Emergence of SARS-CoV-2 Omicron Variant JN.1 in Tamil Nadu, India - Clinical Characteristics and Novel Mutations

In December 2023, we observed a notable shift in the COVID-19 landscape, when the JN.1 emerged as a predominant SARS-CoV-2 variant with a 95% incidence. We characterized the clinical profile, and genetic changes in JN.1, an emerging SARS-CoV-2 variant of interest. Whole genome sequencing was performed on SARS-CoV-2 positive samples, followed by sequence analysis. Mutations within the spike protein sequences were analyzed and compared with the previous lineages and sublineages of SARS-CoV-2, to identify the potential impact of these unique mutations on protein structure and possible functionality. Several unique and dynamic mutations were identified herein. Our data provides key insights into the emergence of newer variants of SARS-CoV-2 in our region and highlights the need for robust and sustained genomic surveillance of SARS-CoV-2.

Chronic Viral Infection Compromises the Quality of Circulating Mucosal-Associated Invariant T Cells and Follicular T Helper Cells via Expression of Inhibitory Receptors

BACKGROUND

Chronic viral infection results in impaired immune responses rendering viral persistence. Here, we compared the quality of T-cell responses among chronic hepatitis B virus (HBV), hepatitis C virus (HCV) and human immunodeficiency virus (HIV)-infected individuals by examining the levels of expression of selected immune activation and exhaustion molecules on circulating MAIT cells and Tfh cells.

METHODS

Cytokines were measured using a commercial Bio-plex Pro Human Cytokine Grp I Panel 17-plex kit (BioRad, Hercules, CA, USA). Inflammation was assessed by measuring an array of plasma cytokines, and phenotypic alterations in CD4+ T cells including circulating Tfh cells, CD8+ T cells, and TCR iVα7.2+ MAIT cells in chronic HBV, HCV, and HIV-infected patients and healthy controls. The cells were characterized based on markers pertaining to immune activation (CD69, ICOS, and CD27) proliferation (Ki67), cytokine production (TNF-α, IFN-γ) and exhaustion (PD-1). The cytokine levels and T cell phenotypes together with cell markers were correlated with surrogate markers of disease progression.

RESULTS

The activation marker CD69 was significantly increased in CD4+hi T cells, while CD8+ MAIT cells producing IFN-γ were significantly increased in chronic HBV, HCV and HIV infections. Six cell phenotypes, viz., TNF-α+CD4+lo T cells, CD69+CD8+ T cells, CD69+CD4+ MAIT cells, PD-1+CD4+hi T cells, PD-1+CD8+ T cells, and Ki67+CD4+ MAIT cells, were independently associated with decelerating the plasma viral load (PVL). TNF-α levels showed a positive correlation with increase in cytokine levels and decrease in PVL.

CONCLUSION

Chronic viral infection negatively impacts the quality of peripheral MAIT cells and Tfh cells via differential expression of both activating and inhibitory receptors.

Genomic surveillance of omicron B.1.1.529 SARS-CoV-2 and its variants between December 2021 and March 2023 in Tamil Nadu, India-A state-wide prospective longitudinal study

A state-wide prospective longitudinal investigation of the genomic surveillance of the omicron B.1.1.529 SARS-CoV-2 variant and its sublineages in Tamil Nadu, India, was conducted between December 2021 and March 2023. The study aimed to elucidate their mutational patterns and their genetic interrelationship in the Indian population. The study identified several unique mutations at different time-points, which likely could attribute to the changing disease characteristics, transmission, and pathogenicity attributes of omicron variants. The study found that the omicron variant is highly competent in its mutating potentials, and that it continues to evolve in the general population, likely escaping from natural as well as vaccine-induced immune responses. Our findings suggest that continuous surveillance of viral variants at the global scenario is warranted to undertake intervention measures against potentially precarious SARS-CoV-2 variants and their evolution.

Clinical characteristics and novel mutations of omicron subvariant XBB in Tamil Nadu, India - a cohort study

BACKGROUND

Despite the continued vaccination efforts, there had been a surge in breakthrough infections, and the emergence of the B.1.1.529 omicron variant of SARS-CoV-2 in India. There is a paucity of information globally on the role of newer XBB variants in community transmission. Here, we investigated the mutational patterns among hospitalised patients infected with the XBB omicron sub-variant, and checked if there was any association between the rise in the number of COVID-19 cases and the observed novel mutations in Tamil Nadu, India.

METHODS

Nasopharyngeal and oropharyngeal swabs, collected from symptomatic and asymptomatic COVID-19 patients were subjected to real-time PCR followed by Next Generation Sequencing (NGS) to rule out the ambiguity of mutations in viruses isolated from the patients (n = 98). Using the phylogenetic association, the mutational patterns were used to corroborate clinico-demographic characteristics and disease severity among the patients.

FINDINGS

Overall, we identified 43 mutations in the S gene across 98 sequences, of which two were novel mutations (A27S and T747I) that have not been reported previously with XBB sub-variants in the available literature. Additionally, the XBB sequences from our cohort had more mutations than omicron B.1.1.529. The phylogenetic analysis comprising six major branches clearly showed convergent evolution of XBB. Our data suggests that age, and underlying conditions (e.g., diabetes, hypertension, and cardiovascular disease) or secondary complications confers increased susceptibility to infection rather than vaccination status or prior exposure. Many vaccinated individuals showed evidence of a breakthrough infection, with XBB.3 being the predominant variant identified in the study population.

INTERPRETATION

Our study indicates that the XBB variant is highly evasive from available vaccines and may be more transmissible, and potentially could emerge as the 'next' predominant variant, which likely could overwhelm the existing variants of SARS-CoV-2 omicron variants.

FUNDING

National Health Mission (India), SIDASARC, VINNMER (Sweden), ORIP/NIH (USA).

Plasma CXCL8 and MCP-1 as surrogate plasma biomarkers of latent tuberculosis infection among household contacts-A cross-sectional study

Early detection of latent tuberculosis infection (LTBI) is critical to TB elimination in the current WHO vision of End Tuberculosis Strategy. The study investigates whether detecting plasma cytokines could aid in diagnosing LTBI across household contacts (HHCs) positive for IGRA, HHCs negative for IGRA, and healthy controls. The plasma cytokines were measured using a commercial Bio-Plex Pro Human Cytokine 17-plex assay. Increased plasma CXCL8 and decreased MCP-1, TNF-α, and IFN-γ were associated with LTBI. Regression analysis showed that a combination of CXCL8 and MCP-1 increased the risk of LTBI among HHCs to 14-fold. Our study suggests that CXCL-8 and MCP-1 could serve as the surrogate biomarkers of LTBI, particularly in resource-limited settings. Further laboratory investigations are warranted before extrapolating CXCL8 and MCP-1 for their usefulness as surrogate biomarkers of LTBI in resource-limited settings.

Plasma CXCL8 and MCP-1 as biomarkers of latent tuberculosis infection

Background

Early detection of latent tuberculosis infection (LTBI) is critical to TB elimination in the current WHO vision of End Tuberculosis Strategy.

Methods

We investigated whether detecting plasma cytokines could aid in diagnosing LTBI across household contacts (HHCs) positive for IGRA, HHCs negative for IGRA, and healthy controls. We also measured the plasma cytokines using a commercial Bio-Plex Pro Human Cytokine 17-plex assay.

Results

Increased plasma CXCL8 and decreased MCP-1, TNF-α, and IFN-γ were associated with LTBI. Regression analysis showed that a combination of CXCL8 and MCP-1 increased the risk of LTBI among HHCs to 14-fold.

Conclusions

We postulated that CXCL8 and MCP-1 could be the surrogate biomarkers of LTBI, especially in resource-limited settings.

Surrogate Biomarkers of Disease Progression in Human Pegivirus Seropositive Human Immunodeficiency Virus-Infected Individuals

Scientific observations indicate that an actively prevailing systemic condition could alleviate the pathology of another disease. Human pegivirus (HPgV), a highly ubiquitous flavivirus is believed to be associated with slow human immunodeficiency virus (HIV) disease progression, and has seldom been linked to hepatic pathology. In this study, we investigated whether HPgV seropositivity had any impact on surrogate markers of HIV disease progression in a cohort of HIV-infected HPgV seropositive (n = 28) and seronegative (n = 12) individuals who were prospectively evaluated for absolute CD4+ T cell counts, plasma viral load (PVL), liver enzymes, and plasma cytokine levels. The HIV PVL was relatively lower in HPgV seropositive than in HPgV seronegative HIV-infected subjects. Clinical markers of hepatic injury were significantly low among HPgV seropositive HIV-infected participants. HPgV seropositive individuals showed significantly higher levels of interleukin-7 (IL-7), and although not significant, the levels of IL-6 were lower among HPgV seropositive subjects. Spearman correlation analysis showed that the absolute CD4+T cell count was inversely correlated with HIV PVL. Exposure to HPgV appears to have a positive prognostic impact on the levels of surrogate biomarkers of HIV disease progression.

Activated peripheral TFH cells and MAIT cells together with increased plasma TNF-α levels mark the pathogenesis of acute dengue virus infection

Dengue virus (DENV) infection has become an increasingly common public health concern in tropical and subtropical regions. Dengue infection appears to cause immune activation in a wide array of immune cells. Here, we estimated Th1 and Th2 cytokines and correlated their levels with primary and secondary dengue. We also investigated the signatures of immune activation of circulating Tfh cells and mucosal-associated invariant T (MAIT) cells in adults with confirmed acute clinical dengue virus infection. We found that IL-2, TNF-α, IL-4, and IL-10 levels were significantly elevated in patients with secondary DENV infection, whereas the level of IL-13 remained unaltered during both primary and secondary infections. No statistically significant difference was noticed with IL-12p70, IL-5, IFN-γ, and GM-CSF between the healthy controls and the primary and secondary dengue. Increase of 1 unit of TNF-α was associated with a decrease of 160 units of blood platelets. We found a higher frequency of activated Tfh cells and pTfh cells in clinical DENV infection. We also found similar activated and expanding phenotypes of MAIT cells. Our study suggests that TNF-α could play a key role in the pathogenesis of dengue along with activated pTfh cells and circulating MAIT cells in acute DENV infection.

Asymptomatic SARS-CoV-2 infection: is it all about being refractile to innate immune sensing of viral spare-parts?-Clues from exotic animal reservoirs

A vast proportion of coronavirus disease 2019 (COVID-19) individuals remain asymptomatic and can shed severe acute respiratory syndrome (SARS-CoV) type 2 virus to transmit the infection, which also explains the exponential increase in the number of COVID-19 cases globally. Furthermore, the rate of recovery from clinical COVID-19 in certain pockets of the globe is surprisingly high. Based on published reports and available literature, here, we speculated a few immunovirological mechanisms as to why a vast majority of individuals remain asymptomatic similar to exotic animal (bats and pangolins) reservoirs that remain refractile to disease development despite carrying a huge load of diverse insidious viral species, and whether such evolutionary advantage would unveil therapeutic strategies against COVID-19 infection in humans. Understanding the unique mechanisms that exotic animal species employ to achieve viral control, as well as inflammatory regulation, appears to hold key clues to the development of therapeutic versatility against COVID-19.

Peripheral Follicular T Helper Cells and Mucosal-Associated Invariant T Cells Represent Activated Phenotypes During the Febrile Phase of Acute Dengue Virus Infection

Peripheral follicular helper T (pTfh) cells represent specialized CD4⁺ T cells that help B cells to secrete antibodies. Dengue infection appears to cause immune activation in a wide array of immune cells. Herein, we investigated the signatures of immune activation of circulating Tfh cells and mucosal-associated invariant T (MAIT) cells in adult subjects with confirmed acute clinical dengue virus (DENV) infection by multiparametric flow cytometry. The acute DENV infection induced a significant expansion of highly activated pTfh cells and circulating MAIT cells during acute febrile infection. We found a higher frequency of activated PD-1⁺ Tfh cells and CD38⁺ pTfh cells in clinical DENV infection. We also found similar activated and expanding phenotypes of MAIT cells in the patients tested. The total counts of activated pTfh cells and circulating MAIT cells were higher in dengue patients relative to healthy controls. We concluded that pTfh cells and circulating MAIT cells represent activated phenotypes in acute DENV infection.

Immune Biomarkers for Diagnosis and Treatment Monitoring of Tuberculosis: Current Developments and Future Prospects

Tuberculosis (TB) treatment monitoring is paramount to clinical decision-making and the host biomarkers appears to play a significant role. The currently available diagnostic technology for TB detection is inadequate. Although GeneXpert detects total DNA present in the sample regardless live or dead bacilli present in clinical samples, all the commercial tests available thus far have low sensitivity. Humoral responses against Mycobacterium tuberculosis (Mtb) antigens are generally low, which precludes the use of serological tests for TB diagnosis, prognosis, and treatment monitoring. Mtb-specific CD4⁺ T cells correlate with Mtb antigen/bacilli burden and hence might serve as good biomarkers for monitoring treatment progress. Omics-based techniques are capable of providing a more holistic picture for disease mechanisms and are more accurate in predicting TB disease outcomes. The current review aims to discuss some of the recent advances on TB biomarkers, particularly host biomarkers that have the potential to diagnose and differentiate active TB and LTBI as well as their use in disease prognosis and treatment monitoring.

Viral Persistence and Chronicity in Hepatitis C Virus Infection: Role of T-Cell Apoptosis, Senescence and Exhaustion

Hepatitis C virus (HCV) represents a challenging global health threat to ~200 million infected individuals. Clinical data suggest that only ~10–15% of acutely HCV-infected individuals will achieve spontaneous viral clearance despite exuberant virus-specific immune responses, which is largely attributed to difficulties in recognizing the pathognomonic symptoms during the initial stages of exposure to the virus. Given the paucity of a suitable small animal model, it is also equally challenging to study the early phases of viral establishment. Further, the host factors contributing to HCV chronicity in a vast majority of acutely HCV-infected individuals largely remain unexplored. The last few years have witnessed a surge in studies showing that HCV adopts myriad mechanisms to disconcert virus-specific immune responses in the host to establish persistence, which includes, but is not limited to viral escape mutations, viral growth at privileged sites, and antagonism. Here we discuss a few hitherto poorly explained mechanisms employed by HCV that are believed to lead to chronicity in infected individuals. A better understanding of these mechanisms would aid the design of improved therapeutic targets against viral establishment in susceptible individuals.

Hyper-Expression of PD-1 Is Associated with the Levels of Exhausted and Dysfunctional Phenotypes of Circulating CD161++TCR iVα7.2+ Mucosal-Associated Invariant T Cells in Chronic Hepatitis B Virus Infection

Mucosal-associated invariant T (MAIT) cells, defined as CD161⁺⁺TCR iVα7.2⁺ T cells, play an important role in the innate defense against bacterial infections, and their functionality is impaired in chronic viral infections. Here, we investigated the frequency and functional role of MAIT cells in chronic hepatitis B virus (HBV) infection. The peripheral CD3⁺CD161⁺⁺TCR iVα7.2⁺ MAIT cells in chronic HBV-infected patients and healthy controls were phenotypically characterized based on CD57, PD-1, TIM-3, and CTLA-4, as well as HLA-DR and CD38 expression. The frequency of MAIT cells was significantly decreased among chronic HBV-infected individuals as compared to controls. Expression of CD57, PD-1, CTLA-4, as well as HLA-DR and CD38 on MAIT cells was significantly elevated in chronic HBV-infected individuals relative to controls. The percentage of T cell receptor (TCR) iVα7.2⁺ CD161⁺ MAIT cells did not correlate with HBV viral load but inversely with HLA-DR on CD4⁺ T cells and MAIT cells and with CD57 on CD8⁺ T cells suggesting that decrease of MAIT cells may not be attributed to direct infection by HBV but driven by HBV-induced chronic immune activation. The percentage and expression levels of PD-1 as well as CTLA-4 on MAIT cells inversely correlated with plasma HBV-DNA levels, which may suggest either a role for MAIT cells in the control of HBV infection or the effect of HBV replication in the liver on MAIT cell phenotype. We report that decrease of TCR iVα7.2⁺ MAIT cells in the peripheral blood and their functions were seemingly impaired in chronic HBV-infected patients likely because of the increased expression of PD-1.

Identifying protein biomarkers in predicting disease severity of dengue virus infection using immune-related protein microarray

Dengue virus is one of the most widespread flaviviruses that re-emerged throughout recent decades. The progression from mild dengue to severe dengue (SD) with the complications such as vascular leakage and hemorrhage increases the fatality rate of dengue. The pathophysiology of SD is not entirely clear. To investigate potential biomarkers that are suggestive of pathogenesis of SD, a small panel of serum samples selected from 1 healthy individual, 2 dengue patients without warning signs (DWS-), 2 dengue patients with warning signs (DWS+), and 5 patients with SD were subjected to a pilot analysis using Sengenics Immunome protein array. The overall fold changes of protein expressions and clustering heat map revealed that PFKFB4, TPM1, PDCL3, and PTPN20A were elevated among patients with SD. Differential expression analysis identified that 29 proteins were differentially elevated greater than 2-fold in SD groups than DWS- and DWS+. From the 29 candidate proteins, pathways enrichment analysis also identified insulin signaling and cytoskeleton pathways were involved in SD, suggesting that the insulin pathway may play a pivotal role in the pathogenesis of SD.

Decrease of CD69 levels on TCR Vα7.2+CD4+ innate-like lymphocytes is associated with impaired cytotoxic functions in chronic hepatitis B virus-infected patients

Hepatitis B virus (HBV) infection is a major cause of chronic liver disease that may progress to liver cirrhosis and hepatocellular carcinoma. Host immune responses represent the key determinants of HBV clearance or persistence. Here, we investigated the role of the early activation marker, CD69 and effector cytokines, granzyme B (GrB) and IFN-γ in the exhaustion of innate-like TCR Vα7.2⁺CD4⁺T cells, in 15 individuals with chronic HBV (CHB) infection where six were HBV DNA⁺ and nine were HBV DNA^-. The percentage of cytokine-producing T cells and MAIT cells were significantly perturbed in HBV patients relative to healthy controls (HCs). The intracellular expression of GrB and IFN-γ was significantly reduced in MAIT cells derived from HBV-infected patients as compared to HCs, and the levels correlated with the percentage and levels [mean fluorescence intensity (MFI)] of CD69 expression. The total expression of CD69 (iMFI) was lower in CHB patients as compared to HCs. The frequency of CD69⁺ cells correlated with the levels of cytokine expression (MFI), particularly in CHB patients as compared to HCs. In summary, the polyfunctionality of peripheral T cells was significantly reduced among CHB patients, especially in the TCR Vα7.2⁺CD4⁺T cells, and the levels of cytokine expression correlated with functional cytokine levels.

Aberrant monocyte responses predict and characterize dengue virus infection in individuals with severe disease

BACKGROUND

Currently, several assays can diagnose acute dengue infection. However, none of these assays can predict the severity of the disease. Biomarkers that predicts the likelihood that a dengue patient will develop a severe form of the disease could permit more efficient patient triage and allows better supportive care for the individual in need, especially during dengue outbreaks.

METHODS

We measured 20 plasma markers i.e. IFN-γ, IL-10, granzyme-B, CX3CL1, IP-10, RANTES, CXCL8, CXCL6, VCAM, ICAM, VEGF, HGF, sCD25, IL-18, LBP, sCD14, sCD163, MIF, MCP-1 and MIP-1β in 141 dengue patients in over 230 specimens and correlate the levels of these plasma markers with the development of dengue without warning signs (DWS-), dengue with warning signs (DWS+) and severe dengue (SD).

RESULTS

Our results show that the elevation of plasma levels of IL-18 at both febrile and defervescence phase was significantly associated with DWS+ and SD; whilst increase of sCD14 and LBP at febrile phase were associated with severity of dengue disease. By using receiver operating characteristic (ROC) analysis, the IL-18, LBP and sCD14 were significantly predicted the development of more severe form of dengue disease (DWS+/SD) (AUC = 0.768, P < 0.0001; AUC = 0.819, P < 0.0001 and AUC = 0.647, P = 0.014 respectively). Furthermore, we also found that the levels of VEGF were directly correlated and sCD14 was inversely correlated with platelet count, suggesting that the endothelial activation and microbial translocation may played a role in pathogenesis of dengue disease.

CONCLUSIONS

Given that the elevation IL-18, LBP and sCD14 among patients with severe form of dengue disease, our findings suggest a pathogenic role for an aberrant inflammasome and monocyte activation in the development of severe form of dengue disease.

Negative Checkpoint Regulatory Molecule 2B4 (CD244) Upregulation Is Associated with Invariant Natural Killer T Cell Alterations and Human Immunodeficiency Virus Disease Progression

The CD1d-restricted invariant natural killer T (iNKT) cells are implicated in innate immune responses against human immunodeficiency virus (HIV). However, the determinants of cellular dysfunction across the iNKT cells subsets are seldom defined in HIV disease. Herein, we provide evidence for the involvement of the negative checkpoint regulator (NCR) 2B4 in iNKT cell alteration in a well-defined cohort of HIV-seropositive anti-retroviral therapy (ART) naïve, ART-treated, and elite controllers (ECs). We report on exaggerated 2B4 expression on iNKT cells of HIV-infected treatment-naïve individuals. In sharp contrast to CD4⁻iNKT cells, 2B4 expression was significantly higher on CD4⁺ iNKT cell subset. Notably, an increased level of 2B4 on iNKT cells was strongly correlated with parameters associated with HIV disease progression. Further, iNKT cells from ART-naïve individuals were defective in their ability to produce intracellular IFN-γ. Together, our results suggest that the levels of 2B4 expression and the downstream co-inhibitory signaling events may contribute to impaired iNKT cell responses.

Genetic polymorphisms in the CD14 gene are associated with monocyte activation and carotid intima-media thickness in HIV-infected patients on antiretroviral therapy

HIV-infected individuals on antiretroviral therapy (ART) are at increased risk of cardiovascular disease (CVD). Given the relationship between innate immune activation and CVD, we investigated the association of single-nucleotide polymorphisms (SNPs) in TLR4 and CD14 and carotid intima-media thickness (cIMT), a surrogate measurement for CVD, in HIV-infected individuals on ART and HIV-uninfected controls as a cross-sectional, case-control study. We quantified the frequency of monocyte subsets (CD14, CD16), markers of monocyte activation (CD38, HLA-DR), and endothelial adhesion (CCR2, CX3CR1, CD11b) by flow cytometry. Plasma levels of lipopolysaccharide, sCD163, sCD14, sCX3CL1, and sCCL2, were measured by ELISA. Genotyping of TLR4 and CD14 SNPs was also performed. The TT genotype for CD14/-260SNP but not the CC/CT genotype was associated with elevated plasma sCD14, and increased frequency of CD11b+CD14+ monocytes in HIV-infected individuals. The TT genotype was associated with lower cIMT in HIV-infected patients (n = 47) but not in HIV-uninfected controls (n = 37). The AG genotype for TLR4/+896 was associated with increased CX3CR1 expression on total monocytes among HIV-infected individuals and increased sCCL2 and fibrinogen levels in HIV-uninfected controls. SNPs in CD14/-260 and TLR4/+896 were significantly associated with different markers of systemic and monocyte activation and cIMT that differed between HIV-infected participants on ART and HIV-uninfected controls. Further investigation on the relationship of these SNPs with a clinical endpoint of CVD is warranted in HIV-infected patients on ART.

Functional role of mucosal-associated invariant T cells in HIV infection

MAIT cells represent an evolutionarily conserved, MR1-restricted, innate-like cell subset that express high levels of CD161; have a canonical semi-invariant TCR iVα7.2; and may have an important role in mucosal immunity against various bacterial and fungal pathogens. Mature MAIT cells are CD161(hi)PLZF(hi)IL-18Rα(+)iVα7.2(+)γδ-CD3(+)CD8(+) T cells and occur in the peripheral blood, liver, and mucosa of humans. MAIT cells are activated by a metabolic precursor of riboflavin synthesis presented by MR1 and, therefore, respond to many bacteria and some fungi. Despite their broad antibacterial properties, their functional role in persistent viral infections is poorly understood. Although there is an increasing line of evidence portraying the depletion of MAIT cells in HIV disease, the magnitude and the potential mechanisms underlying such depletion remain unclear. Recent studies suggest that MAIT cells are vulnerable to immune exhaustion as a consequence of HIV and hepatitis C virus infections and HIV/tuberculosis coinfections. HIV infection also appears to cause functional depletion of MAIT cells resulting from abnormal expression of T-bet and EOMES, and effective ART is unable to completely salvage functional MAIT cell loss. Depletion and exhaustion of peripheral MAIT cells may affect mucosal immunity and could increase susceptibility to opportunistic infections during HIV infection. Here, we review some of the important mechanisms associated with depletion and functional loss of MAIT cells and also suggest potential immunotherapeutic strategies to restore MAIT cell functions, including the use of IL-7 to restore effector functions in HIV disease.

Peripheral loss of CD8(+) CD161(++) TCRVα7·2(+) mucosal-associated invariant T cells in chronic hepatitis C virus-infected patients

BACKGROUND

Mucosal-associated invariant T (MAIT) cells play an important role in innate host defence. MAIT cells appear to undergo exhaustion and are functionally weakened in chronic viral infections. However, their role in chronic hepatitis C virus (HCV) infection remains unclear.

MATERIALS AND METHODS

We investigated the frequency of CD8(+) CD161(++) TCR Vα7.2(+) MAIT cells in a cross-sectional cohort of chronic HCV-infected patients (n = 25) and healthy controls (n = 25). Peripheral blood mononuclear cells were investigated for circulating MAIT cell frequency, liver-homing (CCR5 and CD103), biomarkers of immune exhaustion (PD-1, TIM-3 and CTLA-4), chronic immune activation (CD38 and HLA-DR), and immunosenescence (CD57) by flow cytometry.

RESULTS

The frequency of MAIT cells was significantly decreased, and increased signs of immune exhaustion and chronic immune activation were clearly evident on MAIT cells of HCV-infected patients. Decrease of CCR5 on circulating MAIT cells is suggestive of their peripheral loss in chronic HCV-infected patients. MAIT cells also showed significantly increased levels of HLA-DR, CD38, PD-1, TIM-3 and CTLA-4, besides CD57 in chronic HCV disease.

CONCLUSIONS

Immune exhaustion and senescence of CD8(+) CD161(++) TCR Vα7.2(+) MAIT cells could contribute to diminished innate defence attributes likely facilitating viral persistence and HCV disease progression.

Concurrent loss of co-stimulatory molecules and functional cytokine secretion attributes leads to proliferative senescence of CD8(+) T cells in HIV/TB co-infection

The role of T-cell immunosenescence and functional CD8(+) T-cell responses in HIV/TB co-infection is unclear. We examined and correlated surrogate markers of HIV disease progression with immune activation, immunosenescence and differentiation using T-cell pools of HIV/TB co-infected, HIV-infected and healthy controls. Our investigations showed increased plasma viremia and reduced CD4/CD8 T-cell ratio in HIV/TB co-infected subjects relative to HIV-infected, and also a closer association with changes in the expression of CD38, a cyclic ADP ribose hydrolase and CD57, which were consistently expressed on late-senescent CD8(+) T cells. Up-regulation of CD57 and CD38 were directly proportional to lack of co-stimulatory markers on CD8(+) T cells, besides diminished expression of CD127 (IL-7Rα) on CD57(+)CD4(+) T cells. Notably, intracellular IFN-γ, perforin and granzyme B levels in HIV-specific CD8(+) T cells of HIV/TB co-infected subjects were diminished. Intracellular CD57 levels in HIV gag p24-specific CD8(+) T cells were significantly increased in HIV/TB co-infection. We suggest that HIV-TB co-infection contributes to senescence associated with chronic immune activation, which could be due to functional insufficiency of CD8(+) T cells.

Diagonal control design for atomic force microscope piezoelectric tube nanopositioners

Atomic Force Microscopes (AFM) are used for generating surface topography of samples at micro to atomic resolutions. Many commercial AFMs use piezoelectric tube nanopositioners for scanning. Scanning rates of these microscopes are hampered by the presence of low frequency resonant modes. When inadvertently excited, these modes lead to high amplitude mechanical vibrations causing the loss of accuracy, while scanning, and eventually to break down of the tube. Feedback control has been used to damp these resonant modes. Thereby, enabling higher scanning rates. Here, a multivariable controller is designed to damp the first resonant mode along both the x and y axis. Exploiting the inherent symmetry in the piezoelectric tube, the multivariable control design problem is recast as independent single-input single-output (SISO) designs. This in conjunction with integral resonant control is used for damping the first resonant mode.

Invited review article: high-speed flexure-guided nanopositioning: mechanical design and control issues

Recent interest in high-speed scanning probe microscopy for high-throughput applications including video-rate atomic force microscopy and probe-based nanofabrication has sparked attention on the development of high-bandwidth flexure-guided nanopositioning systems (nanopositioners). Such nanopositioners are designed to move samples with sub-nanometer resolution with positioning bandwidth in the kilohertz range. State-of-the-art designs incorporate uniquely designed flexure mechanisms driven by compact and stiff piezoelectric actuators. This paper surveys key advances in mechanical design and control of dynamic effects and nonlinearities, in the context of high-speed nanopositioning. Future challenges and research topics are also discussed.

High-speed cycloid-scan atomic force microscopy

A key hurdle in achieving high scan speeds in atomic force microscopes is that the probe is required to be scanned over the sample in a zig-zag raster pattern. The fast axis of the AFM scanner must track a signal that contains frequencies beyond its mechanical bandwidth. Consequently, fast raster scans generate distortions in the resulting image. We propose a smooth cycloid-like scan pattern that allows us to achieve scan speeds much higher than a raster scan. We illustrate how the proposed method can be implemented on a commercial AFM with minimal modifications.

Immunological profiles of immune restoration disease presenting as mycobacterial lymphadenitis and cryptococcal meningitis

OBJECTIVES

A proportion of HIV patients beginning antiretroviral therapy (ART) develop immune restoration disease (IRD). Immunological characteristics of IRD were investigated in a cohort of HIV patients beginning therapy in Kuala Lumpur, Malaysia.

METHODS

Peripheral blood mononuclear cells were collected at weeks 0, 6, 12, 24 and 48 of ART from five patients experiencing IRD [two with cryptococcal and three with Mycobacterium tuberculosis (Mtb) disease], eight non-IRD controls who had begun ART with CD4 T-cell counts of <100 cells/microL and 17 healthy controls. Leukocytes producing interferon-gamma (IFNgamma) were quantified by enzyme-linked immunospot assay after stimulation with purified protein derivative (PPD), early secretory antigenic target-6 (ESAT-6), Cryptococcus neoformans or Cytomegalovirus antigens. Plasma immunoglobulin (IgG) antibodies reactive with these antigens were assessed by enzyme-linked immunosorbent assay. Proportions of activated (HLA-DR(hi)) and regulatory (CD25 CD127(lo) and CTLA-4(+)) CD4 T-cells were quantified by flow cytometry.

RESULTS

Plasma HIV RNA declined and CD4 T-cell counts rose within 8-27 weeks on ART. Mtb IRD patients displayed elevated IFNgamma responses and/or plasma IgG to PPD, but none responded to ESAT-6. Cryptococcal IRD occurred in patients with low baseline CD4 T-cell counts and involved clear IFNgamma and antibody responses to cryptococcal antigen. Proportions of activated and regulatory CD4 T-cells declined on ART, but remained higher in patients than in healthy controls. At the time of IRD, proportions of activated CD4 T-cells and regulatory CD4 T-cells were generally elevated relative to other patients.

CONCLUSIONS

Cryptococcal and Mtb IRD generally coincide with peaks in the proportion of activated T-cells, pathogen-specific IFNgamma responses and reactive plasma IgG. IRD does not reflect a paucity of regulatory CD4 T-cells.

Rapid detection and serotyping of dengue virus by multiplex RT-PCR and real-time SYBR green RT-PCR

INTRODUCTION

Dengue fever and dengue haemorrhagic fever currently rank highly among the newly-emerging infectious diseases, and are considered to be the most important arboviral disease worldwide. The definitive diagnosis is culture analysis, but practical considerations limit its use. Also, the period for viral detection is limited. Within a day or two after fever subsides, rising levels of antibodies interfere with viral cultures. An alternative to this quandary is the use of viral RNA detection assays. In our laboratory, a reverse transcriptase polymerase chain reaction (RT-PCR) assay was developed using a set of degenerate primers.

METHODS

This multiplex RT-PCR assay was evaluated with 280 samples collected during the year 2003. These groups include prototype dengue virus (serotypes 1-4), acute serum from which the dengue virus was isolated, seronegative acute samples (culture negative) but whose convalescent samples seroconverted, and sera positive for other microbial diseases. This assay was then modified into a real-time SYBR Green RT-PCR assay. Sensitivity and specificity of both assays were compared.

RESULTS

The multiplex RT-PCR assay was able to detect 134 samples whereas SYBR Green RT-PCR assay was able to detect 178 out of 306 samples. Both assays were 100 percent specific. Further analysis of 53 samples showed that the virus could be amplified at IgM positive/negative values of up to 4.2, and up to six days after onset of fever. The viral detection rate was inversely proportional to the day of fever onset as well as IgM values.

CONCLUSION

The sensitivity and specificity of the conventional multiplex RT-PCR assay are 98.18 percent and 100 percent, respectively, and for the real-time SYBR Green assay, 99.09 percent and 100 percent, respectively. The melting curve analysis allows all four dengue serotypes to be discriminated based on distinct melting temperature value. The accuracy and speed of this multiplex RTPCR assay makes it a suitable test for the diagnosis of dengue and for epidemiological surveillance.

On the accuracy of Mindlin plate predictions for the frequency-temperature behavior of resonant modes in AT- and SC-cut quartz plates

The frequency spectra of resonant modes in AT- and SC-cut quartz plates and their frequency-temperature behavior were studied using Mindlin first- and third-order plate equations. Both straight-crested wave solutions and two-dimensional plate solutions were studied. The first-order Mindlin plate theory with shear correction factors was previously found to yield inaccurate frequency spectra of the modes in the vicinity of the fundamental thickness-shear frequency. The third-order Mindlin plate equations without correction factors, on the other hand, predict well the frequency spectrum in the same vicinity. In general, the frequency-temperature curves of the fundamental thickness-shear obtained from the first-order Mindlin plate theory are sufficiently different from those of the third-order Mindlin plate theory that they raise concerns. The least accurately predicted mode of vibration is the flexure mode, which results in discrepancies in its frequency-temperature behavior. The accuracy of other modes of vibrations depends on the degree of couplings with the flexure mode. Mindlin first-order plate theory with only the shear correction factors is not sufficiently accurate for high frequency crystal vibrations at the fundamental thickness-shear frequency. Comparison with measured resonant frequencies and frequency-temperature results on an AT-cut quartz plate shows that the third-order plate theory is more accurate than the first-order plate theory; this is especially true for the technically important fundamental thickness shear mode in the AT-cut quartz plate.

Numerical algorithms and results for SC-cut quartz plates vibrating at the third harmonic overtone of thickness shear

Finite element matrix equations, derived from two-dimensional piezoelectric high frequency plate theory are solved to study the vibrational behavior of the third overtone of thickness shear in square and circular SC-cut quartz resonators. The mass-loading and electric effects of electrodes are included. A perturbation method which reduces the memory requirements and computational time significantly is employed to calculate the piezoelectric resonant frequencies. A new storage scheme is introduced which reduces memory requirements for mass matrix by about 90% over that of the envelope storage scheme. Substructure techniques are used in eigenvalue calculation to save storage. Resonant frequency and the mode shapes of the harmonic third overtone thickness shear vibrations for square and circular plates are calculated. A predominant third overtone thickness shear displacement, coupled with the third overtone of thickness stretch and thickness twist, is observed. Weak coupling between the third order thickness shear displacement and the zeroth-, first-, and second-order displacements is noted. The magnitudes of the lower order displacements are found to be about two orders smaller than that of the third overtone thickness shear displacement.

A perturbation method for finite element modeling of piezoelectric vibrations in quartz plate resonators

When the piezoelectric stiffening matrix is added to the mechanical stiffness matrix of a finite element model, its sparse matrix structure is destroyed. A direct consequence of this loss in sparseness is a significant rise in memory and computational time requirements for the model. For weakly coupled piezoelectric materials, the matrix sparseness can be retained by a perturbation method which separates the mechanical eigenvalue solution from its piezoelectric effects. Using this approach, a perturbation and finite element scheme for weakly coupled piezoelectric vibrations in quartz plate resonators has been developed. Finite-element matrix equations were derived specifically for third-overtone thickness-shear, SC-cut quartz plate resonators with electrode platings. High-frequency piezoelectric plate equations were employed in the formulation of the finite element matrix equation. Results from the perturbation method compared well with the direct solution of the piezoelectric finite element equations. This method will result in significant savings in the computer memory and computational time. Resonance and antiresonance frequencies of a certain mode could be calculated easily by using the same eigenpair from the purely mechanical stiffness matrix. Numerical results for straight crested waves in a third overtone SC-cut quartz strip with and without electrodes are presented. The steady-state response to an electrical excitation is calculated.

Thickness-shear mode shapes and mass-frequency influence surface of a circular and electroded AT-cut quartz resonator

Finite-element solutions for the fundamental thickness shear mode and the second-anharmonic overtone of a circular, 1.87-MHz AT-cut quartz plate with no electrodes are presented and compared with previously obtained results for a rectangular plate of similar properties. The edge flexural mode in circular plates, a vibration mode not seen in the rectangular plate is also presented. A 5-MHz circular and electroded AT-cut quartz plate is studied. A portion of the frequency spectrum is constructed in the neighborhood of the fundamental thickness-shear mode. A convergence study is also presented for the electroded 5-MHz plate. A new two-dimensional (2-D) technique for visualizing the vibration mode solutions is presented. This method departs substantially from the three-dimensional (3-D) ;wire-frame' plots presented in the previous analysis. The 2-D images can be manipulated to produce nodal line diagrams and can be color coded to illustrate mode shapes and energy trapping phenomenon. A contour plot of the mass-frequency influence surface for the plated 5-MHz resonator is presented. The mass-frequency influence surface is defined as a surface giving the frequency change due to a small localized mass applied to the resonator surface.

Mass-frequency influence surface, mode shapes, and frequency spectrum of a rectangular AT-cut quartz plate

The mass-frequency influence surface and frequency spectrum of a rectangular AT-cut quartz plate are studied. The mass-frequency influence surface is defined as a surface giving the frequency change due to a small localized mass applied on the plate surface. Finite-element solutions of R.D. Mindlin's (1963) two-dimensional plate equations for thickness-shear, thickness-twist, and flexural vibrations are given. Spectrum splicing, and an efficient eigenvalue solver using the C. Lanczos (1950) algorithm are incorporated into the finite-element program. A convergence study of the fundamental thickness-shear mode and its first symmetric, anharmonic overtone is performed for finite-element meshes of increasing fineness. As a general rule, more than two elements must span any half-wave in the plate or spurious mode shapes will be obtained. Two-dimensional (2D) mode shapes and frequency spectrum of a rectangular AT-cut plate in the region of the fundamental thickness-shear frequency are presented. The mass-frequency influence surface for a 5-MHz rectangular, AT-cut plate with patch electrodes is obtained by calculating the frequency change due to a small mass layer moving over the plate surface. The frequency change is proportional to the ratio of mass loading to mass of plate per unit area and is confined mostly within the electrode area, where the magnitude is on the order 10(8) Hz/g.

Modeling resonator frequency fluctuations induced by adsorbing and desorbing surface molecules

Resonator frequency fluctuations due to adsorption and desorption of molecules on plate electrodes are studied using the principle of mass-loading effects of adsorbed molecules. The study is based on a 525 MHz, AT-cut quartz resonator enclosed in a small crystal holder. Equations relating the surface adsorption rates of the crystal holder to pressure were derived and found to be quadratic polynomial functions of the adsorption rates. Calculations based on these equations show that a contaminant gas with a higher desorption energy creates larger changes in pressure when the temperature is varied. The function describing the frequency fluctuations due to any one contaminant site is a continuous-time Markov chain. Kolmogorov equations and an autocorrelation function for the Markov chain are derived. The autocorrelation and spectral density function of resonator frequency fluctuations are derived. The spectral density of frequency fluctuations at 1 Hz is studied as a function of pressure, temperature, and desorption energy of molecules. The noise levels for a contaminant gas with one type of molecules are found to be lower for lower desorption energies, and higher at lower pressures.

Resonator surface contamination-a cause of frequency fluctuations?

The mass loading effects of adsorbing and desorbing contaminant molecules on the magnitude and characteristics of frequency fluctuations in a thickness-shear resonator are studied. The study is motivated by the observation that the frequency of a thickness-shear resonator is determined predominantly by such mechanical parameters as the thickness of the resonator, elastic stiffnesses, mass loading of the electrodes, and energy trapping. An equation was derived relating the spectral density of frequency fluctuations to: (1) rates of adsorption and desorption of one species of contaminant molecules; (2) mass per unit area of a monolayer of molecules: (3) frequency constant; (4) thickness of resonator; and (5) number of molecular sites on one resonator surface. The induced phase noises were found to be significant in very-high-frequency resonators and are not simple functions of the percentage of area contaminated. The spectral density of frequency fluctuations was inversely proportional to the fourth power of the thickness if other parameters were held constant.

Characteristics of a Lagrangian, high-frequency plate element for the static temperature behavior of low-frequency quartz resonators

Finite-element matrix equations based on the Lagrangian, first-order, incremental plate equations of motion superposed on homogeneous thermal strains were formulated using virtual work principles. A program for an isoparametric, four-node quadrilateral element was written and applied to the study of the frequency-temperature (FT) behavior of flexure-mode quartz resonators. The lumped-mass and consistent-mass matrices were found to yield practically the same FT curves. For simple prismatic resonators, two schemes, reduced/selective integration and incompatible modes, produced relatively similar FT curves. The incompatible modes scheme yielded better results for resonators of more complex shapes, such as the tuning fork. It is concluded that the six-degree-of-freedom per node element is needed for the analysis of the FT behavior of a fully anisotropic flexure-mode resonator.