ABSTRACT
The recent emergence of highly mutated SARS-CoV-2 Omicron variant has debilitating effect on public health system of the affected countries worldwide. Currently India is facing third wave of COVID-19 pandemic and going through a severe crisis. Within short span of time, the variant has shown high transmissibility and capability of evading the immune response generated against natural infection and vaccination. The immune escape potential of Omicron is a serious concern and further needs to be explored. In the present study, we have assessed the IgG and neutralizing antibody (NAb) response in breakthrough individuals vaccinated with two doses ChAdOx1 nCoV-19 vaccine (n=25), breakthrough individuals vaccinated with two doses of BNT162b2 mRNA vaccine (n=8) and unvaccinated individuals (n=6). All these individuals were infected with Omicron variant. The IgG antibody activity in the sera of the ChAdOx1 nCoV-19 and BNT162b2 mRNA breakthrough individuals was comparable with S1-RBD, while it was lesser in BNT162b2 mRNA breakthrough individuals with N protein and inactivated whole antigen IgG ELISA. BNT162b2 mRNA breakthrough individuals showed moderate reduction in NAb GMTs compared to ChAdOx1 nCoV-19 against Alpha, Beta and Delta. However, 3-fold higher reduction was observed with omicron variant in BNT162b2 mRNA than ChAdOx1 nCoV-19. Apparently, Alpha variant was modestly resistant to the sera of unvaccinated individuals than Beta, Delta and Omicron. Our study demonstrated substantial immune response in the individuals infected with Omicron. The neutralizing antibodies could effectively neutralize the Omicron and other VOCs including the most prevalent Delta variant.
ABSTRACT
Due to failure of virus isolation of Omicron variant in Vero CCL-81 from the clinical specimens of COVID-19 cases, we infected Syrian hamsters and then passage into Vero CCL-81 cells. The Omicron sequences were studied to assess if hamster could incorporate any mutation to changes its susceptibility. L212C mutation, Tyrosine 69 deletion, and C25000T nucleotide change in spike gene and absence of V17I mutation in E gene was observed in sequences of hamster passage unlike human clinical specimen and Vero CCL-81 passages. No change was observed in the furin cleavage site in any of the specimen sequence which suggests usefulness of these isolates in future studies.
ABSTRACT
BackgroundAccurate rapid antibody detection kits requiring minimum infrastructure are beneficial in detecting post-vaccination antibodies in large populations. ChAdOx1-nCOV (COVISHIELD) and BBV-152 (Covaxin) vaccines are primarily used in India. MethodsIn this single-centre prospective study, performance of Meril ABFind was investigated by comparing with Abbott SARS-CoV-2 IgG II Quant (Abbott Quant), GenScript cPass SARS-CoV-2 neutralization antibody detection kit (GenScript cPass), and COVID Kawach MERILISA (MERILISA) in 62 vaccinated health care workers (HCW) and 40 pre-pandemic samples. ResultsIn the vaccinated subjects, Meril ABFind kit displayed high sensitivity of 93.3% (CI, 89.83%-96.77%), 94.92% (CI, 91.88%-97.96%), and 90.3% (CI, 86.20%-94.4%) in comparison to Abbott Quant, MERILISA, and GenScript cPass respectively. The results of the Meril ABFind in the COVISHIELD-vaccinated group were excellent with 100% sensitivity in comparison to the other three kits. In the Covaxin-vaccinated group, Meril ABFind displayed sensitivity ranging from 80% to 88.9%. In control samples, there were no false positives detected by Meril ABFind, while Abbott Quant, MERILISA, and GenScript cPass reported 2.5%, 10.0%, and 12.5% false positives, respectively. In the pre-pandemic controls, specificity of Meril ABFind was 100%, Abbott Quant 97.5%, MERILISA 90%, and GenScript cPass 87.5%. ConclusionThe Meril ABFind kit demonstrated satisfactory performance when compared with the three commercially available kits and was the only kit without false positives in the pre-pandemic samples. This makes it a viable option for rapid diagnosis of post vaccination antibodies.
ABSTRACT
The aim of this study was to identify the SARS-CoV-2 lineages circulating in the pediatric population of India during the second wave of the pandemic. Clinical and demographic details linked with the nasopharyngeal/oropharyngeal swabs (NPS/OPS) collected from SARS-CoV-2 cases (n=583) aged 0-18 year and tested positive by real-time RT-PCR were retrieved from March to June 2021.Symptoms were reported among 37.2% of patients and 14.8% reported to be hospitalized. The E gene CT value had significant statistical difference at the point of sample collection when compared to that observed in the sequencing laboratory. Out of these 512 sequences 372 were VOCs, 51 were VOIs. Most common lineages observed were Delta, followed by Kappa, Alpha and B.1.36, seen in 65.82%, 9.96%, 6.83% and 4.68%, respectively in the study population. Overall, it was observed that Delta strain was the leading cause of SARS-CoV-2 infection in Indian children during the second wave of the pandemic. We emphasize on the need of continuous genomic surveillance in SARS-CoV-2 infection even amongst children.
ABSTRACT
Immune cell dysregulation and lymphopenia characterize COVID-19 pathology in moderate to severe disease. While underlying inflammatory factors have been extensively studied, homeostatic and mucosal migratory signatures remain largely unexplored as causative factors. In this study we evaluated the association of circulating IL-6, soluble mucosal addressin cell adhesion molecule (sMAdCAM) and IL-15 with cellular dysfunction characterizing mild and hypoxemic stages of COVID-19. A cohort of SARS-CoV-2 infected individuals (n=125) at various stages of disease progression together with healthy controls (n=16) were recruited from COVID Care Centres (CCCs) across Mumbai, India. Multiparametric flow cytometry was used to perform in-depth immune subset characterization and to measure plasma IL-6 levels. sMAdCAM, IL-15 levels were quantified using ELISA. Distinct depletion profiles, with relative sparing of CD8 effector memory and CD4+ regulatory T cells was observed in hypoxemic disease within the lymphocyte compartment. An apparent increase in the frequency of intermediate monocytes characterized both mild as well as hypoxemic disease. IL-6 levels inversely correlated with those of sMAdCAM and both markers showed converse associations with observed lympho-depletion suggesting opposing roles in pathogenesis. Interestingly, IL-15, a key cytokine involved in lymphocyte activation and homeostasis, was detected in symptomatic individuals but not in healthy controls or asymptomatic cases. Further, negative association of plasma IL-15 with depleted T, B and NK subsets suggested a compensatory production of this cytokine in response to the profound lymphopenia. Finally, higher levels of plasma IL-15 and IL-6, but not sMAdCAM, were associated with longer duration of hospitalization.
ABSTRACT
Recent studies positing the gut as a sanctuary site for viral persistence in SARS-CoV-2 infection highlight the importance of assimilating profiles of systemic as well as gut inflammatory mediators to understand the pathology of COVID-19. Also, the role of these markers in governing virus specific immunity following infection remains largely unexplored. A cohort (n=84) of SARS-C0V-2 infected individuals included a group of in-patients (n=60) at various stages of disease progression together with convalescent individuals (n=24) recruited between April and June 2020 from Mumbai, India. Follow-up of 35 in-patients at day 7 post diagnosis was carried out. Th1/Th2/Th17 cytokines along with soluble MAdCAM (sMAdCAM) levels in plasma were measured. Also, anti-viral humoral response as measured by rapid antibody test (IgG, IgM), Chemiluminescent Immunoassay (IgG) and antibodies binding to SARS-CoV-2 proteins were measured by Surface Plasmon Resonance (SPR) from plasma.IL-6 and sMAdCAM levels among in-patients inversely correlated with one another. When expressed as a novel integrated marker -sMIL index (sMAdCAM/IL-6 ratio), these levels were incrementally and significantly higher in various disease states with convalescents exhibiting the highest values. Importantly, sMAdCAM levels as well as sMIL index (fold change) correlated with peak association rates of receptor binding domain and fold change in binding to spike respectively as measured by SPR. Our results highlight key systemic and gutassociated parameters that need to be monitored and investigated further to optimally guide therapeutic and prophylactic interventions for COVID-19.
ABSTRACT
ObjectivesConvalescent plasma (CP) as a passive source of neutralizing antibodies and immunomodulators is a century-old therapeutic option used for the management of viral diseases. We investigated its effectiveness for the treatment of COVID-19. DesignOpen-label, parallel-arm, phase II, multicentre, randomized controlled trial. SettingThirty-nine public and private hospitals across India. ParticipantsHospitalized, moderately ill confirmed COVID-19 patients (PaO2/FiO2: 200-300 or respiratory rate > 24/min and SpO2 [≤] 93% on room air). InterventionParticipants were randomized to either control (best standard of care (BSC)) or intervention (CP + BSC) arm. Two doses of 200 mL CP was transfused 24 hours apart in the intervention arm. Main Outcome MeasureComposite of progression to severe disease (PaO2/FiO2< 100) or all-cause mortality at 28 days post-enrolment. ResultsBetween 22nd April to 14th July 2020, 464 participants were enrolled; 235 and 229 in intervention and control arm, respectively. Composite primary outcome was achieved in 44 (18.7%) participants in the intervention arm and 41 (17.9%) in the control arm [aOR: 1.09; 95% CI: 0.67, 1.77]. Mortality was documented in 34 (13.6%) and 31 (14.6%) participants in intervention and control arm, respectively [aOR) 1.06 95% CI: -0.61 to 1.83]. InterpretationCP was not associated with reduction in mortality or progression to severe COVID-19. This trial has high generalizability and approximates real-life setting of CP therapy in settings with limited laboratory capacity. A priori measurement of neutralizing antibody titres in donors and participants may further clarify the role of CP in management of COVID-19. Trial registrationThe trial was registered with Clinical Trial Registry of India (CTRI); CTRI/2020/04/024775.
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ObjectiveEstimate seroprevalence in representative samples from slum and non-slum communities in Mumbai, India, a mega-city in a low or middle-income country and test if prevalence is different in slums. DesignAfter geographically-spaced community sampling of households, one individual per household was tested for IgG antibodies to SARS-CoV-2 N-protein in a two-week interval. SettingSlum and non-slum communities in three wards, one each from the three main zones of Mumbai. ParticipantsIndividuals over age 12 who consent to and have no contraindications to venipuncture were eligible. 6,904 participants (4,202 from slums and 2,702 from non-slums) were tested. Main outcome measuresThe primary outcomes were the positive test rate for IgG antibodies to the SARS-CoV-2 N-protein by demographic group (age and gender) and location (slums and non-slums). The secondary outcome is seroprevalence at slum and non-slum levels. Sera was tested via chemiluminescence (CLIA) using Abbott Diagnostics ArchitectTM N-protein based test. Seroprevalence was calculated using weights to match the population distribution by age and gender and accounting for imperfect sensitivity and specificity of the test. ResultsThe positive test rate was 54.1% (95% CI: 52.7 to 55.6) and 16.1% (95% CI: 14.9 to 17.4) in slums and non-slums, respectively, a difference of 38 percentage points (P < 0.001). Accounting for imperfect accuracy of tests (e.g., sensitivity, 0.90; specificity 1.00), seroprevalence was as high as 58.4% (95% CI: 56.8 to 59.9) and 17.3% (95% CI: 16 to 18.7) in slums and non-slums, respectively. ConclusionsThe high seroprevalence in slums implies a moderate infection fatality rate. The stark difference in seroprevalence across slums and non-slums has implications for the efficacy of social distancing, the level of herd immunity, and equity. It underlines the importance of geographic specificity and urban structure in modeling SARS-CoV-2.
ABSTRACT
The novel coronavirus SARS-CoV2 has been observed to cause a higher incidence and greater severity of disease in males, as seen in multiple cohorts across the globe. The reasons for gender disparity in disease severity is unclear and can be due to host factors. To determine whether males have delayed viral clearance after infection, we evaluated the time to clearance in symptomatic patients tested by serial oropharyngeal/nasopharyngeal swabs followed by RT-PCR at a reference lab in Mumbai, India. A total of 68 subjects with median age of 37 years (3-75 range) were examined and included 48 (71%) males and 20 (29%) females. We observed that females were able to achieve viral clearance significantly earlier than males, with a median difference of 2 days in achieving a negative PCR result (P value = 0.038). Furthermore, examination of 3 families with both male and female patients followed serially, demonstrated that female members of the same household cleared the SARS-CoV2 infection earlier in each family. To determine reasons for delayed clearance in males, we examined the expression patterns of the SARS-CoV2 receptor, Angiotensin-converting enzyme 2 (ACE2), in tissue specific repositories. We observed that the testes was one of the highest sites of ACE2 expression in 3 independent RNA expression databases (Human Protein Atlas, FAMTOM5 and GETx). ACE2 was also determined to be highly expressed in testicular cells at the protein levels. Interestingly, very little expression of ACE2 was seen in ovarian tissue. Taken together, these observations demonstrate for the first time that male subjects have delayed viral clearance of SARS-CoV2. High expression of ACE2 in testes raises the possibility that testicular viral reservoirs may play a role in viral persistence in males and should be further investigated.
