workflow uses osmotic stress to release HCV RNA and has a limit of detection of 4.3 log10(IU/mL) (95% CI 4.0-4.9). The heat workflow uses a heating step to release HCV RNA and has a limit of detection of 4.2 log10(IU/mL) (95% CI 3.8-5.1). The bead workflow, which uses chemical lysis of the sample and a streamlined paramagnetic solid phase reversible immobilization bead procedure for nucleic acid purification, has a limit of detection of 2.8 log10(IU/mL) (95% CI 2.5-3.4). When used to test whole blood spiked with HCV RNA-positive plasma samples in which most HCV levels were below 5.0 log10(IU/mL), the water, heat, and bead workflows detected HCV RNA in 69%, 75%, and 94% of samples, respectively. These workflows are compatible with visual lateral flow dipsticks, and each takes less than 60 min from sample to result. Each workflow can be performed with minimal and inexpensive equipment. With further procedural simplifications, these workflows may form the basis of assays for the point-of-care diagnosis of HCV infections.
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Affiliation(s)
- Matthew D. Pauly
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
| | - Sabrina Weis-Torres
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
| | - Tonya M. Hayden
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
| | - Lilia M. Ganova-Raeva
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
| | - Saleem Kamili
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
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Breakwell L, Marke D, Kaiser R, Tejada-Strop A, Pauly MD, Jabbi S, Yambasu S, Kabore HJ, Stewart B, Sesay T, Samba TT, Hayden T, Kamili S, Jambai A, Drobeniuc J, Singh T, Tohme RA, Wasley A. Assessing the impact of the routine childhood hepatitis B immunization program and the need for hepatitis B vaccine birth dose in Sierra Leone, 2018. Vaccine 2022; 40:2741-2748. [PMID: 35361502 PMCID: PMC10406334 DOI: 10.1016/j.vaccine.2022.03.049] [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: 09/10/2021] [Revised: 03/18/2022] [Accepted: 03/20/2022] [Indexed: 11/19/2022]
Abstract
Sierra Leone is highly endemic for hepatitis B virus (HBV) infection and thus recommends three doses of hepatitis B vaccine (HepB3) from 6 weeks of age but does not recommend a birth dose (HepB-BD) to prevent mother-to-child transmission (MTCT). We evaluated impact of the existing HepB3 schedule and risk for MTCT of HBV. We conducted a community-based serosurvey among 4-30-month-olds, their mothers, and 5-9-year-olds in three districts in Sierra Leone. Participants had an HBV surface antigen (HBsAg) rapid test; all HBsAg-positive and one HBsAg-negative mother per cluster were tested for HBV markers. We collected children's HepB3 vaccination history. Among 1889 children aged 4-30 months, HepB3 coverage was 85% and 20 (1·3% [95% CI 0·8-2·0]) were HBsAg-positive, of whom 70% had received HepB3. Among 2025 children aged 5-9 years, HepB3 coverage was 77% and 32 (1·6% [1·1-2·3]) were HBsAg-positive, of whom 56% had received HepB3. Of 1776 mothers, 169 (9·8% [8·1-11·7]) were HBsAg-positive. HBsAg prevalence was 5·9% among children of HBsAg-positive mothers compared to 0·7% among children of HBsAg-negative mothers (adjusted OR = 10·6 [2·8-40·8]). HBsAg positivity in children was associated with maternal HBsAg (p = 0·026), HBV e antigen (p < 0·001), and HBV DNA levels ≥ 200 000 IU/mL (p < 0·001). HBsAg prevalence was lower among children than mothers, for whom HepB was not available, suggesting routine infant HepB vaccination has lowered HBV burden. Since HBsAg positivity in children was strongly associated with maternal HBV infection and most of the HBsAg-positive children in the survey received HepB3, HepB-BD may prevent MTCT and chronic HBV infection.
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Affiliation(s)
- Lucy Breakwell
- U.S. Centers for Disease Control and Prevention, Atlanta, GA, United States.
| | - Dennis Marke
- Sierra Leone Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Reinhard Kaiser
- U.S. Centers for Disease Control and Prevention, Freetown, Sierra Leone
| | | | - Matthew D Pauly
- U.S. Centers for Disease Control and Prevention, Atlanta, GA, United States
| | | | | | - Hyacinte J Kabore
- World Health Organization Regional Office for Africa, Brazzaville, People's Republic of Congo
| | - Brock Stewart
- U.S. Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Tom Sesay
- Sierra Leone Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Thomas T Samba
- Sierra Leone Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Tonya Hayden
- U.S. Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Saleem Kamili
- U.S. Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Amara Jambai
- Sierra Leone Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Jan Drobeniuc
- U.S. Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Tushar Singh
- U.S. Centers for Disease Control and Prevention, Freetown, Sierra Leone
| | - Rania A Tohme
- U.S. Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Annemarie Wasley
- U.S. Centers for Disease Control and Prevention, Atlanta, GA, United States
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Pauly MD, Kamili S, Hayden TM. Impact of nucleic acid extraction platforms on hepatitis virus genome detection. J Virol Methods 2019; 273:113715. [PMID: 31419455 DOI: 10.1016/j.jviromet.2019.113715] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 07/19/2019] [Revised: 08/07/2019] [Accepted: 08/12/2019] [Indexed: 02/06/2023]
Abstract
Detection and quantification of viral nucleic acids are important for diagnosing current viral infections and monitoring response to antiviral therapy. Automated nucleic acid extraction and purification platforms are routinely used during the first step in these processes in clinical and research laboratories. Here, we compare the extraction efficiencies of four MagNA Pure magnetic bead-based nucleic acid extraction platforms and associated kits using samples positive for nucleic acids from HAV, HBV, HCV, HDV, and HEV. These five hepatitis viruses are diverse in their virion structures and type of nucleic acid that compose their genomes. We found that the most efficient nucleic acid extraction platform and corresponding kit, when averaged across all tested viruses, was the MagNA Pure 96, which yielded twice as much detectable nucleic acid as the other platforms. However, the relative efficiencies of the different platforms varied by virus type, suggesting that an extraction platform that is more efficient for one virus type will not necessarily function better with a different virus type. Our results show that the choice of a nucleic acid extraction platform influences the sensitivity of the methodology and has the potential to generate false-negative results especially in samples with low levels of viral nucleic acids.
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Affiliation(s)
- Matthew D Pauly
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, Atlanta, GA, USA
| | - Saleem Kamili
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, Atlanta, GA, USA
| | - Tonya M Hayden
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, Atlanta, GA, USA.
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Pauly MD, Bautista MA, Black JA, Whitaker RJ. Diversified local CRISPR-Cas immunity to viruses of Sulfolobus islandicus. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180093. [PMID: 30905292 PMCID: PMC6452263 DOI: 10.1098/rstb.2018.0093] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/29/2019] [Indexed: 12/26/2022] Open
Abstract
The population diversity and structure of CRISPR-Cas immunity provides key insights into virus-host interactions. Here, we examined two geographically and genetically distinct natural populations of the thermophilic crenarchaeon Sulfolobus islandicus and their interactions with Sulfolobus spindle-shaped viruses (SSVs) and S. islandicus rod-shaped viruses (SIRVs). We found that both virus families can be targeted with high population distributed immunity, whereby most immune strains target a virus using unique unshared CRISPR spacers. In Kamchatka, Russia, we observed high immunity to chronic SSVs that increases over time. In this context, we found that some SSVs had shortened genomes lacking genes that are highly targeted by the S. islandicus population, indicating a potential mechanism of immune evasion. By contrast, in Yellowstone National Park, we found high inter- and intra-strain immune diversity targeting lytic SIRVs and low immunity to chronic SSVs. In this population, we observed evidence of SIRVs evolving immunity through mutations concentrated in the first five bases of protospacers. These results indicate that diversity and structure of antiviral CRISPR-Cas immunity for a single microbial species can differ by both the population and virus type, and suggest that different virus families use different mechanisms to evade CRISPR-Cas immunity. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.
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Affiliation(s)
- Matthew D. Pauly
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 South Goodwin Avenue, Urbana, IL 61801, USA
| | - Maria A. Bautista
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 South Goodwin Avenue, Urbana, IL 61801, USA
| | - Jesse A. Black
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 South Goodwin Avenue, Urbana, IL 61801, USA
| | - Rachel J. Whitaker
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 South Goodwin Avenue, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA
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Pauly MD, Procario MC, Lauring AS. A novel twelve class fluctuation test reveals higher than expected mutation rates for influenza A viruses. eLife 2017; 6. [PMID: 28598328 PMCID: PMC5511008 DOI: 10.7554/elife.26437] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [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: 03/01/2017] [Accepted: 06/09/2017] [Indexed: 12/21/2022] Open
Abstract
Influenza virus’ low replicative fidelity contributes to its capacity for rapid evolution. Clonal sequencing and fluctuation tests have suggested that the influenza virus mutation rate is 2.7 × 10–6 - 3.0 × 10–5 substitutions per nucleotide per strand copied (s/n/r). However, sequencing assays are biased toward mutations with minimal fitness impacts and fluctuation tests typically investigate only a subset of all possible single nucleotide mutations. We developed a fluctuation test based on reversion to fluorescence in a set of virally encoded mutant green fluorescent proteins, which allowed us to measure the rates of selectively neutral mutations representative of the twelve different mutation types. We measured an overall mutation rate of 1.8 × 10–4 s/n/r for PR8 (H1N1) and 2.5 × 10–4 s/n/r for Hong Kong 2014 (H3N2) and a transitional bias of 2.7–3.6. Our data suggest that each replicated genome will have an average of 2–3 mutations and highlight the importance of mutational load in influenza virus evolution. DOI:http://dx.doi.org/10.7554/eLife.26437.001
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Affiliation(s)
- Matthew D Pauly
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, United States
| | - Megan C Procario
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, United States
| | - Adam S Lauring
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, United States.,Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, United States
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