COVID-19 variants in India: Potential role in second wave and impact on vaccination

COVID-19 pandemic - Cocktail of variants, a study from Northern India

Context

The aim of the study was to identify and monitor the circulating strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the samples received at our center and update the existing national and international genomic surveillance data.

Introduction

SARS-CoV-2 is no exception to the basic nature of the viruses ability to change and evolve. Since its first report in December 2019 from Wuhan, China, multiple variants of the virus have emerged and been reported. Five variants of concern have been recognized and reported by the Centers for Disease Control and Prevention, which are associated with variable degrees of transmissibility and mortality.

Materials and Methods

Nasopharyngeal and oropharyngeal swabs received in viral transport medium at the Viral Research Diagnostic Laboratory were processed for reverse transcription-polymerase chain reaction for SARS-CoV-2. Whole genome sequencing (WGS) was performed for selective positive samples using Oxford Nanopore sequencing technology, using MinKNOW software for data acquisition.

Statistical Analysis

The clades were assigned using Nextclade v2.4.1 software. The statistical analysis was calculated using OpenEpi version 3, an open-source calculator, and two by two.

Results

Variants reported over the study period included Alpha, Kappa, Delta, and Omicron. Delta dominated in the year 2021, while Omicron was the dominant variant in 2022. In both the dominant variants, asymptomatics contributed to around 30-40% of positives. Intensive care unit admissions and mortality were higher in the Delta variant, while vaccination history and travel history were higher in the patients with Omicron variant.

Conclusion

The trend tracking of these variants has been important in view of public health, enabling early interventions to control the spread of the disease and foresight in preparation for the situation.

The Role of Platelet Parameters in Predicting the Disease Severity of COVID-19 Patients: A Hospital-Based Study

Background and objective Globally, a large number of people have been impacted by the extremely contagious coronavirus disease 2019 (COVID-19) infection, and several pieces of literature were published on hematological parameter changes in this infection, particularly focusing on leucocytes. In this study, we have analyzed the platelet parameters and platelet-leucocyte ratios in COVID-19 patients and correlated them with the disease severity. Methods The COVID-19 patients who were hospitalized during the second peak of the pandemic were assessed. The platelet count and indices, platelet to lymphocyte ratio (PLR), neutrophil to platelet ratio (NPR), and clinical severity of each patient were analyzed. The significance of parameters and clinical severity was evaluated using analysis of variance (ANOVA) and the Kruskal Wallis test. A bivariate analysis was performed to assess the strength of the association. Receiver operating characteristic (ROC) curves were plotted to detect the predictive value of parameters for disease severity. Results The data of 132 COVID-19 patients has been evaluated. The average mean age was 45.60 ± 15.76 years with slight female predominance. Thrombocytopenia was found in 33% of cases with the majority of them being mild. Age, platelet distribution width (PDW), and PLR and NPR parameters were significantly (p-value <0.05) associated with disease severity. ROC curves showed age, PDW, PLR, NPR, absolute neutrophil count (ANC), and absolute lymphocyte count (ALC) had significant prediction values for clinical severity. Conclusions Platelet parameters may not accurately reflect the severity of the disease, but when combined with leucocyte parameters and their ratios (PLR and NPR), they offer important information about disease severity.

Semen proteomics reveals alterations in fertility-related proteins post-recovery from COVID-19

Introduction: Changes to sperm quality and decline in reproductive function have been reported in COVID-19-recovered males. Further, the emergence of SARS-CoV-2 variants has caused the resurgences of COVID-19 cases globally during the last 2 years. These variants show increased infectivity and transmission along with immune escape mechanisms, which threaten the already burdened healthcare system. However, whether COVID-19 variants induce an effect on the male reproductive system even after recovery remains elusive. Methods: We used mass-spectrometry-based proteomics approaches to understand the post-COVID-19 effect on reproductive health in men using semen samples post-recovery from COVID-19. The samples were collected between late 2020 (1st wave, n = 20), and early-to-mid 2021 (2nd wave, n = 21); control samples were included (n = 10). During the 1st wave alpha variant was prevalent in India, whereas the delta variant dominated the second wave. Results: On comparing the COVID-19-recovered patients from the two waves with control samples, using one-way ANOVA, we identified 69 significantly dysregulated proteins among the three groups. Indeed, this was also reflected by the changes in sperm count, morphology, and motility of the COVID-19- recovered patients. In addition, the pathway enrichment analysis showed that the regulated exocytosis, neutrophil degranulation, antibacterial immune response, spermatogenesis, spermatid development, regulation of extracellular matrix organization, regulation of peptidase activity, and regulations of calcium ion transport were significantly dysregulated. These pathways directly or indirectly affect sperm parameters and function. Our study provides a comprehensive landscape of expression trends of semen proteins related to male fertility in men recovering from COVID-19. Discussion: Our study suggests that the effect of COVID-19 on the male reproductive system persists even after recovery from COVID-19. In addition, these post-COVID-19 complications persist irrespective of the prevalent variants or vaccination status.

The Role of "Hierarchical and Classified Prevention and Control Measures (HCPC)" Strategy for SARS-CoV-2 Delta Variant in Guangzhou: A Modeling Study

BACKGROUND

The Delta variant of SARS-COV-2 has replaced previously circulating strains around the world in 2021. Sporadic outbreaks of the Delta variant in China have posed a concern about how to properly respond to the battle against evolving COVID-19. Here, we analyzed the "hierarchical and classified prevention and control (HCPC)" measures strategy deployed during the recent Guangzhou outbreak.

METHODS

A modified susceptible-exposed-pre-symptomatic-infectious-recovered (SEPIR) model was developed and applied to study a range of different scenarios to evaluate the effectiveness of policy deployment. We simulated severe different scenarios to understand policy implementation and timing of implementation. Two outcomes were measured: magnitude of transmission and duration of transmission. The outcomes of scenario evaluations were presented relative to the reality case (i.e., 368 cases in 34 days) with 95% confidence interval (CI).

RESULTS

Based on our simulation, the outbreak would become out of control with 7 million estimated infections under the assumption of the absence of any interventions than the 153 reported cases in reality in Guangzhou. The simulation on delayed implementation of interventions showed that the total case numbers would also increase by 166.67%-813.07% if the interventions were delayed by 3 days or 7 days.

CONCLUSIONS

It may be concluded that timely and more precise interventions including mass testing and graded community management are effective measures for Delta variant containment in China.

Plausible explanation for the third COVID-19 wave in India and its implications

Recently some of us used a random-walk Monte Carlo simulation approach to study the spread of COVID-19. The calculations were reasonably successful in describing secondary and tertiary waves of infection, in countries such as the USA, India, South Africa and Serbia. However, they failed to predict the observed third wave for India. In this work we present a more complete set of simulations for India, that take into consideration two aspects that were not incorporated previously. These include the stochastic movement of an erstwhile protected fraction of the population, and the reinfection of some recovered individuals because of their exposure to a new variant of the SARS-CoV-2 virus. The extended simulations now show the third COVID-19 wave for India that was missing in the earlier calculations. They also suggest an additional fourth wave, which was indeed observed during approximately the same time period as the model prediction.

Myocarditis post-SARS-CoV-2 vaccination: a systematic review

Variable clinical criteria taken by medical professionals across the world for myocarditis following coronavirus disease 2019 (COVID-19) vaccination along with wide variation in treatment necessitates understanding and reviewing the same. A systematic review was conducted to elucidate the clinical findings, laboratory parameters, treatment and outcomes of individuals with myocarditis after COVID-19 vaccination after registering with PROSPERO. Electronic databases including MEDLINE, EMBASE, PubMed, LitCovid, Scopus, ScienceDirect, Cochrane Library, Google Scholar and Web of Science were searched. A total of 85 articles encompassing 2184 patients were analysed. It was a predominantly male (73.4%) and young population (mean age: 25.5 ± 14.2 years) with most having taken an mRNA-based vaccine (99.4%). The mean duration from vaccination to symptom onset was 4.01 ± 6.99 days. Chest pain (90.1%), dyspnoea (25.7%) and fever (11.9%) were the most common symptoms. Only 2.3% had comorbidities. CRP was elevated in 83.3% and cardiac troponin in 97.6% patients. An abnormal ECG was reported in 979/1313 (74.6%) patients with ST-segment elevation being most common (34.9%). Echocardiographic data were available for 1243 patients (56.9%), of whom 288 (23.2%) had reduced left ventricular ejection fraction. Non-steroidal antiinflammatory drugs (76.5%), steroids (14.1%) followed by colchicine (7.3%) were used for treatment. Only 6 patients died among 1317 of whom data were available. Myocarditis following COVID-19 vaccination is often mild, seen more commonly in young healthy males and is followed by rapid recovery with conservative treatment. The emergence of this adverse event calls for harmonizing case definitions and definite treatment guidelines, which require wider research.

Delta variant (B.1.617.2) of SARS-CoV-2: current understanding of infection, transmission, immune escape, and mutational landscape

The Delta variant is one of the alarming variants of the SARS-CoV-2 virus that have been immensely detrimental and a significant cause of the prolonged pandemic (B.1.617.2). During the SARS-CoV-2 pandemic from December 2020 to October 2021, the Delta variant showed global dominance, and afterwards, the Omicron variant showed global dominance. Delta shows high infectivity rate which accounted for nearly 70% of the cases after December 2020. This review discusses the additional attributes that make the Delta variant so infectious and transmissible. The study also focuses on the significant mutations, namely the L452R and T478K present on the receptor-binding domain of spike (S)-glycoprotein, which confers specific alterations to the Delta variant. Considerably, we have also highlighted other notable factors such as the immune escape, infectivity and re-infectivity, vaccine escape, Ro number, S-glycoprotein stability, cleavage pattern, and its binding affinity with the host cell receptor protein. We have also emphasized clinical manifestations, symptomatology, morbidity, and mortality for the Delta variant compared with other significant SARS-CoV-2 variants. This review will help the researchers to get an elucidative view of the Delta variant to adopt some practical strategies to minimize the escalating spread of the SARS-CoV-2 Delta variant.

Perspective Chapter: SARS-CoV-2 Variants - Two Years Post-Onset of the Pandemic

Since the pandemic began in China in December 2019, thousands of variants of SARS-CoV-2 have emerged globally since late 2020. The World Health Organization (WHO) defined the SARS-CoV-2 variant of concern (VOC) as a variant with increased transmissibility, virulence, and decreased response to available diagnostics, vaccines, and therapeutics. Areas of the emerging variant of concern arise from countries like the United Kingdom, South Africa, Brazil, and India. These mutations carry a lineage from N501Y, D614G, N439K, Y453F, and others, which are globally dominated by clades 20A, 20B, and 20C. SARS-CoV-2 VOC emerged after 11 months of evolution since the onset through massive human-to-human transmission with five major VOCs recognized by the WHO, namely Alpha, Beta, Gamma, Delta, and Omicron. Their emergence could be attributed to changing immunological dynamics in the human population, which has resulted in resistance or escape from neutralizing antibodies, or to mutations and/or recombinations that increase transmission or pathogenicity. This literature review intends to identify and report on SARS-CoV-2 variants that have evolved two years post-onset of the pandemic and their disease implications.

Effect of COVID-19 vaccination status on outcome of adult patients admitted at a tertiary care centre in India

COVID-19 vaccination was initially started in India on 16th January 2021 after approval from national authorities. This study was carried out to assess the effect of vaccination status on the severity and clinical outcome among patients infected with COVID-19. The study included all adult COVID-19 patients admitted to our hospital from 1st April to 30th June 2021. A total of 819 patients were enrolled in the study out of which only 183 (22.3%) were vaccinated. The study documented a statistically significant reduction in the severity of illness among the vaccinated (single/double dose) (33% severe COVID-19) against the unvaccinated (43% severe COVID-19) groups; along with a reduction in mortality. On univariate and multivariate analysis, age, severity of illness and lack of COVID-19 vaccination status were associated with a statistically significant increased mortality. To conclude, this study demonstrates the role of vaccination in decreasing the severity and mortality of COVID-19 infection.

Impact of prior vaccination with CovishieldTM and Covaxin® on mortality among symptomatic COVID-19 patients during the second wave of the pandemic in South India during April and May 2021: a cohort study

BACKGROUND

COVID-19 vaccines were authorised for emergency use to mitigate the impact of the pandemic. This study evaluated the effect of prior vaccination with either Oxford Astra Zeneca's Covishield™ or Bharath Biotech's Covaxin® on mortality among symptomatic COVID-19 patients during the second wave of the pandemic in India.

METHODOLOGY

In this cohort study comprising of RT-PCR confirmed symptomatic COVID-19 patients presenting during April and May 2021, the effect of prior vaccination on mortality (primary outcome), need for hospitalization, oxygen therapy, non-invasive ventilation (NIV) and intensive care unit (ICU) admission were assessed and expressed as risk ratio (RR) with 95% confidence intervals (CI).

RESULTS

The mean (SD) age of the cohort (n = 4183) was 46.3 (15.5) years; 17.9% (748/4183) had received at least one dose of Covishield™ and 4.8% (201/4183) had received Covaxin®. Mortality was 0.2% (95% CI: 0.2% - 0.7%), 3.5% (1.9-5.2%), 6.2% (0.3-12%) and 12.9% (11.8-14.1%) among fully vaccinated (>2 weeks after two doses), partially vaccinated (>2 weeks after one dose or <2 weeks after two doses), indeterminate (<2 weeks after one dose) and unvaccinated patients respectively. The difference in mortality among unvaccinated vs. fully vaccinated was 12.7% (95% CI: 11.4-13.9%), unvaccinated vs. partially vaccinated was 9.4% (7.4-11.4%) and unvaccinated vs. indeterminate vaccinated was 6.8% (0.8-12.7%). On adjusted analysis, as compared to unvaccinated patients, at least one dose of vaccine reduced the need for hospitalization (RR: 0.40; 95% CI: 0.35-0.47), oxygen (0.33; 0.27-0.40), NIV (0.23; 0.17-0.32), ICU admission (0.18; 0.12-0.27) and mortality (0.18; 0.11-0.29).

CONCLUSION

Among symptomatic COVID-19 patients, prior vaccination with Covishield ™ or Covaxin® impacted the severity of illness and reduced mortality during a period of widespread delta variant circulation. Full vaccination conferred greater protection than partial vaccination.

SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines

With the high rate of COVID-19 infections worldwide, the emergence of SARS-CoV-2 variants was inevitable. Several mutations have been identified in the SARS-CoV-2 genome, with the spike protein as one of the mutational hot spots. Specific amino acid substitutions such as D614G and N501Y were found to alter the transmissibility and virulence of the virus. The WHO has classified the variants identified with fitness-enhancing mutations as variants of concern (VOC), variants of interest (VOI) or variants under monitoring (VUM). The VOCs pose an imminent threat as they exhibit higher transmissibility, disease severity and ability to evade vaccine-induced and natural immunity. Here we review the mutational landscape on the SARS-CoV-2 structural and non-structural proteins and their impact on diagnostics, therapeutics and vaccines. We also look at the effectiveness of approved vaccines, antibody therapy and convalescent plasma on the currently prevalent VOCs, which are B.1.17, B.1.351, P.1, B.1.617.2 and B.1.1.529. We further discuss the possible factors influencing mutation rates and future directions.

Positivity rate: an indicator for the spread of COVID-19

OBJECTIVE

This paper investigates the relationship between the positivity rate and numbers of deaths and intensive care unit (ICU) patients. In addition, it explores the use of the positivity rate as an indicator for the spread of COVID-19.

METHODS

We used COVID-19 datasets for eight countries - Canada, USA, UK, Italy, Belgium, Ireland, Colombia and South Africa - and considered two correlation cases. The first case considers the correlation of the number of confirmed cases with each of deaths and ICU patients. The second case considers the correlation of the positivity rate with each of deaths and ICU patients. When obtaining the correlation, we considered different lagging periods between the date of confirming a case and the date of its ICU admittance or death. We compared the obtained correlation coefficient values for each of the two considered cases to explore whether the positivity rate is a better indicator for the spread of the disease than confirmed cases. For each of the eight considered countries, we obtained the daily reproduction number using each of confirmed cases and positivity rate. The two obtained sets of reproduction number values for each country were statistically compared to investigate whether they are significantly different.

RESULTS

When considering the daily positivity rate instead of the daily number of confirmed cases, the maximum correlation with deaths is increased by 349.9% for the USA (the country with the highest increase) and 4.5% for the UK (the country with the lowest increase), with an average increase of 60.8% considering the eight countries. Considering the daily positivity rate instead of the daily number of confirmed cases caused the maximum correlation with the number of ICU patients to be increased by 74.7% for the USA (the country with the highest increase) and 2.2% for the UK (the country with the lowest increase), with an average increase of 25% over the considered countries. The results for the daily reproduction number obtained using the positivity rate are statistically different from those obtained using daily confirmed cases.

CONCLUSION

The results indicate that positivity rate is a better indicator for the spread of the disease than the number of confirmed cases. Therefore, it is highly advised to use measures based on the positivity rate when indicating the spread of the disease and considering responses accordingly because these measures consider the daily number of tests and confirmed cases.

Mortality among adult hospitalized patients during the first wave and second wave of COVID-19 pandemic at a tertiary care center in India

The similarities and differences between the mortality patterns of the two waves in India remain largely unknown. This was a retrospective study of medical records conducted in the COVID data center of our hospital This study analyzed data of patients who died in the month of August, 2020 to October 2020 (one month before and after the peak of first wave i.e., 16th September, 2020) & April 2021 to June 2021 (one month before and after the peak of second wave i.e., 6th May, 2021), corresponding to an equal part of the pandemic during first (2020) and second (2021) wave. Out of 1893 patients in the study, 764 patients were admitted during the first wave and 1129 patients during the second wave of pandemic. In total, 420 patients died during the entire study period. Of those, 147 (35%) deaths occurred during the first wave and 273 (65%) during the second wave, reflecting a case fatality rate (CFR) of 19.2% during the first wave and a CFR of 24.18%. There were no significant differences in the Age Group, Gender, Presenting Complaints, Duration of Stay and Comorbidities. However, the deceased COVID-19 patients had an increase in Case Fatality Rate, average duration of symptoms from onset to Hospital Admission (DOSHA) and a major shift from MODS to ARDS being the Cause of Death during the second wave of Pandemic. This study demonstrates increased CFR, average DOSHA and a paradigm shift to ARDS as cause of mortality during the second peak of the Pandemic. It is necessary to remain vigilant of newer COVID-19 variants of concern, follow COVID-19 appropriate behaviors and keep emphasizing on care of high-risk groups including patients with comorbidities and elderly population to prevent mortality.

Second Wave of the COVID-19 Pandemic in Delhi, India: High Seroprevalence Not a Deterrent?

Background We report the findings of a large follow-up, community-based, cross-sectional serosurvey and correlate it with the coronavirus disease (COVID-19) test-positivity rate and the caseload observed between the peaks of the first and the second wave of the COVID-19 pandemic in Delhi, India. Methodology Individuals aged five and above were recruited from 274 wards of the state (population approximately 19.6 million) from January 11 to January 22, 2021. A total of 100 participants each were included from all wards for a net sample size of approximately 28,000. A multistage sampling technique was employed to select participants for the household serosurvey. Anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunoglobulin (IgG) antibodies were detected by using the VITROS® (Ortho Clinical Diagnostics, Raritan, NJ, USA) assay (90% sensitivity, 100% specificity). Results Antibody positivity was observed in 14,298 (50.76%) of 28,169 samples. The age, sex, and district population-weighted seroprevalence of the SARS-CoV-2 IgG was 50.52% (95% confidence interval [CI] = 49.94-51.10), and after adjustment for assay characteristics, it was 56.13% (95% CI = 55.49-56.77). On adjusted analysis, participants aged ≥50 years, of female gender, housewives, having ever lived in containment zones, urban slum dwellers, and diabetes or hypertensive patients had significantly higher odds of SARS-CoV-2 antibody positivity. The peak infection rate and the test-positivity rate since October 2020 were initially observed in mid-November 2020, with a subsequent steep declining trend, followed by a period of persistently low case burden lasting until the first week of March 2021. This was followed by a steady increase followed by an exponential surge in infections from April 2021 onward culminating in the second wave of the pandemic. Conclusions The presence of infection-induced immunity from SARS-CoV-2 even in more than one in two people can be ineffective in protecting the population. Despite such high seroprevalence, population susceptibility to COVID-19 can be accentuated by variants of concern having the ability for rapid transmission and depletion of antibody levels with the threat of recurrent infections, signifying the need for mass vaccination.

Impact of preoperative COVID infection on the outcomes of planned curative-intent cancer surgeries in the second wave of the pandemic from a tertiary care center in India

Background

Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) pandemic was an unforeseen calamity. Sudden disruption of nonemergency services led to disruption of treatment across all specialties. Oncology revolves around the tenet of timely detection and treatment. Disruption of any sort will jeopardize cure rates. The time interval between coronavirus infection and cancer surgery is variable and needs to be tailored to avoid the progression of the disease.

Methods

We analyzed the impact of preoperative coronavirus disease 2019 (COVID‐19) infection on the planned cancer surgery, delay, disease progression, and change of intent of treatment from April 1 to May 31, 2021 at a tertiary care center. All preoperative positive patients were retested after 2 weeks and were considered for surgery if the repeat test was negative and asymptomatic.

Findings

Our study included 432 preoperative patients of which 91 (21%) were COVID‐19 positive. Amongst this cohort, 76% were operated and the morbidity and mortality were comparable to the COVID‐19 negative cohort. Around 10% of the COVID‐19 positive were lost to follow up and 10% had disease progression and were deemed palliative

Interpretation

SARS‐CoV‐2 infection has adversely impacted cancer care and a 2‐week waiting period postinfection seems to be a safe interval in asymptomatic individuals to consider radical cancer surgery.

Genetic emergence of B.1.617.2 in COVID-19

Many proactive steps have been taken worldwide to fight against the SARS-CoV-2 pandemic and to prevent COVID-19 spread with realistic approaches. Recently, a novel variant B.1.617.2 has been identified in India, which is rapidly transmitting to other countries, challenging current therapeutics, wide vaccination and future research in COIVD-19.