Pan-India influenza-like illness (ILI) and Severe acute respiratory infection (SARI) surveillance: epidemiological, clinical and genomic analysis

Background

Over time, COVID-19 testing has significantly declined across the world. However, it is critical to monitor the virus through surveillance. In late 2020, WHO released interim guidance advising the use of the existing Global Influenza Surveillance and Response System (GISRS) for the integrated surveillance of influenza and SARS-CoV-2.

Methods

In July 2021, we initiated a pan-India integrated surveillance for influenza and SARS-CoV-2 through the geographically representative network of Virus Research and Diagnostic Laboratories (VRDLs) across 26 hospital and laboratory sites and 70 community sites. A total of 34,260 cases of influenza-like illness (ILI) and Severe acute respiratory infection (SARI) were enrolled from 4 July 2021 to 31 October 2022.

Findings

Influenza A(H3) and B/Victoria dominated during 2021 monsoon season while A(H1N1)pdm09 dominated during 2022 monsoon season. The SARS-CoV-2 "variants of concern" (VoC) Delta and Omicron predominated in 2021 and 2022, respectively. Increased proportion of SARI was seen in extremes of age: 90% cases in < 1 year; 68% in 1 to 5 years and 61% in ≥ 8  years age group. Approximately 40.7% of enrolled cases only partially fulfilled WHO ILI and SARI case definitions. Influenza- and SARS-CoV-2-infected comorbid patients had higher risks of hospitalization, ICU admission, and oxygen requirement.

Interpretation

The results depicted the varying strains and transmission dynamics of influenza and SARS-CoV-2 viruses over time, thus emphasizing the need to continue and expand surveillance across countries for improved decision making. The study also describes important information related to clinical outcomes of ILI and SARI patients and highlights the need to review existing WHO ILI and SARI case definitions.

External quality assessment of COVID-19 real time reverse transcription PCR laboratories in India

Sudden emergence and rapid spread of COVID-19 created an inevitable need for expansion of the COVID-19 laboratory testing network across the world. The strategy to test-track-treat was advocated for quick detection and containment of the disease. Being the second most populous country in the world, India was challenged to make COVID-19 testing available and accessible in all parts of the country. The molecular laboratory testing network was augmented expeditiously, and number of laboratories was increased from one in January 2020 to 2951 till mid-September, 2021. This rapid expansion warranted the need to have inbuilt systems of quality control/ quality assurance. In addition to the ongoing inter-laboratory quality control (ILQC), India implemented an External Quality Assurance Program (EQAP) with assistance from World Health Organization (WHO) and Royal College of Pathologists, Australasia. Out of the 953 open system rRTPCR laboratories in both public and private sector who participated in the first round of EQAP, 891(93.4%) laboratories obtained a passing score of > = 80%. The satisfactory performance of Indian COVID-19 testing laboratories has boosted the confidence of the public and policy makers in the quality of testing. ILQC and EQAP need to continue to ensure adherence of the testing laboratories to the desired quality standards.

Can paraoxonase activity serve as a comparable marker than high density lipoprotein in the follow-up of patients of coronary artery disease?

Funding Acknowledgements

Type of funding sources: None.

Background

Human serum paraoxonase (PON1) produced by the liver and residing almost exclusively on high density lipoproteins (HDL), has been demonstrated to prevent the oxidation of low density lipoprotein (LDL), which is  the central initiating factor in the causation of atherosclerosis. (1,2) Thus, PON1 along with HDL, plays an important role in the pathophysiology of atherosclerosis and consequently coronary artery disease. Statins are commonly used in clinical practice for the management of dyslipidemia , a known risk factor for coronary artery disease (CAD).Keeping this in mind,  it was deemed necessary to set up an observational study to explore whether the changes in PON1 activity after 3 months of statin therapy could help in the follow up of CAD patients.

Purpose

The purpose of the study was to evaluate the alterations in the PON1 activity along with the concentrations of HDL and LDL in patients of CAD before and after 3 months of statin therapy and to explore whether PON1 can be used as a comparable marker for assessment of the atherosclerotic risk in the follow up of these patients.

Materials and Methods

The study included 30 new patients who were put on statin therapy following the diagnosis of acute coronary syndrome in the Cardiology outpatients department. The activity of PON1 and the lipid profile parameters were estimated before starting statin therapy and again three months later. Patients with co-morbidities like diabetes, chronic kidney disease, chronic liver disease and other cardiac diseases of infectious etiology were excluded from the study. The data thus obtained was compiled and tabulated in Excel and statistically analyzed.

Results

The mean, median and standard deviation of the PON1, LDL and HDL, both before and after starting statin therapy, were calculated and the distribution of the individual parameters were determined. Analysis of the compiled data revealed that there was a statistically significant increase in both PON1 (p &lt; 0.05) and HDL (p &lt; 0.001) and a decrease (p &lt;0.05, also statistically significant) in LDL after 3 months of statin therapy. The results both before and after 3 months of statin therapy are summarised in the table attached.(Table 1)

Conclusion

It may be concluded from the above study that the activity of PON1 may be used to indicate the changes in the lipid profile in the follow up of patients of CAD being treated with statins. It is however necessary to conduct larger, well designed studies in future to explore whether it may be used as a comparable marker better than HDL in the follow up of these patients. Abstract Figure.

Neutralization assays for SARS-CoV-2: Implications for assessment of protective efficacy of COVID-19 vaccines

The WHO emergency use-listed (EUL) COVID-19 vaccines were developed against early strains of SARS-CoV-2. With the emergence of SARS-CoV-2 variants of concern (VOCs) - Alpha, Beta, Gamma, Delta and Omicron, it is necessary to assess the neutralizing activity of these vaccines against the VOCs. PubMed and preprint platforms were searched for literature on neutralizing activity of serum from WHO EUL vaccine recipients, against the VOCs, using appropriate search terms till November 30, 2021. Our search yielded 91 studies meeting the inclusion criteria. The analysis revealed a drop of 0-8.9-fold against Alpha variant, 0.3-42.4-fold against Beta variant, 0-13.8-fold against Gamma variant and 1.35-20-fold against Delta variant in neutralization titres of serum from the WHO EUL COVID-19 vaccine recipients, as compared to early SARS-CoV-2 isolates. The wide range of variability was due to differences in the choice of virus strains selected for neutralization assays (pseudovirus or live virus), timing of serum sample collection after the final dose of vaccine (day 0 to 8 months) and sample size (ranging from 5 to 470 vaccinees). The reasons for this variation have been discussed and the possible way forward to have uniformity across neutralization assays in different laboratories have been described, which will generate reliable data. Though in vitro neutralization studies are a valuable tool to estimate the performance of vaccines against the backdrop of emerging variants, the results must be interpreted with caution and corroborated with field-effectiveness studies.

Inter-laboratory testing as a strategy for external quality assessment for qualitative detection of SARS-CoV-2 by real-time RT-PCR testing in India

To implement the strategy of test, track and treat to tackle the ongoing COVID-19 pandemic, the number of real-time RT-PCR-based testing laboratories was increased for diagnosis of SARS-CoV-2 in the country. To ensure reliability of the laboratory results, the Indian Council of Medical Research initiated external quality assessment (EQA) by deploying inter-laboratory quality control (ILQC) activity for these laboratories by nominating 34 quality control (QC) laboratories. This report presents the results of this activity for a period of September 2020 till November 2020. A total of 597 laboratories participated in this activity and 86 per cent of these scored ≥90 per cent concordance with QC laboratories. This ILQC activity showcased India's preparedness in quality diagnosis of SARS-CoV-2.

Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India

From March to June 2021, India experienced a deadly second wave of COVID-19, with an increased number of post-vaccination breakthrough infections reported across the country. To understand the possible reason for these breakthroughs, we collected 677 clinical samples (throat swab/nasal swabs) of individuals from 17 states/Union Territories of the country who had received two doses (n = 592) and one dose (n = 85) of vaccines and tested positive for COVID-19. These cases were telephonically interviewed and clinical data were analyzed. A total of 511 SARS-CoV-2 genomes were recovered with genome coverage of higher than 98% from both groups. Analysis of both groups determined that 86.69% (n = 443) of them belonged to the Delta variant, along with Alpha, Kappa, Delta AY.1, and Delta AY.2. The Delta variant clustered into four distinct sub-lineages. Sub-lineage I had mutations in ORF1ab A1306S, P2046L, P2287S, V2930L, T3255I, T3446A, G5063S, P5401L, and A6319V, and in N G215C; Sub-lineage II had mutations in ORF1ab P309L, A3209V, V3718A, G5063S, P5401L, and ORF7a L116F; Sub-lineage III had mutations in ORF1ab A3209V, V3718A, T3750I, G5063S, and P5401L and in spike A222V; Sub-lineage IV had mutations in ORF1ab P309L, D2980N, and F3138S and spike K77T. This study indicates that majority of the breakthrough COVID-19 clinical cases were infected with the Delta variant, and only 9.8% cases required hospitalization, while fatality was observed in only 0.4% cases. This clearly suggests that the vaccination does provide reduction in hospital admission and mortality.

Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India

From March to June 2021, India experienced a deadly second wave of COVID-19, with an increased number of post-vaccination breakthrough infections reported across the country. To understand the possible reason for these breakthroughs, we collected 677 clinical samples (throat swab/nasal swabs) of individuals from 17 states/Union Territories of the country who had received two doses (n = 592) and one dose (n = 85) of vaccines and tested positive for COVID-19. These cases were telephonically interviewed and clinical data were analyzed. A total of 511 SARS-CoV-2 genomes were recovered with genome coverage of higher than 98% from both groups. Analysis of both groups determined that 86.69% (n = 443) of them belonged to the Delta variant, along with Alpha, Kappa, Delta AY.1, and Delta AY.2. The Delta variant clustered into four distinct sub-lineages. Sub-lineage I had mutations in ORF1ab A1306S, P2046L, P2287S, V2930L, T3255I, T3446A, G5063S, P5401L, and A6319V, and in N G215C; Sub-lineage II had mutations in ORF1ab P309L, A3209V, V3718A, G5063S, P5401L, and ORF7a L116F; Sub-lineage III had mutations in ORF1ab A3209V, V3718A, T3750I, G5063S, and P5401L and in spike A222V; Sub-lineage IV had mutations in ORF1ab P309L, D2980N, and F3138S and spike K77T. This study indicates that majority of the breakthrough COVID-19 clinical cases were infected with the Delta variant, and only 9.8% cases required hospitalization, while fatality was observed in only 0.4% cases. This clearly suggests that the vaccination does provide reduction in hospital admission and mortality.

Comparison of the immunogenicity & protective efficacy of various SARS-CoV-2 vaccine candidates in non-human primates

BACKGROUND & OBJECTIVES

The COVID-19 pandemic has emerged as a global public health crisis and research groups worldwide are engaged in developing vaccine candidates to curb its transmission, with a few vaccines having progressed to advanced stages of clinical trials. The aim of this systematic review was to compare immunogenicity and protective efficacy of various SARS-CoV-2 vaccine candidates tested in non-human primate (NHP) models.

METHODS

Literature on effect of SARS-CoV-2 vaccines in NHP models reported on PubMed and preprint platforms (medRxiv and bioRxiv) till October 22, 2020, was searched with the following terms: coronavirus vaccine, COVID-19 vaccine, SARS-CoV-2 vaccine, nonhuman primate, and rhesus macaque.

RESULTS

Our search yielded 19 studies, which reported immune response elicited by 18 vaccine candidates in NHP. All the vaccines induced detectable neutralizing antibody (NAb) titres in the serum of vaccinated animals, with some showing effective viral clearance from various organs. The vaccinated animals also showed nil to mild histopathological changes in their lungs compared to placebo groups in the trials that performed necropsy.

INTERPRETATION & CONCLUSIONS

Our findings highlighted onset of quick immunogenicity and protective efficacy of mRNA-1273, followed by Ad26.CoV2.S, NVX-CoV2373, BNT162b2, RBD and BBV152 vaccine candidates in preclinical trials as compared to the others. NHP data also showed correlation with clinical trial data available for a few vaccines. Preclinical trials of COVID-19 vaccine candidates in NHPs yielded promising results, with some candidates faring better than others.

Expression patterns of inhibitor of apoptosis proteins in malignant pleural mesothelioma

Inhibitor of apoptosis proteins (IAPs) comprise a family of structurally similar proteins, five of which are widely studied in the context of cancer: IAP-1/MIHC/cIAP2, IAP-2/MIHB/cIAP1, livin/ML-IAP/KIAP, survivin, and XIAP/MIHA/hILP. IAPs are overexpressed by most neoplasms, promote tumour cell survival after a wide variety of apoptotic stimuli, and frequently have gene and/or protein expression patterns associated with a relatively poor prognosis. However, many IAPs are also expressed by normal tissues, can facilitate apoptotic cell death, and have expression patterns associated with a relatively favourable prognosis in some cases. The result is that the precise role(s) of IAPs in human tumours is not exactly known. It has been previously reported that IAP-1 is overexpressed in malignant pleural mesothelioma (MPM) and is responsible for a large degree of the resistance of cultured MPM cells to cisplatin. Given the high homology of IAP family members, it is likely that other IAPs will be important in MPM. In the present study, the gene and protein expression patterns of IAP-1, IAP-2, survivin, livin, and XIAP have been determined in MPM cell lines (n=9) and a large number of MPM tumours using high-density oligonucleotide microarrays (n=40) and an MPM tissue array (n=66). Human tumours were linked to clinical data and it was found that IAP-1 and survivin mRNA expression patterns were associated with a relatively shorter patient survival, while those of XIAP and livin were associated with a relatively longer patient survival. Abundant protein for all IAPs was also detected in MPM tumours, where they were expressed primarily in the cytoplasm. Only IAP-1 and livin protein was expressed in the nucleus of MPM tumours. These results provide the rationale for additional study of this gene family in MPM and cancer in general.

Inhibitor of apoptosis proteins are regulated by tumour necrosis factor-alpha in malignant pleural mesothelioma

Inhibitor of apoptosis proteins (IAPs) are overexpressed by most neoplasms and promote tumour cell survival after a wide variety of apoptotic stimuli elicited via intrinsic (ie mitochondrial) and extrinsic (ie death receptor) pathways. It has previously been reported that one of these proteins, IAP-1(MIHC/cIAP2), is overexpressed in malignant pleural mesothelioma (MPM) and is responsible for a large degree of the resistance of cultured MPM cells to cisplatin. Subsequent analysis in a larger number of human tumours revealed that additional IAPs (eg IAP-2/MIHB/cIAP1, livin/ML-IAP/KIAP, survivin, and XIAP/MIHA/hILP) are also overexpressed in MPM and, with the exception of IAP-2, have expression patterns that correlate with prognosis. In the present study, potential regulatory mechanisms of IAP genes in MPM were investigated and it was found that tumour necrosis factor-alpha (TNF-alpha) can increase mRNA and protein levels of IAP-1, IAP-2, and XIAP, but not livin or survivin in MPM cell lines (n=4). It was also found that IAP gene expression levels are increased concomitantly with translocation to the nucleus of the TNF-responsive transcription factor NF-kappaB. Co-incubation of MPM cells with TNF-alpha and pyrrolidine dithiocarbamate (PDTC), an NF-kappaB inhibitor, prevented TNF-mediated up-regulation of IAP gene expression levels. In survival studies, TNF-alpha was not toxic to MPM cells at any concentration examined. However, MPM cells exposed to TNF-alpha were twice as resistant to cisplatin in dose response survival assays compared with unstimulated controls and were found to have a significantly greater fraction of surviving cells at multiple cisplatin concentrations (p<0.0087). Finally, it was found that levels of circulating TNF-alpha were statistically significantly (p=0.031) (median 312.5 pg/ml) higher in MPM patients (n=6) prior to surgical tumour debulking compared with those after surgery (median 0 pg/ml). These results when combined with previous observations by our laboratory and others strongly suggest that IAPs act synergistically with TNF family members to promote survival of MPM tumour cells after exposure to cisplatin and possibly other chemotherapeutic drugs.

Thermodynamics of Formation of Biological Microemulsion (with Cinnamic Alcohol, Aerosol OT, Tween 20, and Water) and Kinetics of Alkaline Fading of Crystal Violet in Them

The ternary phase diagrams for the formation of biological microemulsions of the combinations CA/AOT/water and CA/Tween 20/water have been presented. The thermodynamics of solution of water in AOT/CA as well as in Tween 20/CA forming w/o microemulsions and solution of oil in Tween 20/water forming o/w microemulsions have been calorimetrically studied. The solution processes are essentially exothermic (with a few exceptions) and have yielded negative entropies, i.e., producing an ordering effect. This has been supported by the measured specific heats of the resulting solution. The pseudo-first-order rate constants (k1) for the alkaline fading of crystal violet in w/o microemulsion medium for the CA/AOT/water and CA/TW 20/water have been found to depend on [water]/[AOT] mole ratio (omega) with maxima at omega = 10. For o/w preparations of CA/TW-20/water, k1 has shown maximum at [CA]/[TW-20] mole ratio omega' = 2, whereas the k2 value has increased with omega'. The salt effect on the reaction has shown significant deviation from expectation in w/o microemulsion. The free energies of activation for the w/o and o/w systems are of the same order, whereas both DeltaHdouble dagger and DeltaSdouble dagger values differ significantly.

Activity of alkaline phosphatase in water-in-oil microemulsions containing vegetable oil

The hydrolysis of p-nitrophenyl phosphate by the enzyme alkaline phosphatase has been studied in vegetable oil containing water-in-oil (W/O) microemulsions of six different compositions at four different (water)/(surfactant) mole ratios of 10, 17.6, 24.7 and 37. The vegetable oils used are ricebran oil (RO) and clove oil (CO) and the amphiphiles used are Aerosol OT (AOT), cinnamic alcohol (CA) and Tween-20 (T-20). The hydrolytic process does not follow conventional Michaelis Menten equation normally observed for enzymatic process. In the water/vegetable oil microemulsions, the enzyme seems to lose its activity when AOT is the amphiphile. The amount of p-nitrophenol generated as a result of hydrolysis is independent of the presence of the enzyme. With Tween-20 as the amphiphile, the microemulsion produces an initial retarding effect which ultimately gets appreciably compensated.

Biological microemulsions: Part IV--Phase behaviour and dynamics of microemulsions prepared with vegetable oils mixed with aerosol-OT, cinnamic alcohol and water

Microemulsification of vegetable oils (ricebran, saffola, soyabean, sesame, palm and linseed) with water using aerosol-OT and cinnamic alcohol as mixed amphiphiles was studied. The biological microemulsions formed covered on the average approximately 27% of single phase area in the triangular phase diagram. The multiphasic zone for saffola was studied in detail, two- and three-phase zones were identified with patches of thick gel. The effect of temperature on the multiphase formation in the range 29-55 degrees C was also studied. The formation of multiphase and their proportions found to depend on the type of oil. The biological microemulsions at reasonable water/AOT mole ratio showed moderate increase in conductance with temperature. The viscosity of the microemulsions was high. Of the studied systems (sesame, saffola and ricebran) the viscosity of the first two decreased with the rate of shear whereas that of ricebran increased. When cinnamic alcohol was used as the oil, the trend of viscosity was similar to that of sesame and saffola.

Thermodynamics of water-induced precipitation of cholesterol and its acetate, benzoate and stearate derivatives dissolved in 1,4-dioxane and 2-propanol

The energetics of the precipitation process depended on the solute-solvent combination and the enthalpy and entropy of precipitation compensated each other. The partial molal volumes of the lipids in both the solvents were greater than the anhydrous molar volumes, except for cholesterol in 1,4-dioxane and cholesteryl acetate in 2-propanol where the order was reverse. While the partial molal compressibilities of all the solutes studied were negative in 1,4-dioxane, those of cholesterol and cholesteryl acetate in 2-propanol were, respectively, negative and positive. The negative values were supported by considerable solvation of the solutes, particularly in 1,4-dioxane.

Water-induced precipitation of cholesterol dissolved in organic solvents in the absence and presence of surfactants and salts

The precipitation of cholesterol dissolved in organic solvents, viz. methanol, ethanol, n-propanol, isopropanol, acetone and 1,4-dioxane, by the addition of water has been studied. The effects of the solvents towards the precipitation follow the order: methanol greater than ethanol greater than acetone greater than dioxane greater than n-propanol greater than iso-propanol, the solvent dioxane however exhibits a change in the order at higher concentration. Additives like Triton X-100, sodium cholate, sodium deoxycholate, sodium dehydro cholate, sodium salicylate and sodium chloride have some protective action against precipitation, the maximum protection being that of Triton X-100. The additives have shown better protective action in propanols and dioxane than in methanol, ethanol and acetone. Analysis of solvent composition and dielectric constant has revealed specific solvent effects on the water-induced precipitation of cholesterol. Thermodynamic analysis of the precipitation phenomenon and the unique role of solvent structure on cholesterol precipitation has been discussed.