Comparison of the performance of two targeted metagenomic virus capture probe-based methods using reference control materials and clinical samples

Viral enrichment by probe hybridization has been reported to significantly increase the sensitivity of viral metagenomics. This study compares the analytical performance of two targeted metagenomic virus capture probe-based methods: (i) SeqCap EZ HyperCap by Roche (ViroCap) and (ii) Twist Comprehensive Viral Research Panel workflow, for diagnostic use. Sensitivity, specificity, and limit of detection were analyzed using 25 synthetic viral sequences spiked in increasing proportions of human background DNA, eight clinical samples, and American Type Culture Collection (ATCC) Virome Virus Mix. Sensitivity and specificity were 95% and higher for both methods using the synthetic and reference controls as gold standard. Combining thresholds for viral sequence read counts and genome coverage [respectively 500 reads per million (RPM) and 10% coverage] resulted in optimal prediction of true positive results. Limits of detection were approximately 50-500 copies/mL for both methods as determined by ddPCR. Increasing proportions of spike-in cell-free human background sequences up to 99.999% (50 ng/mL) did not negatively affect viral detection, suggesting effective capture of viral sequences. These data show analytical performances in ranges applicable to clinical samples, for both probe hybridization metagenomic approaches. This study supports further steps toward more widespread use of viral metagenomics for pathogen detection, in clinical and surveillance settings using low biomass samples.

IMPORTANCE

Viral metagenomics has been gradually applied for broad-spectrum pathogen detection of infectious diseases, surveillance of emerging diseases, and pathogen discovery. Viral enrichment by probe hybridization methods has been reported to significantly increase the sensitivity of viral metagenomics. During the past years, a specific hybridization panel distributed by Roche has been adopted in a broad range of different clinical and zoonotic settings. Recently, Twist Bioscience has released a new hybridization panel targeting human and animal viruses. This is the first report comparing the performance of viral metagenomic hybridization panels.

A comparison of five Illumina, Ion Torrent, and nanopore sequencing technology-based approaches for whole genome sequencing of SARS-CoV-2

Rapid identification of the rise and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern remains critical for monitoring of the efficacy of diagnostics, therapeutics, vaccines, and control strategies. A wide range of SARS-CoV-2 next-generation sequencing (NGS) methods have been developed over the last years, but cross-sequence technology benchmarking studies have been scarce. In the current study, 26 clinical samples were sequenced using five protocols: AmpliSeq SARS-CoV-2 (Illumina), EasySeq RC-PCR SARS-CoV-2 (Illumina/NimaGen), Ion AmpliSeq SARS-CoV-2 (Thermo Fisher), custom primer sets (Oxford Nanopore Technologies (ONT)), and capture probe-based viral metagenomics (Roche/Illumina). Studied parameters included genome coverage, depth of coverage, amplicon distribution, and variant calling. The median SARS-CoV-2 genome coverage of samples with cycle threshold (Ct) values of 30 and lower ranged from 81.6 to 99.8% for, respectively, the ONT protocol and Illumina AmpliSeq protocol. Correlation of coverage with PCR Ct values varied per protocol. Amplicon distribution signatures differed across the methods, with peak differences of up to 4 log₁₀ at disbalanced positions in samples with high viral loads (Ct values ≤ 23). Phylogenetic analyses of consensus sequences showed clustering independent of the workflow used. The proportion of SARS-CoV-2 reads in relation to background sequences, as a (cost-)efficiency metric, was the highest for the EasySeq protocol. The hands-on time was the lowest when using EasySeq and ONT protocols, with the latter additionally having the shortest sequence runtime. In conclusion, the studied protocols differed on a variety of the studied metrics. This study provides data that assist laboratories when selecting protocols for their specific setting.

AB0021 FEATURES OF IMMUNOLOGICAL MANIFESTATIONS OF СOMMON VARIABLE IMMUNODEFICIENCY COMBINED WITH RHEUMATOID ARTHRITIS

Background

The prevalence rate of сommon variable immunodeficiency (CVID), the most common symptomatic form of primary immunodeficiency disease (PID), is growing every year. In the Republican Register of PID in the Chuvash Republic (Russia) there are 32 patients with CVID, 5 (15.6%) of whom have CVID combined with an autoimmune disease - rheumatoid arthritis (RA). The immunological studies occupy a large place in the diagnosis of PID and autoimmune diseases.

Objectives

The aim of the study was to search for immunological criteria for the differentiation of RA from CVID combined with RA.

Methods

The object of the study were 2 groups of patients. Group 1 consisted of 20 RA patients; group 2 consisted of 5 patients with CVID in combination with RA. Patients with CVID, who had the results of an immunological study conducted before the appointment of immunoglobulin replacement therapy, were selected for this study. The control group consisted of 20 practically healthy people.

Results

The significant changes were revealed in the concentration of serum immunoglobulins in the studied groups of patients, in particular, a sharp decrease in IgG levels in group 2 (1.9±0.3 g/l vs. 15.2±2.3 in group 1, p<0.001), IgA (0.1±0.02 g/l vs. 3.1±0.7 g/l in group 1, p<0.001), IgM (0.2±0.03 g/l vs. 1.7±0.2 g/l in group 1, p<0.001). Immunoglobulin levels in both groups of patients were lower (p<0.001) compared to the control group. In both groups, the number of regulatory cells – Treg (CD4+CD25+FoxP3) was reduced: in group 1 - to 2.5±0.03%; in group 2 - to 2.3± 0.02%, while in the control group it was 4.2± 0.5%, p<0.001. The result of our study confirms that the development of RA and CVID is associated with the decrease in the number of Treg cells responsible for ensuring peripheral tolerance and preventing the development of autoimmune diseases.

Conclusion

CVID and RA have a common immunopathological sign - a decrease in the content of Treg cells in the blood. In the differential diagnosis between RA and CVID, combined with RA, it is necessary to rely on the results of the determination of immunoglobulins in the blood serum.

Disclosure of Interests

None declared

Haem is crucial for medium-dependent metronidazole resistance in clinical isolates of Clostridioides difficile

Background

Until recently, metronidazole was the first-line treatment for Clostridioides difficile infection and it is still commonly used. Though resistance has been reported due to the plasmid pCD-METRO, this does not explain all cases.

Objectives

To identify factors that contribute to plasmid-independent metronidazole resistance of C. difficile.

Methods

Here, we investigate resistance to metronidazole in a collection of clinical isolates of C. difficile using a combination of antimicrobial susceptibility testing on different solid agar media and WGS of selected isolates.

Results

We find that nearly all isolates demonstrate a haem-dependent increase in the MIC of metronidazole, which in some cases leads to isolates qualifying as resistant (MIC >2 mg/L). Moreover, we find an SNP in the haem-responsive gene hsmA, which defines a metronidazole-resistant lineage of PCR ribotype 010/MLST ST15 isolates that also includes pCD-METRO-containing strains.

Conclusions

Our data demonstrate that haem is crucial for medium-dependent metronidazole resistance in C. difficile.

POS1374 RHEUMATOLOGIC DISEASES AS PRESENTATIONS OF PRIMARY IMMUNODEFICIENCY DISEASES

Background:

Primary immunodeficiency diseases (PID) occur on average with a frequency of 1: 100 000 of the population. In accordance with the classification of PIDS of the International Union of Immunological Societies (IUIS) 9 different groups of innate errors of immunity are distinguished [1]. The polymorphism of the clinical picture, difficulties in recognizing PID cause their late diagnosis and the associated development of irreversible organ damage, complications and high mortality. According to the traditional view, the clinical marker of PID is an infectious syndrome. However, in some cases, PID is detected as a rheumatologic disease.

Objectives:

The aim of the study is to analyze the frequency of rheumatologic diseases in adult patients with PID living in one of the subjects of Russia –Chuvashia.

Methods:

The material of the study was patient data obtained during a retrospective analysis of 49 outpatient records included in the Republican Register of PID. Diagnosis of various forms of PIDS was carried out in accordance with the criteria developed by the IUIS [1].

Results:

During the period from 1993 to January 2020, 49 cases of PID were registered in the adult population of Chuvashia. According to the frequency of PID, сommon variable immunodeficiency (CVID) is the most common in Chuvashia (26 people). In the second place there is selective IgA deficiency (10 people); in third place there are X-linked agammaglobulinemia (4 people) and hereditary angioedema (4 people). The remaining forms of PID account for 5 cases: 2 cases of Louis-Bar syndrome, 1 case of DiGeorge syndrome, 1 case of Wiskott-Aldrich syndrome and 1 case of Hyper IgE syndrome. The main symptom of PID in 35 (71.4%) patients was heightened susceptibility to infection. In 14 (28.6%) patients, the clinical picture was dominated by non-infectious presentations (autoimmune, lymphoproliferative and oncological diseases). In 9 patients (18.3%), it was manifested by rheumatologic diseases (rheumatoid arthritis, psoriatic arthritis, scleroderma-like syndrome). These symptoms were more characteristic of CVID. With selective IgA deficiency and X-linked agammaglobulinemia, rheumatic symptoms were observed only in isolated cases. CVID debuted in 2 cases as rheumatoid arthritis, resulting in the delay in the diagnosis of an average of 5.2 years. Only the detailed immunological and genetic study made it possible to diagnose PID and prescribe adequate treatment – replacement immunoglobulin therapy. This treatment reduced the frequency of infectious manifestations of the disease and it did not significantly improve the course of rheumatological diseases. Therefore, the use of methotrexate and targeted therapy was continued.

Conclusion:

In the clinical picture of PID, rheumatic symptoms predominate in 28.6% of cases, which requires a thorough immunological and genetic examination of patients with rheumatic diseases in order to diagnose PID in a timely manner.

References:

[1]Picard C, Bobby Gaspar H, Al-Herz W, et al. J Clin Immunol. 2018;38(1):96-128.

Disclosure of Interests:

None declared

Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting

Metagenomic next-generation sequencing (mNGS) is an untargeted technique for determination of microbial DNA/RNA sequences in a variety of sample types from patients with infectious syndromes. mNGS is still in its early stages of broader translation into clinical applications. To further support the development, implementation, optimization and standardization of mNGS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mNGS for viral diagnostics to share methodologies and experiences, and to develop application guidelines. Following the ENNGS publication Recommendations for the introduction of mNGS in clinical virology, part I: wet lab procedure in this journal, the current manuscript aims to provide practical recommendations for the bioinformatic analysis of mNGS data and reporting of results to clinicians.

SARS-coronavirus-2 replication in Vero E6 cells: replication kinetics, rapid adaptation and cytopathology

The sudden emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the end of 2019 from the Chinese province of Hubei and its subsequent pandemic spread highlight the importance of understanding the full molecular details of coronavirus infection and pathogenesis. Here, we compared a variety of replication features of SARS-CoV-2 and SARS-CoV and analysed the cytopathology caused by the two closely related viruses in the commonly used Vero E6 cell line. Compared to SARS-CoV, SARS-CoV-2 generated higher levels of intracellular viral RNA, but strikingly about 50-fold less infectious viral progeny was recovered from the culture medium. Immunofluorescence microscopy of SARS-CoV-2-infected cells established extensive cross-reactivity of antisera previously raised against a variety of non-structural proteins, membrane and nucleocapsid protein of SARS-CoV. Electron microscopy revealed that the ultrastructural changes induced by the two SARS viruses are very similar and occur within comparable time frames after infection. Furthermore, we determined that the sensitivity of the two viruses to three established inhibitors of coronavirus replication (remdesivir, alisporivir and chloroquine) is very similar, but that SARS-CoV-2 infection was substantially more sensitive to pre-treatment of cells with pegylated interferon alpha. An important difference between the two viruses is the fact that – upon passaging in Vero E6 cells – SARS-CoV-2 apparently is under strong selection pressure to acquire adaptive mutations in its spike protein gene. These mutations change or delete a putative furin-like cleavage site in the region connecting the S1 and S2 domains and result in a very prominent phenotypic change in plaque assays.

STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies

The term metagenomics refers to the use of sequencing methods to simultaneously identify genomic material from all organisms present in a sample, with the advantage of greater taxonomic resolution than culture or other methods. Applications include pathogen detection and discovery, species characterisation, antimicrobial resistance detection, virulence profiling, and study of the microbiome and microecological factors affecting health. However, metagenomics involves complex and multistep processes and there are important technical and methodological challenges that require careful consideration to support valid inference. We co-ordinated a multidisciplinary, international expert group to establish reporting guidelines that address specimen processing, nucleic acid extraction, sequencing platforms, bioinformatics considerations, quality assurance, limits of detection, power and sample size, confirmatory testing, causality criteria, cost, and ethical issues. The guidance recognises that metagenomics research requires pragmatism and caution in interpretation, and that this field is rapidly evolving.

SARS-coronavirus-2 replication in Vero E6 cells: replication kinetics, rapid adaptation and cytopathology

The sudden emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the end of 2019 from the Chinese province of Hubei and its subsequent pandemic spread highlight the importance of understanding the full molecular details of coronavirus infection and pathogenesis. Here, we compared a variety of replication features of SARS-CoV-2 and SARS-CoV and analysed the cytopathology caused by the two closely related viruses in the commonly used Vero E6 cell line. Compared to SARS-CoV, SARS-CoV-2 generated higher levels of intracellular viral RNA, but strikingly about 50-fold less infectious viral progeny was recovered from the culture medium. Immunofluorescence microscopy of SARS-CoV-2-infected cells established extensive cross-reactivity of antisera previously raised against a variety of non-structural proteins, membrane and nucleocapsid protein of SARS-CoV. Electron microscopy revealed that the ultrastructural changes induced by the two SARS viruses are very similar and occur within comparable time frames after infection. Furthermore, we determined that the sensitivity of the two viruses to three established inhibitors of coronavirus replication (remdesivir, alisporivir and chloroquine) is very similar, but that SARS-CoV-2 infection was substantially more sensitive to pre-treatment of cells with pegylated interferon alpha. An important difference between the two viruses is the fact that - upon passaging in Vero E6 cells - SARS-CoV-2 apparently is under strong selection pressure to acquire adaptive mutations in its spike protein gene. These mutations change or delete a putative furin-like cleavage site in the region connecting the S1 and S2 domains and result in a very prominent phenotypic change in plaque assays.

Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients

Viruses are the main cause of respiratory tract infections. Metagenomic next-generation sequencing (mNGS) enables unbiased detection of all potential pathogens. To apply mNGS in viral diagnostics, sensitive and simultaneous detection of RNA and DNA viruses is needed. Herein, were studied the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection. The sequencing protocol and bioinformatics analysis were designed and optimized, including exogenous internal controls. Subsequently, the protocol was retrospectively validated using 25 clinical respiratory samples. The developed protocol using Illumina NextSeq 500 sequencing showed high repeatability. Use of the National Center for Biotechnology Information's RefSeq database as opposed to the National Center for Biotechnology Information's nucleotide database led to enhanced specificity of classification of viral pathogens. A correlation was established between read counts and PCR cycle threshold value. Sensitivity of mNGS, compared with PCR, varied up to 83%, with specificity of 94%, dependent on the cutoff for defining positive mNGS results. Viral pathogens only detected by mNGS, not present in the routine diagnostic workflow, were influenza C, KI polyomavirus, cytomegalovirus, and enterovirus. Sensitivity and analytical specificity of this mNGS protocol were comparable to PCR and higher when considering off-PCR target viral pathogens. One single test detected all potential viral pathogens and simultaneously obtained detailed information on detected viruses.

The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease

INTRODUCTION

Exacerbations are major contributors to morbidity and mortality in patients with chronic obstructive pulmonary disease (COPD), and respiratory bacterial and viral infections are an important trigger. However, using conventional diagnostic techniques, a causative agent is not always found. Metagenomic next-generation sequencing (mNGS) allows analysis of the complete virome, but has not yet been applied in COPD exacerbations.

OBJECTIVES

To study the respiratory virome in nasopharyngeal samples during COPD exacerbations using mNGS.

STUDY DESIGN

88 nasopharyngeal swabs from 63 patients from the Bergen COPD Exacerbation Study (2006-2010) were analysed by mNGS and in-house qPCR for respiratory viruses. Both DNA and RNA were sequenced simultaneously using an Illumina library preparation protocol with in-house adaptations.

RESULTS

By mNGS, 24/88 samples tested positive. Sensitivity and specificity, as compared with PCR, were 96% and 98% for diagnostic targets (23/24 and 1093/1120, respectively). Additional viral pathogens detected by mNGS were herpes simplex virus type 1 and coronavirus OC43. A positive correlation was found between Cq value and mNGS viral normalized species reads (log value) (p = 0.002). Patients with viral pathogens had lower percentages of bacteriophages (p<0.001). No correlation was found between viral reads and clinical markers.

CONCLUSIONS

The mNGS protocol used was highly sensitive and specific for semi-quantitative detection of respiratory viruses. Excellent negative predictive value implicates the power of mNGS to exclude any pathogenic respiratory viral infectious cause in one test, with consequences for clinical decision making. Reduced abundance of bacteriophages in COPD patients with viral pathogens implicates skewing of the virome during infection, with potential consequences for the bacterial populations, during infection.

Distance sensing to rough semitransparent and multiscattering materials using dynamic speckles

Noncontact methods of distance measurements to a moving surface using laser light are relevant for many industrial applications, such as surface profile and position monitoring, thickness measurements, and wear estimation. Application of existing methods (e.g., triangulation) is limited especially for nonhomogeneous, semitransparent and rough materials (paper, wood, plastic). The task is even more challenging for fast moving objects. We present a novel online method of distance sensing to semitransparent and multiscattering surfaces (papers, woods, polymers) based on spatial filtering of dynamic speckles. We validated a proposed method at the speed of the test surface as high as 35 m/s.

Accuracy of measuring systems using dynamic speckles

Diffraction-limited accuracy is estimated for measuring systems exploiting dynamic speckles. Statistical properties of the signal in the systems with spatial filtering are used to evaluate the signal frequency with precision sufficient to achieve the diffraction-limited accuracy. The results of the analysis allow for designing an optimal measuring system in which components are matched with each other to provide the highest accuracy. Experiments carried out with a range sensor using spatially filtered dynamic speckles are in good agreement with theory.

Leukocyte telomere dynamics and human hematopoietic stem cell kinetics during somatic growth

OBJECTIVE

A central question in stem cell research is knowing the frequency of human hematopoietic stem cells (HSC) replication in vivo.

MATERIALS AND METHODS

We have constructed a model that characterizes HSC kinetics and the relative sizes of the hematopoietic progenitor cell (HPC) and HSC pools from birth onward. The model capitalizes on leukocyte telomere length (LTL) data and body weight-gain charts from birth to the age of 20 years. The core premise of the model is that during human growth, LTL dynamics (birth LTL and age-dependent LTL shortening afterward) chronicle the expansions of the HSC and HPC pools.

RESULTS

The model estimates that by the end of the first year of life, HSC have replicated approximately 17 times and they replicate approximately 2.5 times/year between the ages of 3 and 13 years. Subsequently, HSC replication slows considerably. In adults HSC replicate at a rate of approximately 0.6 times/year. In addition, the model predicts that newborns with small birth weight would have shorter LTL as adults and that women would have longer LTL than men.

CONCLUSION

Our findings will be useful in bone marrow transplantations and might explain a body of clinical observations related to LTL distribution in the general population.

Identification of a novel CD4i human monoclonal antibody Fab that neutralizes HIV-1 primary isolates from different clades

A new human monoclonal antibody (hmAb), designated m16, was selected by sequential antigen panning (SAP) of a human phage display library against recombinant soluble HIV-1 envelope glycoproteins (Envs) (gp140s) and their complexes with soluble CD4. It bound with high (nM) affinity to gp120 and gp140; the binding was further enhanced by interactions of the Envs with CD4. m16 inhibited cell fusion mediated by the Envs of 9 HIV-1 isolates from clades A, B, E and G with potency on average comparable to that of the broadly neutralizing human monoclonal antibody Fab X5. The identification of a new hmAb with broad neutralizing activity that exhibits differential inhibitory profile suggests a potential for its use as a component of anti-HIV-1 treatments.

Dissection of human immunodeficiency virus type 1 entry with neutralizing antibodies to gp41 fusion intermediates

Human immunodeficiency virus type 1 (HIV-1) entry requires conformational changes in the transmembrane subunit (gp41) of the envelope glycoprotein (Env) involving transient fusion intermediates that contain exposed coiled-coil (prehairpin) and six-helix bundle structures. We investigated the HIV-1 entry mechanism and the potential of antibodies targeting fusion intermediates to block Env-mediated membrane fusion. Suboptimal temperature (31.5 degrees C) was used to prolong fusion intermediates as monitored by confocal microscopy. After transfer to 37 degrees C, these fusion intermediates progressed to syncytium formation with enhanced kinetics compared with effector-target (E/T) cell mixtures that were incubated only at 37 degrees C. gp41 peptides DP-178, DP-107, and IQN17 blocked fusion more efficiently (5- to 10-fold-lower 50% inhibitory dose values) when added to E/T cells at the suboptimal temperature prior to transfer to 37 degrees C. Rabbit antibodies against peptides modeling the N-heptad repeat or the six-helix bundle of gp41 blocked fusion and viral infection at 37 degrees C only if preincubated with E/T cells at the suboptimal temperature. Similar fusion inhibition was observed with human six-helix bundle-specific monoclonal antibodies. Our data demonstrate that antibodies targeting gp41 fusion intermediates are able to bind to gp41 and arrest fusion. They also indicate that six-helix bundles can form prior to fusion and that the lag time before fusion occurs may include the time needed to accumulate preformed six-helix bundles at the fusion site.

Renal transplant patients show variations in their self-reactive repertoires: a serial study

We addressed the question of whether allo-transplantation (Tx) induces breakdown of tolerance to self-antigens or alteration of the autoreactive T cell repertoire in humans. The serial variation of T cell autoreactivity was studied in the peripheral blood of 12 renal transplant patients, by autologous limiting dilution assay and autologous mixed lymphocyte reaction. Ten of 12 patients presented a positive response in autologous peripheral blood mononuclear cells in the post-Tx period, in contrast to four of 12 patients before Tx (P = 0.038). Multi-hit kinetics was found in 57% of the assays analyzed, indicating frequent regulatory control of the autologous response. Quantitative analysis performed in eight patients showed an increase in precursor frequency at >1 year post-Tx in five patients. These data indicate that autoreactivity increases or develops following Tx, in humans. Post-Tx events such as alloreactivity, infections or immunosuppression could interfere with the balance of autoreactive and regulatory cells, leading to changes in the T cell repertoires to self-antigens and eventually breakdown of self-tolerance. Further investigation is needed to elucidate whether post-Tx autoreactivity contributes to rejection, plays a regulatory role over alloreactivity or both, at separate times.

Purification and properties of polyphosphatase from Saccharomyces cerevisiae cytosol

A homogenous polyphosphatase preparation was obtained from Saccharomyces cerevisiae cytosol with a 3.8% yield and 3540-fold purification. The enzyme hydrolysed polyphosphate (polyP) with various chain lengths, including polyP3, and split Pi off the end of the chain. It was inactive with respect to ATP, PPi, and p-nitrophenylphosphate. Its specific activity with polyP15 was 283 U/mg protein. The polyphosphatase was a monomeric protein with a molecular mass of 40 kDa. This enzyme was inactive without divalent cations and with Cu2+ and Ca2+. The ability of other divalent cations to activate the enzyme decreased in the following order; Co2+ > Mn2+ > Mg2+ > Zn2+. A kinetic model of the hydrolysis of polyP3 and action of Mg2+ is proposed.