scholarly journals A comprehensive genomics solution for HIV surveillance and clinical monitoring in a global health setting

2018 ◽  
Author(s):  
David Bonsall ◽  
Tanya Golubchik ◽  
Mariateresa de Cesare ◽  
Mohammed Limbada ◽  
Barry Kosloff ◽  
...  
Keyword(s):  
Public Health ◽  
Drug Resistance ◽  
Viral Load ◽  
High Throughput ◽  
Genetic Sequencing ◽  
Hiv Surveillance ◽  
Viral Loads ◽  
True Variant ◽  
Technical Challenges ◽  
Additional Value

AbstractHigh-throughput viral genetic sequencing is needed to monitor the spread of drug resistance, direct optimal antiretroviral regimes, and to identify transmission dynamics in generalised HIV epidemics. Public health efforts to sequence HIV genomes at scale face three major technical challenges: (i) minimising assay cost and protocol complexity, (ii) maximising sensitivity, and (iii) recovering accurate and unbiased sequences of both the genome consensus and the within-host viral diversity. Here we present a novel, high-throughput, virus-enriched sequencing method and computational pipeline tailored specifically to HIV (veSEQ-HIV), which addresses all three technical challenges, and can be used directly on leftover blood drawn for routine CD4 testing. We demonstrate its performance on 1,620 plasma samples collected from consenting individuals attending 10 large urban clinics in Zambia, partners of HPTN 071 (PopART). We show that veSEQ-HIV consistently recovers complete HIV genomes from the majority of samples of different subtypes, and is also quantitative: the number of HIV reads per sample obtained by veSEQ-HIV estimates viral load without the need for additional testing. Both quantitativity and sensitivity were assessed on a subset of 126 samples with clinically measured viral loads, and with standardized quantification controls (VL 100 – 5,000,000 RNA copies/ml). Complete HIV genomes were recovered from 93% (85/91) of samples when viral load was over 1,000 copies per ml. The quantitative nature of the assay implies that variant frequencies estimated with veSEQ-HIV are representative of true variant frequencies in the sample. Detection of minority variants can be exploited for epidemiological analysis of transmission and drug resistance, and we show how the information contained in individual reads of a veSEQ-HIV sample can be used to detect linkage between multiple mutations associated with resistance to antiretroviral therapy. Less than 2% of reads obtained by veSEQ-HIV were identified as in silico contamination events using updates to the phyloscanner software (phyloscanner clean) that we show to be 95% sensitive and 99% specific at ‘decontaminating’ NGS data. The cost of the assay — approximately 45 USD per sample — compares favourably with existing VL and HIV genotyping tests, and provides the additional value of viral load quantification and inference of drug resistance with a single test. veSEQ-HIV is well suited to large public health efforts and is being applied to all ∼9000 samples collected for the HPTN 071-2 (PopART Phylogenetics) study.

scholarly journals Performance of a high-throughput next-generation sequencing method for analysis of HIV drug resistance and viral load

2020 ◽  
Vol 75 (12) ◽  
pp. 3510-3516 ◽  
Author(s):  
Jessica M Fogel ◽  
David Bonsall ◽  
Vanessa Cummings ◽  
Rory Bowden ◽  
Tanya Golubchik ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Viral Load ◽  
Next Generation Sequencing ◽  
High Throughput ◽  
Whole Genome ◽  
Hiv Viral Load ◽  
Viral Loads ◽  
Viral Load Assay ◽  
Generation Sequencing ◽  
Hiv 1

Abstract Objectives To evaluate the performance of a high-throughput research assay for HIV drug resistance testing based on whole genome next-generation sequencing (NGS) that also quantifies HIV viral load. Methods Plasma samples (n = 145) were obtained from HIV-positive MSM (HPTN 078). Samples were analysed using clinical assays (the ViroSeq HIV-1 Genotyping System and the Abbott RealTime HIV-1 Viral Load assay) and a research assay based on whole-genome NGS (veSEQ-HIV). Results HIV protease and reverse transcriptase sequences (n = 142) and integrase sequences (n = 138) were obtained using ViroSeq. Sequences from all three regions were obtained for 100 (70.4%) of the 142 samples using veSEQ-HIV; results were obtained more frequently for samples with higher viral loads (93.5% for 93 samples with >5000 copies/mL; 50.0% for 26 samples with 1000–5000 copies/mL; 0% for 23 samples with <1000 copies/mL). For samples with results from both methods, drug resistance mutations (DRMs) were detected in 33 samples using ViroSeq and 42 samples using veSEQ-HIV (detection threshold: 5.0%). Overall, 146 major DRMs were detected; 107 were detected by both methods, 37 were detected by veSEQ-HIV only (frequency range: 5.0%–30.6%) and two were detected by ViroSeq only. HIV viral loads estimated by veSEQ-HIV strongly correlated with results from the Abbott RealTime Viral Load assay (R2 = 0.85; n = 142). Conclusions The NGS-based veSEQ-HIV method provided results for most samples with higher viral loads, was accurate for detecting major DRMs, and detected mutations at lower levels compared with a method based on population sequencing. The veSEQ-HIV method also provided HIV viral load data.

scholarly journals A Comprehensive Genomics Solution for HIV Surveillance and Clinical Monitoring in Low-Income Settings

2020 ◽  
Vol 58 (10) ◽  
Author(s):  
David Bonsall ◽  
Tanya Golubchik ◽  
Mariateresa de Cesare ◽  
Mohammed Limbada ◽  
Barry Kosloff ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Viral Load ◽  
Low Income ◽  
Cost Effective ◽  
Clinical Monitoring ◽  
Resistance Mutations ◽  
Middle Income ◽  
Cd4 Cell Count ◽  
Genetic Sequencing ◽  
Hiv Surveillance

ABSTRACT Viral genetic sequencing can be used to monitor the spread of HIV drug resistance, identify appropriate antiretroviral regimes, and characterize transmission dynamics. Despite decreasing costs, next-generation sequencing (NGS) is still prohibitively costly for routine use in generalized HIV epidemics in low- and middle-income countries. Here, we present veSEQ-HIV, a high-throughput, cost-effective NGS sequencing method and computational pipeline tailored specifically to HIV, which can be performed using leftover blood drawn for routine CD4 cell count testing. This method overcomes several major technical challenges that have prevented HIV sequencing from being used routinely in public health efforts; it is fast, robust, and cost-efficient, and generates full genomic sequences of diverse strains of HIV without bias. The complete veSEQ-HIV pipeline provides viral load estimates and quantitative summaries of drug resistance mutations; it also exploits information on within-host viral diversity to construct directed transmission networks. We evaluated the method’s performance using 1,620 plasma samples collected from individuals attending 10 large urban clinics in Zambia as part of the HPTN 071-2 study (PopART Phylogenetics). Whole HIV genomes were recovered from 91% of samples with a viral load of >1,000 copies/ml. The cost of the assay (30 GBP per sample) compares favorably with existing VL and HIV genotyping tests, proving an affordable option for combining HIV clinical monitoring with molecular epidemiology and drug resistance surveillance in low-income settings.

scholarly journals Changes in SARS-CoV-2 viral load and mortality during the initial wave of the pandemic in New York City

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0257979
Author(s):  
Michael J. Satlin ◽  
Jason Zucker ◽  
Benjamin R. Baer ◽  
Mangala Rajan ◽  
Nathaniel Hupert ◽  
...  
Keyword(s):  
Public Health ◽  
New York ◽  
New York City ◽  
Viral Load ◽  
Hospital Mortality ◽  
York City ◽  
Health Interventions ◽  
Public Health Interventions ◽  
Viral Loads ◽  
The Impact

Public health interventions such as social distancing and mask wearing decrease the incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but it is unclear whether they decrease the viral load of infected patients and whether changes in viral load impact mortality from coronavirus disease 2019 (COVID-19). We evaluated 6923 patients with COVID-19 at six New York City hospitals from March 15-May 14, 2020, corresponding with the implementation of public health interventions in March. We assessed changes in cycle threshold (CT) values from reverse transcription-polymerase chain reaction tests and in-hospital mortality and modeled the impact of viral load on mortality. Mean CT values increased between March and May, with the proportion of patients with high viral load decreasing from 47.7% to 7.8%. In-hospital mortality increased from 14.9% in March to 28.4% in early April, and then decreased to 8.7% by May. Patients with high viral loads had increased mortality compared to those with low viral loads (adjusted odds ratio 2.34). If viral load had not declined, an estimated 69 additional deaths would have occurred (5.8% higher mortality). SARS-CoV-2 viral load steadily declined among hospitalized patients in the setting of public health interventions, and this correlated with decreases in mortality.

scholarly journals Peginterferon-lambda for the treatment of COVID-19 in outpatients

2020 ◽  
Author(s):  
Jordan J. Feld ◽  
Christopher Kandel ◽  
Mia J. Biondi ◽  
Robert A. Kozak ◽  
Muhammad Atif Zahoor ◽  
...  
Keyword(s):  
Public Health ◽  
Viral Load ◽  
Adverse Events ◽  
Outpatient Setting ◽  
Viral Clearance ◽  
Clinical Deterioration ◽  
Baseline Viral Load ◽  
High Baseline ◽  
Viral Loads ◽  
Viral Shedding

SummaryBackgroundThere are currently no effective treatments for outpatients with coronavirus disease 2019 (COVID-19). Interferon-lambda-1 is a Type III interferon involved in the innate antiviral response with activity against respiratory pathogens.MethodsIn this double-blind, placebo-controlled trial, outpatients with laboratory-confirmed COVID-19 were randomized to a single subcutaneous injection of peginterferon-lambda 180μg or placebo within 7 days of symptom onset or first positive swab if asymptomatic. The primary endpoint was proportion negative for SARS-CoV-2 RNA on Day 7 post-injection.FindingsThere were 30 patients per arm, with median baseline SARS-CoV-2 viral load of 6.71 (IQR 1.3-8.0) log copies/mL. The decline in SARS-CoV-2 RNA was greater in those treated with peginterferon-lambda than placebo (p=0.04). On Day 7, 24 participants (80%) in the peginterferon-lambda group had an undetectable viral load compared to 19 (63%) in the placebo arm (p=0.15). After controlling for baseline viral load, peginterferon lambda treatment resulted in a 4.12-fold (95CI 1.15-16.7, p=0.029) higher likelihood of viral clearance by Day 7. Of those with baseline viral load above 10E6 copies/mL, 15/19 (79%) in the peginterferon-lambda group were undetectable on Day 7 compared to 6/16 (38%) in the placebo group (p=0.012). Adverse events were similar between groups with only mild reversible transaminase elevations more frequently observed in the peginterferon-lambda group.InterpretationPeginterferon-lambda accelerated viral decline in outpatients with COVID-19 resulting in a greater proportion with viral clearance by Day 7, particularly in those with high baseline viral load. Peginterferon-lambda may have potential to prevent clinical deterioration and shorten duration of viral shedding.(NCT04354259)FundingThis study was supported by the Toronto COVID-19 Action Initiative, University of Toronto and the Ontario First COVID-19 Rapid Research Fund. Medication was supplied by Eiger BioPharma.Research in ContextTreatment trials for COVID-19 have largely focused on hospitalized patients and no treatments are approved for people with mild to moderate disease in the outpatient setting. A number of studies in ambulatory populations have been registered but no controlled studies in the outpatient setting have been reported to date (Pubmed Search October 20, 2020, COVID-19 treatment; controlled trials). Uncontrolled case series of hydroxychloroquine with or without azithromycin have been reported with mixed results but no clear signal of efficacy and some concerns raised about cardiac toxicity. Treamtent in the outpatient setting has potential to prevent infected individuals from deteriorating and perhaps more importantly, may shorten the duration of viral shedding, reducing the risk of transmission and the duration required for self-isolation, with significant public health and societal impact.Added value of this studyThis is the first study to show an antiviral effect in outpatients with COVID-19. After controlling for baseline viral load, those treated with peginterferon-lambda had a 4.12-fold (95%CI 1.15-16.7, p=0.029) higher odds of viral clearance by Day 7 compared to those who received placebo. The viral load decline was faster with pegterferon-lambda and the effect was most pronounced in those with high viral loads. In individuals with a baseline viral load of 10E6 copies/mL or higher, 15/19 (79%) in the peginterferon-lambda arm cleared by Day 7 compared to 6/16 (38%) (p=0.012) in the placebo arm (OR 6.25, 95%CI 1.49-31.1, p=0.012), translating to a median time to viral clearance of 7 days (95%CI 6.2-7.8 days) with peginterferon-lambda compared to 10 days (95%CI 7.8-12.2 days) with placebo (p=0.038). Those with low viral loads (<10E6 copies/mL) cleared quickly in both groups. Peginterferon-lambda was well-tolerated with a similar side effect profile to placebo and no concerning laboratory adverse events.Implications of all available evidenceThere is no currently approved therapy for outpatients with COVID-19. This study showed that peginterferon-lambda accelerated viral clearance, particularly in those with high baseline viral loads, highlighting the importance of quantitative viral load testing in the evaluation of antiviral agents for COVID-19. Treatment early in the course of disease may prevent clinical deterioration and shorenting of the duration of viral shedding may have important public health impact by limiting transmission and reducing the duration required for self-isolation. Additional trials of peginterferon-lambda and other antiviral strategies in the outpatient setting are required.

scholarly journals What Should Health Departments Do with HIV Sequence Data?

Viruses ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 1018
Author(s):  
Ethan Romero-Severson ◽  
Arshan Nasir ◽  
Thomas Leitner
Keyword(s):  
Public Health ◽  
Sequence Data ◽  
Public Health Practice ◽  
Health Benefit ◽  
Routine Care ◽  
Health Departments ◽  
Genetic Sequencing ◽  
Hiv Surveillance ◽  
Hiv Epidemic ◽  
Health Authorities

Many countries and US states have mandatory statues that require reporting of HIV clinical data including genetic sequencing results to the public health departments. Because genetic sequencing is a part of routine care for HIV infected persons, health departments have extensive sequence collections spanning years and even decades of the HIV epidemic. How should these data be used (or not) in public health practice? This is a complex, multi-faceted question that weighs personal risks against public health benefit. The answer is neither straightforward nor universal. However, to make that judgement—of how genetic sequence data should be used in describing and combating the HIV epidemic—we need a clear image of what a phylogenetically enhanced HIV surveillance system can do and what benefit it might provide. In this paper, we present a positive case for how up-to-date analysis of HIV sequence databases managed by health departments can provide unique and actionable information of how HIV is spreading in local communities. We discuss this question broadly, with examples from the US, as it is globally relevant for all health authorities that collect HIV genetic data.

scholarly journals Estimating epidemiologic dynamics from single cross-sectional viral load distributions

2020 ◽  
Author(s):  
James A. Hay ◽  
Lee Kennedy-Shaffer ◽  
Sanjat Kanjilal ◽  
Marc Lipsitch ◽  
Michael J. Mina
Keyword(s):  
Public Health ◽  
Growth Rate ◽  
Viral Load ◽  
Population Level ◽  
Accurate Estimation ◽  
Cross Sectional ◽  
Individual Level ◽  
Viral Loads ◽  
Single Cross ◽  
Testing Practices

AbstractVirologic testing for SARS-CoV-2 has been central to the COVID-19 pandemic response, but interpreting changes in incidence and fraction of positive tests towards understanding the epidemic trajectory is confounded by changes in testing practices. Here, we show that the distribution of viral loads, in the form of Cycle thresholds (Ct), from positive surveillance samples at a single point in time can provide accurate estimation of an epidemic’s trajectory, subverting the need for repeated case count measurements which are frequently obscured by changes in testing capacity. We identify a relationship between the population-level cross-sectional distribution of Ct values and the growth rate of the epidemic, demonstrating how the skewness and median of detectable Ct values change purely as a mathematical epidemiologic rule without any change in individual level viral load kinetics or testing. Although at the individual level measurement variation can complicate interpretation of Ct values for clinical use, we show that population-level properties reflect underlying epidemic dynamics. In support of these theoretical findings, we observe a strong relationship between the time-varying effective reproductive number, R(t), and the distribution of Cts among positive surveillance specimens, including median and skewness, measured in Massachusetts over time. We use the observed relationships to derive a novel method that allows accurate inference of epidemic growth rate using the distribution of Ct values observed at a single cross-section in time, which, unlike estimates based on case counts, is less susceptible to biases from delays in test results and from changing testing practices. Our findings suggest that instead of discarding individual Ct values from positive specimens, incorporation of viral loads into public health data streams offers a new approach for real-time resource allocation and assessment of outbreak mitigation strategies, even where repeat incidence data is not available. Ct values or similar viral load data should be regularly reported to public health officials by testing centers and incorporated into monitoring programs.

scholarly journals Prevalence of and Viral Outcomes Associated with Primary HIV-1 Drug Resistance

2012 ◽  
Vol 6 (1) ◽  
pp. 181-187 ◽  
Author(s):  
SE Buskin ◽  
S Zhang ◽  
CS Thibault
Keyword(s):  
Drug Resistance ◽  
Viral Load ◽  
Statistical Power ◽  
Laboratory Data ◽  
Primary Resistance ◽  
Hiv Surveillance ◽  
Subtype B ◽  
Primary Drug Resistance ◽  
Hiv 1 ◽  
Primary Drug

Primary, or transmitted, HIV antiretroviral resistance is an ongoing concern despite continuing development of new antiretroviral therapies. We examined HIV surveillance data, including both patient demographic characteristics and laboratory data, combined with HIV genotypic test results to evaluate the comprehensiveness of drug resistance surveillance, prevalence of primary drug resistance, and impact, if any, of primary resistance on population-based virological outcomes. The King County, WA Variant, Atypical, and Resistant HIV Surveillance (VARHS) system increased coverage of eligible genotypic testing – within three months of an HIV diagnosis among antiretroviral naïve individuals -- from – 15% in 2003 to 69% in 2010. VARHS under-represented females, Blacks, Native Americans, and injection drug users. Primary drug resistance was more common among males, individuals aged 20 – 29 years, men who had sex with men, and individuals with an initial CD4+ lymphocyte count of 200 cells/µL and higher. High level resistance to two or three antiretroviral classes declined over time. Over 90% of sequences were HIV-1 subtype B. The proportion of individuals with a most recent viral load (closest to April 2011) that was undetectable (<50 copies/mL) was not statistically significantly associated with primary drug resistance. This was true for both number and type of antiretroviral drug class; although small numbers of specimens with drug resistance may have limited our statistical power. In summary, although we found disparities in testing coverage and prevalence of drug resistance, we were unable to detect a significantly deleterious impact of primary drug resistance based on a most recent viral load.

scholarly journals SARS-CoV-2 viral load distribution reveals that viral loads increase with age: a retrospective cross-sectional cohort study

2021 ◽  
Author(s):  
Sjoerd Euser ◽  
Sem Aronson ◽  
Irene Manders ◽  
Steven van Lelyveld ◽  
Bjorn Herpers ◽  
...  
Keyword(s):  
Public Health ◽  
Viral Load ◽  
Health Services ◽  
Load Distribution ◽  
Lower Sensitivity ◽  
Symptom Duration ◽  
Public Health Services ◽  
Viral Loads ◽  
Limited Role ◽  
Antigen Tests

ABSTRACTObjectiveTo describe the SARS-CoV-2 viral load distribution in different patient groups and age categories.MethodsAll SARS-CoV-2 RT-PCR results from nasopharyngeal (NP) and oropharyngeal (OP) swabs (first PCR from unique patients only) that were collected between January 1 and December 1, 2020, predominantly in the Public Health Services regions Kennemerland and Hollands Noorden, province of North Holland, the Netherlands were included in this study. Swabs were derived from patients with respiratory symptoms who were presented at the general practitioner (GP), hospital, or hospital health care workers (HCWs) of four regional hospitals, nursing home residents and HCWs of multiple nursing homes, and in majority (>75%) from Public Health testing facilities of the two Public Health Services. SARS-CoV-2 PCR crossing point (Cp) values were used to estimate viral loads (higher Cp-values indicate lower viral loads).ResultsIn total, 278.455 unique patients were tested of whom 9·1% (n=25.374) were SARS-CoV-2 positive. As there were differences in viral load distribution between tested populations, further analyses focused on PCRs performed by public health services (n=211.914) where sampling and inclusion were uniform. These data reveal a clear relation between age and SARS-CoV-2 viral load, with especially children aged<12 years showing lower viral loads than shown in adults (β: −0·03, 95CI% −0·03 to −0·02, p<0·001), independent of sex and/or symptom duration. Interestingly, the median Cp-values between the oldest (>79 years) and youngest (<12 years) population differed by over 4 PCR cycles, suggesting approximately a 16-fold difference in viral load. In addition, the proportion of children aged <12 years with a low load (Cp-value >30) was significantly higher compared to the other patients (31·1% vs. 17·2%, p-value<0.001).ConclusionWe observed that in patients tested by Public Health Services, SARS-CoV2 viral load increases significantly with age. Previous studies suggest that young children (<12 years) play a limited role in SARS-CoV-2 transmission. Currently, the relation between viral load and infectivity is not yet well understood, and further studies should elucidate whether the lower viral load in children is indeed related to their suggested limited role in SARS-CoV-2 transmission. Moreover, as rapid antigen tests are less sensitive than PCR, these results suggest that SARS-CoV-2 antigen tests could have lower sensitivity in children than in adults.

scholarly journals The Search for a Schistosomiasis Vaccine: Australia’s Contribution

Vaccines ◽  
2021 ◽  
Vol 9 (8) ◽  
pp. 872
Author(s):  
Donald P. McManus
Keyword(s):  
Public Health ◽  
Drug Resistance ◽  
Sub Saharan Africa ◽  
Effective Vaccine ◽  
Neglected Tropical Disease ◽  
Vaccine Research ◽  
Health Measures ◽  
Leading Role ◽  
Invaluable Tool ◽  
Sub Saharan

Schistosomiasis, a neglected tropical disease caused by parasitic flatworms of the genus Schistosoma, results in considerable human morbidity in sub-Saharan Africa, in particular, but also parts of the Middle East, South America, and Southeast Asia. The anti-schistosome drug praziquantel is efficacious and safe against the adult parasites of all Schistosoma species infecting humans; however, it does not prevent reinfection and the development of drug resistance is a constant concern. The need to develop an effective vaccine is of great importance if the health of many in the developing world is to be improved. Indeed, vaccination, in combination with other public health measures, can provide an invaluable tool to achieve lasting control, leading to schistosomiasis elimination. Australia has played a leading role in schistosomiasis vaccine research over many years and this review presents an overview of some of the significant contributions made by Australian scientists in this important area.

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