COVID, Volume 2, Issue 6 (June 2022) – 8 articles

Coronavirus disease 2019 (COVID-19) has been causing negative impacts on various sectors in Sri Lanka, as a result of the public health interventions that the government had to implement in order to reduce the spread of the disease. Equivalent work carried out in this context is outdated and close to ideal models. This paper presents a mathematical epidemiological model, called SEQIJRDS, having additional compartments for quarantine and infected people divided into two compartments as diagnosed and non diagnosed, compared to the SEIR model. We have presented the rate equations for the model and the basic reproduction number is derived. This model considers the effect of vaccination, the viral load of the variants, mask use, mobility, contact tracing and quarantine, natural immunity development of the infected people, and immunity waning of the recovered group as key developments of the model. The model has been validated for the COVID-19 pandemic in Sri Lanka by parameter derivation using mathematical formulations with the help of the existing data, the literature, and by model fitting for historical data. We present a comparison of the model projections for hospitalized infected people, the cumulative death count, and the daily death count against the ground truth values and projections of the SEIR and SIR models during the model validation. The validation results show that the proposed SEQIJRDS model’s 12-week projection performance is significantly better than both the SEIR and SIR models; the 2-, 6-, 8-, and 10-week projection performance is always better, and the 4-week projection performance is only slightly inferior to other models. Using the proposed SEQIJRDS model, we project mortality under different lockdown procedures, vaccination procedures, quarantine practices, and different mask-use cases. We further project hospital resource usage to understand the best intervention that does not exhaust hospital resources. At the end, based on an understanding of the effect of individual interventions, this work recommends combined public health interventions based on the projections of the proposed model. Specifically, three recommendations—called minimum, sub-optimum, and optimum recommendations—are provided for public health interventions. Full article

In the past, epidemics such as AIDS, measles, SARS, H1N1 influenza, and tuberculosis caused the death of millions of people around the world. In response, intensive research is evolving to design efficient drugs and vaccines. However, studies warn that new pandemics such as Coronavirus (COVID-19), variants, and even deadly pandemics can emerge in the future. The existing epidemic confinement approaches rely on a large amount of available data to determine policies. Such dependencies could cause an irreversible effect before proper strategies are developed. Furthermore, the existing approaches follow a one-size-fits-all control technique, which might not be effective. To overcome this, in this work, we develop a game-theory-inspired approach that considers societal and economic impacts and formulates epidemic control as a non-zero-sum game. Further, the proposed approach considers the demographic information that provides a tailored solution to each demography. We explore different strategies, including masking, social distancing, contact tracing, quarantining, partial-, and full-lockdowns and their combinations, and present demography-aware optimal solutions to confine a pandemic with minimal history information and optimal impact on the economy. To facilitate scalability, we propose a novel graph learning approach, which learns from the previously obtained COVID-19 game outputs and mobility rates of one state (region) depending on the other to produce an optimal solution. Our optimal solution is strategized to restrict the mobility between states based on the impact they are causing on COVID-19 spread. We aim to control the COVID-19 spread by more than 50% and model a dynamic solution that can be applied to different strains of COVID-19. Real-world demographic conditions specific to each state are created, and an optimal strategic solution is obtained to reduce the infection rate in each state by more than 50%. Full article

SARS-CoV-2 emerged as a new respiratory virus spreading rapidly to all areas of the world. A systematic review with meta-analysis concerning the use of Loop-Mediated Isothermal Amplification (LAMP) methodology targeting the SARS-CoV-2 nucleoprotein (N) gene was conducted. The search resulted in 229 articles, of which 19 articles were selected to compose the final review. In general, LAMP showed a high specificity in the detection of SARS-CoV-2 and a wide variation of sensitivity values. The LAMP method was considered a fast and highly specific method for SARS-CoV-2 detection; however, some variables may affect its sensitivity and overall performance. Full article

Background: Antigen tests for SARS-CoV-2 testing are rapid and inexpensive but usually have lower sensitivity than RT-qPCR and are only validated for nasopharyngeal/throat swabs; the latter are considered the gold standard in terms of material collection but are not tolerated by patients with frequent sampling. The present study, therefore, investigates the extent to which SARS-CoV-2 antigen testing is comparable to RT-qPCR from an easily obtained gargle solution compared to nasopharyngeal swabs. Methods: The performance of a high-quality POC fluorescence immune antigen test in single nasal swab samples and gargle samples compared to RT-qPCR was investigated (total n = 620 samples (gargle samples = 309, and nasal swabs = 311)). Findings: In our setting, the detection of SARS-CoV2 with an antigen test was reliable up to a Ct value of 30 for single nasal swab samples and was reduced to Ct:20 for single gargle samples. The overall antigen-test sensitivity is 83.92% (swab samples) and 75.72% (gargle samples). Interpretation: Antigen tests showed reliable results up to a detection limit of Ct: 30 with only nasal swab samples but not gargle samples. If the use of gargle samples is preferred due to their advantages, such as painless testing, easy handling, and the lack of a need to involve trained personnel for sample taking, reliable results can only be achieved with RT-qPCR. Full article

A new class of coronavirus, known as the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been discovered, which is responsible for the occurrence of the disease, COVID-19. A comparative study with SARS, MERS and other human viruses was conductedand concluded that SARS-CoV-2 spread more rapidly due to increased globalization and adaptation of the virus in every environment. According to recent WHO reports, by 16 May 2021, the current outbreak of COVID-19 had affected over 174,054,314 people and killed more than 3,744,116 people in more than 222 countries acrossthe world. Finding a solution against the deadly COVID-19 has become an enormous challenge for researchers and virologists. A ring vaccination trial, which recruits subjects connected to a known case either socially or geographically, is a solution to evaluate vaccine efficacy and control the spread of the disease simultaneously, although its implementation is challenging. This review aims to summarize the noteworthy features of the world-intimidating SARS-CoV-2 global pandemic along with its evaluation, problems and challenges in the treatment strategies, clinical efficiency and detection methods proposed so far. This paper describes the impact of the lockdown in response to the COVID-19 pandemic on social, economic, health, and National Health Programs in India; possible ways to control the disease are also discussed. Full article

Tracheomegaly (TM) is a rare appearance that is radiologically defined as an excessive enlargement of the tracheal diameter. We present a comprehensive analysis of tracheal diameter measurements and TM incidence in patients admitted and treated due to COVID-19 pneumonitis and its association with possible respiratory complications. In this retrospective study, we included 1015 patients divided into three groups: 383 patients treated using mechanical ventilation (MV), 132 patients treated using high-flow ventilation (HFV), and 500 randomly selected patients using nasal catheter (NC) oxygenation. The tracheal lumen diameter was measured continuously using a chest X-ray, and the cuff/trachea (C/T) diameter ratio was calculated. We detected TM in 71 patients (18.54%). Regression analysis showed statistical significance in MV patients for the trachea diameter at the level of the cuff, maximal trachea diameter and C/T diameter ratio, and days on MV. Respiratory complications showed a significant association with the C/T diameter ratio. The C/T diameter ratio was shown to be a reliable potential predictor of the occurrence of respiratory complications. The results of the study highlight the importance of the early detection and prevention of TM in COVID-19 patients on MV using a chest X-ray and measurement of the C/T diameter ratio. Full article

The COVID-19 global pandemic necessitated adequate compliance to safe and effective vaccinations developed against the disease. Vaccination reduces high infection, morbidity, and mortality rates, develops herd immunity, and alleviates overburdened healthcare systems and massive economic costs. COVID-19 also raised awareness about the importance of robust health systems, notably public health competence and the number and training of community health workers. Using the World Health Organization, Global Development of Applied Community Studies project, and other available cross-sectional secondary data on 89 countries, we found that the strength of community health training and research (CHTR), the importance of religion, and freedom score (political rights, civil liberties) are associated with COVID-19 full-vaccination rate. Significant bivariate correlations included per-capita-GDP, number of nurses, per-capita health spending, aged population, noncommunicable disease rate, life satisfaction, government response stringency, nonviolent activism, education, and strength of community development, urban planning, and liberation theology fields. Our assessment of CHTR contribution to the COVID-19 response revealed a great resource for effectively targeting vaccine-hesitant individuals and increasing vaccination rates. The results suggest that to motivate vaccine adherence countries need adequate community health workforce training and research, a population not hesitant to adhere to public health measures based on religion, and societal-level freedoms. Full article

Background: In Senegal, the incidence of SARS-CoV-2 evolved with four successive epidemic waves. The first wave started in March 2020 with low virus variability, whilst the second outbreak, which started in December 2020, was dominated by the Alpha variant. The third wave took place in June 2021, and the fourth at the end of November 2021. Our interest was to investigate the involvement of variants of concern during these four waves and to track the viral diversity of SARS-CoV-2. Methodology: During the four waves of the pandemic, 276,876 nasopharyngeal swabs were analyzed at the Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation (IRESSEF). Of these, 22,558 samples tested positive for SARS-CoV-2 by RT-PCR. Then, the virus genomes were sequenced in 817 positive samples using the ARTIC Network of Oxford Nanopore Technologies (ONT). In addition, 10% of the negative samples in RT-PCR new variants were also targeted for the detection of new and previously undescribed variants. Results: Our data have overall shown that the Senegalese strains are very similar to each other or closely related to other strains, such as Gambia, France etc. During the first wave, the most common clade found was 19A (67.5%) and a majority of the samples were of the B.1 (50%) lineage. We noted more diversity during the second wave where clade 20A (38.4%) was more frequent, followed by clade 20B (31.52%) and 20I (9.74%). At the level of lineages, we identified variants of concern as B.1.1.7 (9.74%) and B.1.617.2 (0.86%). In the third wave, we observed at the clade level with mainly 21A (32.63%) and 21J (16.84%). During the fourth wave at the end of November 2021, we mainly identified clade 21K Omicron variant 21K (B.1.1.529 and BA.1) (80.47%) and Delta variant (21A, 21J, and 21I) (AY.103, AY.122, AY.122.1, AY.26, AY.34, AY.36, AY.4, AY.48, AY.57, AY.61, and AY.87) (14.06%). Impact: SARS-CoV-2 diversity may affect the virus’s properties, such as how it spreads, disease severity, or the performance of vaccines, tools, or other public health and social measures. Therefore, such tracking of SARS-CoV-2 variants is not only of public interest, but also highlights the role some African institutes such as IRESSEF with surveillance capabilities through the real-time sequencing of SARS-CoV-2 genomes in the local context. Conclusion: In Senegal, the SARS-CoV-2 pandemic has disrupted the organization of the health system. IRESSEF contributed to put in place strategies to respond effectively to the expectations of medical authorities by providing them with data on the strains circulating in Senegal at each moment of the epidemic. Full article