Natural immunity against COVID-19 significantly reduces the risk of reinfection: findings from a cohort of sero-survey participants

Conflicting reports on the persistence of antibody levels in individuals recovered from COVID-19 infection, suggest that the immunity against COVID-19 may not be lasting for long. In India, by 30th June, 2021, not less than 30 million people were infected with COVID-19 and 0.39 million people were reported to have lost their life to the disease in India. I the current study we followed up with a subsample of our previous sero-survey participants to assess whether natural immunity against SARS-CoV-2 was associated with a reduced risk of re-infection. We conducted telephonic interview of a total of 3038 participants, out of which 2238 participants responded and 5 participants were found to be not alive, as conveyed by their close relatives. There was a non-response rate of 26.1%. Out of the 2238 participants, 1170 were sero-positive and 1068 were sero-negative for antibody against COVID-19. Our survey found that only 3 individuals in the sero-positive group got infected with COVID-19 whereas 127 individuals reported contracting the infection the sero-negative group. Interestingly, from the 127 sero-negative individuals who later contracted COVID-19 infection, 30 needed hospitalization, out of which 12 were on oxygen therapy, four in ICU and one was on ventilator. At the other hand, from the 3 sero-positives re-infected with COVID-19, one had hospitalization, but didnnot require oxygen support or critical care. These findings reinforce the strong plausibility that development of antibody following natural infection not only protects against re-infection by the virus to a great extent, but also safeguards against progression to severe COVID-19 disease.

Seroprevalence of anti-SARS-CoV-2 IgG antibody among health care workers of anaesthesia departments from various hospital settings in India

BackgroundHealth care workers (HCWs) are the most susceptible group to get COVID-19 infection and this group always need special attention as they are the key human resource to contain this pandemic. ObjectiveTo track down the seroprevalence among a particular group of HCWs working in the anaesthesia department in hospital settings. Study designTwo rounds of serosurvey were done to track the dynamicity among the 128 and 164 HCWs participants in the first round and second round, respectively. 5 mL of blood was collected and anti-SARS-CoV-2 IgG antibody was tested in Abbott Architect i1000SR. ResultsThe seroprevalence found in the first and second round was 12.5% and 38.4%, respectively. A significant number (n=61, 77.21%) of seropositivity came from the asymptomatic HCWs group as found in both the survey. There was no significant association among different age, gender and RT-PCR tested groups. ConclusionRoutine diagnosis of COVID-19 should be referred among HCWs to identify and act upon unrecognized SARS-CoV-2 infection.

SARS-CoV-2 IgG antibody responses in rt-PCR positive cases: first report from India

The SARS-CoV-2 antibody responses remain poorly understood and the clinical utility of serological testing is still unclear. As it is thought to confer some degree of immunity, this study is carried out to know the relationship between demographics and ct value of confirmed rt-PCR patients. A total of 384 serum samples were collected between 4-6 weeks after confirmed SARS-CoV-2 infection. IgG positivity was found to be 80.2% (95% CI, 76.2 - 84.2). The IgG positivity increased with the decrease in the ct value, with highest of 87.6% positivity in individuals with <20 ct value. The mean ({+/-} SD) ct value of IgG positives and og IgG negatives was 23.34 ({+/-} 6.09) and 26.72 ({+/-} 7.031) respectively. There was no significant difference found between the demographic characteristics such as age, sex, symptoms and antibody response. The current study is first of its kind wherein we have assessed the correlation of ct of RT-PCR with development of IgG against SARS-CoV-2. Our study showed that although Ct value might not have any relation with severity of the diseases but is associated with the antibody response among the SARS-CoV-2 infected individual.

Situation of labour room documentation at secondary level public health facilities of Cuttack district, Odisha, India - A SWOT analysis.

BACKGROUND: Poor documentation practices in labour rooms have been a challenge especially in resource limited countries. This hinders the efforts towards improving quality of maternal healthcare services. Little effort has been made on this regard in many countries including India. SWOT analysis on labour room documentation would be the first step in understanding the situation, barriers and to formulate strategies for improvement. MATERIALS AND METHODS: Facility based cross-sectional study was carried out in five secondary health facilities of Cuttack district, Odisha, India. A qualitative method using in-depth interviews among 26 healthcare providers was adopted for data collection and inductive content analysis approach for analysis. Strategies like pioneering, positive, conservative and resistive were formulated under each of the three major components identified. RESULTS: Three major components emerged were i) Adherence and completeness of labour room records and reports, ii) Status of the monitoring and supervision and iii) Utilization of labour room data. Improving knowledge and skill through training and supportive supervision, adopting computer-based application for data management, better coordination among supervisors and labour room staff, infrastructural strengthening for documentation and its security, making documentation a priority, more accountability would improve the documentation. Ensuring data analysis and interpretation, discussion in review meetings and regular monitoring and supervision will improve performance. CONCLUSION: Ensuring documentation of labour room records, regular quality monitoring and supervision, and analysis and interpretation of data are critical to improve labour room performance. Making it a priority and adopting the strategies will achieve the same, thereby better labour outcome.

Findings from serological surveys (in August 2020) to assess the exposure of adult population to SARS Cov-2 infection in three cities of Odisha, India.

BackgroundThere is always an uncertainty of epidemiological, serological infectivity and virulence of the emerging novel coronavirus. Antibody test can be used for assessing whether immunity has developed in the infected person after 5-7 days of illness and understand cumulative exposure levels to the infection, make inferences on the actual burden of infection, its geographical spread, effect on specific demographic/risk groups, gaps in testing and infection fatality rates. ObjectiveTo estimate and compare the sero-prevalence, hidden prevalence and determine the demographic risk factors associated with SARS-CoV-2 infection among adults in three largest cities of Odisha, India. MethodologyThis was a population based cross sectional serological survey carried out in August 2020 in the three largest cities of the state of Odisha. Sample size per city was estimated to be 1500 and participants were enrolled from the community using multi-stage random sampling from 25 clusters from each city. Data was collected using ODK based tools by household visits and 3-4 ml of blood samples were collected after informed consent. Samples were transported to testing lab where Serum was separated and tested for anti-SARS CoV-2 antibodies using automated CLIA platform. Statistical analysis was done using R-software packages. ResultsA total of 4146 participants from the 3 cities of Bhubaneswar (BBS), Berhampur (BAM) and Rourkela (RKL) participated. A total of 5635 households were approached and the average non response rate in the community was 17.4%. The gender weighted seroprevalence across the three cities was 20.78% (95% CI: 19.56%-22.05%). Seroprevalence was highest in BAM at 31.14% (95% CI: 28.69-33.66%) followed by 24.59% (95% CI: 22.39-26.88%) in RKL and 5.24% (95% CI: 4.10-6.58%) in BBS. While females reported a higher seroprevalence (22.8%) as compared to males (18.8%), there was no significant difference in seroprevalence across age groups. A majority of the seropositive participants were asymptomatic (93.87%). Among those who reported symptoms, the most common symptom was fever (68.89%) followed by cough (46.06%) and myalgia (32.67%). The case to infection ratio on the date of serosurvey was 1: 6.6 in BBS, 1:61 in BAM and 1:29.8 in RKL. ConclusionThe study found a high seroprevalence against COVID-19 in urban Odisha as well as high numbers of asymptomatic infections.

Diagnostic comparison of three fully automated chemiluminescent immunoassay platforms for the detection of SARS-CoV-2 antibodies

The whole world is battling against coronavirus disease-19 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Various strategies are taken to curb the spread of the virus and to move out from the enforced lockdown stage. Serological tests are the neediest diagnostic and surveillance tool to complement the gold standard molecular diagnostic method to track down the transmission rate of SARS-CoV-2. Automated chemiluminescent immunoassay (CLIA) based analyzers become highly demanding platforms both to clinicians and policy makers for the detection anti-SARS-CoV-2 antibodies. In this study, serum from 594 patients positive for COVID-19 and 100 samples from pre-COVID cases were tested by three automated platforms: Abbott architect i2000SR, Roche cobas e411 and Yhlo iFlash 1800 and their diagnostic accuracy were compared. All three platforms showed high specificity as claimed by manufacturer. Clinical sensitivities of the machines were calculated as 64.48% (58.67-70.3) for Abbott, 80.48% (76.62-84.34) for Roche and 76.94% (72.65-81.23) for Yhlo. The Cohens kappa value was determined from 0.69-0.89 when inter-rater agreements were calculated. The area under the curves (AUC) values demonstrated Roche Cobas e411 as the diagnostically most accurate platform among the three CLIA analyzers.

Saliva as a potential clinical specimen for diagnosis of SARS-CoV-2

Background It is almost nine months, still there is no sign to stop the spreading of the COVID-19 pandemic. Rapid and early detection of the virus is the master key to cease the rapid spread and break the human transmission chain. There are very few studies in search of an alternate and convenient diagnostic tool which can substitute nasopharyngeal swab (NPS) specimen for detection of SARS-CoV-2. We aimed to analyse the comparison and agreement between the feasibility of using the saliva in comparison to NPS for diagnosis of SARS-CoV-2. Methods A total number of 74 patients were enrolled for this study. We analysed and compared the NPS and saliva specimen collected within 48 h after the symptom onset. We used real time quantitative polymerase chain reaction (RT-qPCR), gene sequencing for the detection and determination SARS-CoV-2 specific genes. Phylogenetic tree was constructed to establish the isolation of viral RNA from saliva. We use Bland-Altman model to identify the agreement between two sampling methods. Findings This study shows a lower CT mean value for the detection of SARS-CoV-2 ORF1 gene (27.07; 95% CI, 25.62 to 28.52) in saliva methods than that of NPS (28.24; 95% CI, 26.62 to 29.85) sampling method. Bland-Altman analysis produces relatively smaller bias and high agreement between these specimen tools. Phylogenetic analysis with the RdRp and Spike gene confirmed the presence of SARS-CoV-2 in the saliva samples. Interpretation: In conclusion, our study highlights that saliva represents a promising tool in COVID-19 diagnosis and would reduce the exposure risk of frontline health workers which is one of biggest concern in primary healthcare settings.

Sequence analysis of Indian SARS-CoV-2 isolates shows a stronger interaction of mutated receptor binding domain with ACE2 receptor

SARS-CoV-2 is a RNA Coronavirus responsible for the pandemic of the Severe Acute Respiratory Syndrome (COVID-19). It has affected the whole world including Odisha, a state in eastern India. Many people migrated in the state from different countries as well as states during this SARS-CoV-2 pandemic. As per the protocol laid by ICMR and Health & Family welfare of India, all the suspected cases were tested for SARS-CoV-2 infection. The aim of this study was to analyze the RNA binding domain (RBD) sequence of spike protein from the isolates collected from the throat swab samples of COVID-19 positive cases and further to assess the RBD affinity with ACE2 of different species including human. Whole genome sequencing for 35 clinical SARS-CoV-2 isolates from COVID-19 positive patients was performed using ARTIC amplicon based sequencing. Sequence analysis and phylogenetic analysis was carried out for the Spike and RBD region of all isolates. The interaction between the RBD and ACE2 receptor of five different species was also analysed. Except three isolates, spike region of 32 isolates showed one/multiple alterations in nucleotide bases in comparison to the Wuhan reference strain. One of the identified mutation at 1204 (Ref A, RMRC 22 C) in the RBD of spike protein was identified which depicted a stronger binding affinity with human ACE2 receptor compared to the wild type RBD. Furthermore, RBDs of all the Indian isolates are capable of binding to ACE2 of human, bat, hamster and pangolin. As mutated RBD showed stronger interaction with human ACE2, it could potentially result in higher infectivity. The study shows that RBDs of all the studied isolates have binding affinity for all the five species, which suggests that the virus can infect a wide variety of animals which could also act as natural reservoir for SARS-CoV-2.

PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Reveals Important Insights into the Outbreak

The PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Consortium has achieved its initial goal of completing the sequencing of 1000 SARS-CoV-2 genomes from nasopharyngeal and oropharyngeal swabs collected from individuals testing positive for COVID-19 by Real Time PCR. The samples were collected across 10 states covering different zones within India. Given the importance of this information for public health response initiatives investigating transmission of COVID-19, the sequence data is being released in GISAID database. This information will improve our understanding on how the virus is spreading, ultimately helping to interrupt the transmission chains, prevent new cases of infection, and provide impetus to research on intervention measures. This will also provide us with information on evolution of the virus, genetic predisposition (if any) and adaptation to human hosts. One thousand and fifty two sequences were used for phylodynamic, temporal and geographic mutation patterns and haplotype network analyses. Initial results indicate that multiple lineages of SARS-CoV-2 are circulating in India, probably introduced by travel from Europe, USA and East Asia. A2a (20A/B/C) was found to be predominant, along with few parental haplotypes 19A/B. In particular, there is a predominance of the D614G mutation, which is found to be emerging in almost all regions of the country. Additionally, mutations in important regions of the viral genome with significant geographical clustering have also been observed. The temporal haplotype diversities landscape in each region appears to be similar pan India, with haplotype diversities peaking between March-May, while by June A2a (20A/B/C) emerged as the predominant one. Within haplotypes, different states appear to have different proportions. Temporal and geographic patterns in the sequences obtained reveal interesting clustering of mutations. Some mutations are present at particularly high frequencies in one state as compared to others. The negative estimate Tajimas D (D = -2.26817) is consistent with the rapid expansion of SARS-CoV-2 population in India. Detailed mutational analysis across India to understand the gradual emergence of mutants at different regions of the country and its possible implication will help in better disease management.

SARS-CoV2 genome analysis of Indian isolates and molecular modelling of D614G mutated spike protein with TMPRSS2 depicted its enhanced interaction and virus infectivity

COVID-19 that emerged as a global pandemic is caused by SARS-CoV-2 virus. The virus genome analysis during disease spread reveals about its evolution and transmission. We did whole genome sequencing of 225 clinical strains from the state of Odisha in eastern India using ARTIC protocol-based amplicon sequencing. Phylogenetic analysis identified the presence of all five reported clades 19A, 19B, 20A, 20B and 20C in the population. The analyses revealed two major routes for the introduction of the disease in India i.e. Europe and South-east Asia followed by local transmission. Interestingly, 19B clade was found to be much more prevalent in our sequenced genomes (17%) as compared to other genomes reported so far from India. The haplogroup analysis for clades showed evolution of 19A and 19B in parallel whereas the 20B and 20C appeared to evolve from 20A. Majority of the 19A and 19B clades were present in cases that migrated from Gujarat state in India suggesting it to be one of the major initial points of disease transmission in India during month of March and April. We found that with the time 20A and 20B clades evolved drastically that originated from central Europe. At the same time, it has been observed that 20A and 20B clades depicted selection of four common mutations i.e. 241 C>T (5UTR), P323L in RdRP, F942F in NSP3 and D614G in the spike protein. We found an increase in the concordance of G614 mutation evolution with the viral load in clinical samples as evident from decreased Ct value of spike and Orf1ab gene in qPCR. Molecular modelling and docking analysis identified that D614G mutation enhanced interaction of spike with TMPRSS2 protease, which could impact the shedding of S1 domain and infectivity of the virus in host cells.

A pilot study to investigate the fecal dissemination of SARS-CoV-2 virus genome in COVID-19 patients in Odisha, India

In infectious diseases, the routes of transmission play major roles in determining the rate and extent of disease spread. Though fomites and aerosol droplets are major sources of SARS-CoV-2 human to human transmission, studies have also reported possible involvement of other routes of transmission like fecal-oral. Multiple studies around the world have reported shedding of the SARS-CoV-2 viral genome in certain COVID-19 patient fecal samples. Hence, the major objective of this study was to get the experimental evidence whether in Indian COVID-19 patients fecal dissemination of the SARS-CoV-2 genome occurs or not. Information obtained from twelve number of patients from a COVID-19 hospital of Odisha has demonstrated that both symptomatic and asymptomatic Indian patients could be positive for the SARS-CoV-2 genome in their fecal component. The findings have also established a protocol to collect and extract viral RNA for SARS-CoV-2 detection in fecal samples. Together, the study supports the hypothesis of possible fecal-oral transmission of SARS-CoV-2 virus and provides a rationale to extend this study in a larger cohort of patient samples and correlate the significance of the SARS-CoV-2 virus genome detection in fecal samples with disease severity and transmission.