Clinical Characteristics and Risk Factors for Disease Severity and Death in Patients With Coronavirus Disease 2019 in Wuhan, China

From Detection to Protection: Antibodies and Their Crucial Role in Diagnosing and Combatting SARS-CoV-2

Understanding the antibody response to SARS-CoV-2, the virus responsible for COVID-19, is crucial to comprehending disease progression and the significance of vaccine and therapeutic development. The emergence of highly contagious variants poses a significant challenge to humoral immunity, underscoring the necessity of grasping the intricacies of specific antibodies. This review emphasizes the pivotal role of antibodies in shaping immune responses and their implications for diagnosing, preventing, and treating SARS-CoV-2 infection. It delves into the kinetics and characteristics of the antibody response to SARS-CoV-2 and explores current antibody-based diagnostics, discussing their strengths, clinical utility, and limitations. Furthermore, we underscore the therapeutic potential of SARS-CoV-2-specific antibodies, discussing various antibody-based therapies such as monoclonal antibodies, polyclonal antibodies, anti-cytokines, convalescent plasma, and hyperimmunoglobulin-based therapies. Moreover, we offer insights into antibody responses to SARS-CoV-2 vaccines, emphasizing the significance of neutralizing antibodies in order to confer immunity to SARS-CoV-2, along with emerging variants of concern (VOCs) and circulating Omicron subvariants. We also highlight challenges in the field, such as the risks of antibody-dependent enhancement (ADE) for SARS-CoV-2 antibodies, and shed light on the challenges associated with the original antigenic sin (OAS) effect and long COVID. Overall, this review intends to provide valuable insights, which are crucial to advancing sensitive diagnostic tools, identifying efficient antibody-based therapeutics, and developing effective vaccines to combat the evolving threat of SARS-CoV-2 variants on a global scale.

Altered Anti-Viral Immune Responses in Monocytes in Overweight Heavy Drinkers

Alcohol abuse causes increased susceptibility to respiratory syndromes like bacterial pneumonia and viral infections like SARS-CoV-2. Heavy drinkers (HD) are at higher risk of severe COVID-19 if they are also overweight, yet the molecular mechanisms are unexplored. Single-cell RNA-seq (scRNA-seq) was performed on peripheral blood mononuclear cells from lean or overweight HD and healthy controls (HC) after challenge with a dsRNA homopolymer (PolyI:C) to mimic a viral infection and/or with lipopolysaccharide (LPS). All monocyte populations responded to both PolyI:C and LPS with pro-inflammatory gene expression. However, expression of interferon stimulated genes, essential for inhibiting viral pathogenesis, was greatly reduced in overweight patients. Interestingly, the number of upregulated genes in response to PolyI:C challenge was far greater in monocytes from HD compared to HC, including much stronger pro-inflammatory cytokine and interferon-γ signaling responses. These results suggest increased body weight reduced anti-viral responses while heavy drinking increased pro-inflammatory cytokines.

Complement activation in COVID-19 and targeted therapeutic options: A scoping review

Increasing evidence suggests that activation of the complement system plays a key role in the pathogenesis and disease severity of Coronavirus disease 2019 (COVID-19). We used a systematic approach to create an overview of complement activation in COVID-19 based on histopathological, preclinical, multiomics, observational and clinical interventional studies. A total of 1801 articles from PubMed, EMBASE and Cochrane was screened of which 157 articles were included in this scoping review. Histopathological, preclinical, multiomics and observational studies showed apparent complement activation through all three complement pathways and a correlation with disease severity and mortality. The complement system was targeted at different levels in COVID-19, of which C5 and C5a inhibition seem most promising. Adequately powered, double blind RCTs are necessary in order to further investigate the effect of targeting the complement system in COVID-19.

Association between Hypocalcemia and Outcome in COVID-19 Patients: A Retrospective Study

Background Calcium has been shown to play a vital role in the pathophysiology of severe acute respiratory syndrome-coronavirus-2 and middle east respiratory syndrome coronavirus diseases, but less is known about hypocalcemia in coronavirus disease 2019 (COVID-19) patients and its association with the disease severity and the final outcome. Therefore, this study was conducted with an aim to assess clinical features in COVID-19 patients having hypocalcemia and to observe its impact on COVID-19 disease severity and the final outcome.

Methods In this retrospective study, consecutive COVID-19 patients of all age groups were enrolled. Demographical, clinical, and laboratory details were collected and analyzed. On the basis of albumin-corrected calcium levels, patients were classified into normocalcemic (n = 51) and hypocalcemic (n = 110) groups. Death was the primary outcome.

Results The mean age of patients in the hypocalcemic group was significantly lower (p < 0.05). A significantly higher number of hypocalcemic patients had severe COVID-19 infection (92.73%; p < 0.01), had comorbidities (82.73%, p < 0.05), and required ventilator support (39.09%; p < 0.01) compared with normocalcemic patients. The mortality rate was significantly higher in the hypocalcemic patients (33.63%; p < 0.05). Hemoglobin (p < 0.01), hematocrit (p < 0.01), and red cell count (p < 0.01) were significantly lower with higher levels of absolute neutrophil count (ANC; p < 0.05) and neutrophil-to-lymphocyte ratio (NLR; p < 0.01) in the hypocalcemic patients.

Albumin-corrected calcium levels had a significant positive correlation with hemoglobin levels, hematocrit, red cell count, total protein, albumin, and albumin-to-globulin ratio and a significant negative correlation with ANC and NLR.

Conclusion The disease severity, ventilator requirement, and mortality were considerably higher in hypocalcemic COVID-19 patients.

Proteomic and Metabolomic Characterization of SARS-CoV-2-Infected Cynomolgus Macaque at Early Stage

Although tremendous effort has been exerted to elucidate the pathogenesis of severe COVID-19 cases, the detailed mechanism of moderate cases, which accounts for 90% of all patients, remains unclear yet, partly limited by lacking the biopsy tissues. Here, we established the COVID-19 infection model in cynomolgus macaques (CMs), monitored the clinical and pathological features, and analyzed underlying pathogenic mechanisms at early infection stage by performing proteomic and metabolomic profiling of lung tissues and sera samples from COVID-19 CMs models. Our data demonstrated that innate immune response, neutrophile and platelet activation were mainly dysregulated in COVID-19 CMs. The symptom of neutrophilia, lymphopenia and massive "cytokines storm", main features of severe COVID-19 patients, were greatly weakened in most of the challenged CMs, which are more semblable as moderate patients. Thus, COVID-19 model in CMs is rational to understand the pathogenesis of moderate COVID-19 and may be a candidate model to assess the safety and efficacy of therapeutics and vaccines against SARS-CoV-2 infection.

Associations between perceived discrimination and immune cell composition in the Jackson Heart Study

African American adults suffer disproportionately from several non-communicable and infectious diseases. Among numerous contributing factors, perceived discrimination is considered a stressor for members of historically marginalized groups that contributes to health risk, although biological pathways are incompletely understood. Previous studies have reported associations between stress and both an up-regulation of non-specific (innate) inflammation and down-regulation of specific (adaptive) immunity. While associations between perceived discrimination and markers of inflammation have been explored, it is unclear if this is part of an overall shift that also includes down-regulated adaptive immunity. Relying on a large cross-section of African American adults (n = 3,319) from the Jackson Heart Study (JHS) in Jackson, Mississippi, we tested whether perceived everyday and lifetime discrimination as well as perceived burden from lifetime discrimination were associated with counts of neutrophils (innate), monocytes (innate), lymphocytes (adaptive), and the neutrophil-to-lymphocyte ratio (NLR), derived from complete white blood cell counts with differential. In addition, DNA methylation (DNAm) was measured on the EPIC array in a sub-sample (n = 1,023) of participants, allowing estimation of CD4T, CD8T and B lymphocyte proportions. Unexpectedly, high lifetime discrimination compared to low was significantly associated with lower neutrophils (b : -0.14, [95% CI: -0.24, -0.04]) and a lower NLR (b : -0.15, [95% CI: -0.25, -0.05]) after controlling for confounders. However, high perceived burden from lifetime discrimination was significantly associated with higher neutrophils (b : 0.17, [95% CI: 0.05, 0.30]) and a higher NLR (b : 0.16, [95% CI: 0.03, 0.29]). High perceived burden was also associated with lower lymphocytes among older men, which our analysis suggested might have been attributable to differences in CD4T cells. These findings highlight immune function as a potentially important pathway linking perceived discrimination to health outcomes.

Elevated Levels of Pleiotropic Interleukin-6 (IL-6) and Interleukin-10 (IL-10) are Critically Involved With the Severity and Mortality of COVID-19: An Updated Longitudinal Meta-Analysis and Systematic Review on 147 Studies

Objectives

Disruption in the natural immune reaction due to SARS-CoV-2 infection can initiate a potent cytokine storm among COVID-19 patients. An elevated level of IL-6 and IL-10 during a hyperinflammatory state plays a vital role in increasing the risk of severity and mortality. In this study, we aimed to evaluate the potential of circulating IL-6 and IL-10 levels as biomarkers for detecting the severity and mortality of COVID-19.

Methods

This study was conducted according to the Cochrane Handbook and PRISMA guidelines. Authorized databases were searched to extract suitable studies using specific search terms. RevMan 5.4 was applied for performing the meta-analysis. Mean differences in IL-6 and IL-10 levels were calculated among COVID-19 patients via a random-effects model. NOS scoring, publication bias and sensitivity analyses were checked to ensure study quality.

Results

A total of 147 studies were selected, with 31 909 COVID-19 patients under investigation. In the severity analysis, the mean concentration of IL-6 was significantly higher in the severe COVID-19 cases than in the non-severe cases (MD: 19.98; P < .001; 95% CI: 17.56, 22.40). Similar result was observed for IL-10 mean concentration in severe COVID-19 cases (MD: 1.35; P < .001; 95% CI: 0.90, 1.80). In terms of mortality analysis, circulating IL-6 showed sharp elevation in the deceased patients (MD: 42.11; P < .001; 95% CI: 36.86, 47.36). IL-10 mean concentration was higher in the dead patients than in the survived patients (MD: 4.79; P < .001; 95% CI: 2.83, 6.75). Publication bias was not found except for comparing IL-6 levels with disease severity. Sensitivity analysis also reported no significant deviation from the pooled outcomes.

Conclusions

Elevated levels of circulating IL-6 and IL-10 signifies worsening of COVID-19. To monitor the progression of SARS-CoV-2 infection, IL-6 and IL-10 should be considered as potential biomarkers for severity and mortality detection in COVID-19.

Systematic review registration

INPLASY registration number: INPLASY202240046.

Associations between Serum Interleukins (IL-1β, IL-2, IL-4, IL-6, IL-8, and IL-10) and Disease Severity of COVID-19: A Systematic Review and Meta-Analysis

Background. To investigate the association between interleukins (IL-1β, IL-2, IL-4, IL-6, IL-8, and IL-10) and the disease severity of coronavirus disease 2019 (COVID-19). Materials and Methods. We systematically searched records investigating the role of interleukins (IL-1β, IL-2, IL-4, IL-6, IL-8, and IL-10) in COVID-19 patients in Web of Science, Pubmed, and Embase through December 2020. Data were extracted and pooled, and the weighted mean difference (WMD) and its 95% confidence interval (CI) were calculated. The funnel plot and the nonparametric trim and fill method were used to visualize and adjust the publication bias. Results. In total, 61 studies enrolled 14,136 subjects (14,041 patients and 95 healthy subjects) were enrolled in this meta-analysis. Our results showed that serum IL-2, IL-4, IL-6, and IL-10 levels were elevated in COVID-19 patients compared to healthy controls, and IL-6, IL-8, and IL-10 levels were increased in severe COVID-19 cases compared to nonsevere patients. Additionally, the levels of IL-1β, IL-6, and IL-8 were elevated in nonsurvivor patients compared to survivors. For patients in the intensive care unit (ICU), IL-6 and IL-8 levels were increased than that in non-ICU patients. Conclusions. Elevated levels of IL-6, IL-8, and IL-10 were associated with the disease severity of COVID-19, and elevated levels of IL-1β, IL-6, and IL-8 were related to the prognosis of COVID-19 patients, which could be used to evaluate COVID-19 patients’ disease severity and prognosis.

T-Cell Subsets and Interleukin-10 Levels Are Predictors of Severity and Mortality in COVID-19: A Systematic Review and Meta-Analysis

Background

Many COVID-19 patients reveal a marked decrease in their lymphocyte counts, a condition that translates clinically into immunodepression and is common among these patients. Outcomes for infected patients vary depending on their lymphocytopenia status, especially their T-cell counts. Patients are more likely to recover when lymphocytopenia is resolved. When lymphocytopenia persists, severe complications can develop and often lead to death. Similarly, IL-10 concentration is elevated in severe COVID-19 cases and may be associated with the depression observed in T-cell counts. Accordingly, this systematic review and meta-analysis aims to analyze T-cell subsets and IL-10 levels among COVID-19 patients. Understanding the underlying mechanisms of the immunodepression observed in COVID-19, and its consequences, may enable early identification of disease severity and reduction of overall morbidity and mortality.

Methods

A systematic search was conducted covering PubMed MEDLINE, Scopus, Web of Science, and EBSCO databases for journal articles published from December 1, 2019 to March 14, 2021. In addition, we reviewed bibliographies of relevant reviews and the medRxiv preprint server for eligible studies. Our search covered published studies reporting laboratory parameters for T-cell subsets (CD4/CD8) and IL-10 among confirmed COVID-19 patients. Six authors carried out the process of data screening, extraction, and quality assessment independently. The DerSimonian-Laird random-effect model was performed for this meta-analysis, and the standardized mean difference (SMD) and 95% confidence interval (CI) were calculated for each parameter.

Results

A total of 52 studies from 11 countries across 3 continents were included in this study. Compared with mild and survivor COVID-19 cases, severe and non-survivor cases had lower counts of CD4/CD8 T-cells and higher levels of IL-10.

Conclusion

Our findings reveal that the level of CD4/CD8 T-cells and IL-10 are reliable predictors of severity and mortality in COVID-19 patients. The study protocol is registered with the International Prospective Register of Systematic Reviews (PROSPERO); registration number CRD42020218918.

Systematic Review Registration

https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42020218918, identifier: CRD42020218918.

Endocrine risk factors for COVID-19: Endogenous and exogenous glucocorticoid excess

Patients with endogenous or exogenous glucocorticoid (GC) excess exhibit a range of side effects, including an increased risk of infections. Via both mechanism, immune impairments and cardiometabolic concomitant diseases, patients with GC excess could be at increased risk for COVID-19. The impact on incidence and outcome of a SARS-CoV-2 infection in this population are not yet completely clear. This review aims to compile the data available to date and to discuss the existing literature on this topic. Further we highlight potential effects of SARS-CoV-2 on the hypothalamic-pituitary-adrenal axis as well as the influence of endogenous or exogenous GC excess on SARS-CoV-2 mRNA vaccination. There is growing evidence suggesting an increased risk of infection and severe outcome in patients with high-dose GC therapy after contracting SARS-CoV-2. The few data and case reports on patients with endogenous GC excess and SARS-CoV-2 infection point in a similar direction: chronic GC excess seems to be associated with an unfavorable course of COVID-19. Whether this is mainly a primary immune-mediated effect, or also triggered by the many GC-associated comorbidities in this population, is not yet fully understood. Patients with endogenous or exogenous GC excess should be considered as a vulnerable group during the SARS-CoV-2 pandemic. Regardless of the cause, vaccination and consistent surveillance and control of associated comorbidities are recommended.

Clinical Characteristics and Risk Factors Associated with Severe Disease Progression among COVID-19 Patients In Wad Medani Isolation Centers: A Multicenter Retrospective Cross-Sectional Study

Background

Since December 2019, (COVID-19) has had a significant impact on global health systems. Because little is known about the clinical characteristics and risk factors connected with COVID-19 severity in Sudanese patients, it is vital to summarize the clinical characteristics of COVID-19 patients and to investigate the risk factors linked to COVID-19 severity.

Objectives

We aimed to assess the clinical characteristics of COVID-19 patients and look into risk factors associated with COVID-19 severity.

Methods

This is a retrospective cross-sectional study that took place in two Isolation Centers in Wad Medani, Gezira State, Sudan. Four hundred and eighteen patients were included between May 2020 and May 2021. All COVID-19 patients over the age of 18 who were proven COVID-19 positive by nucleic acid testing or had characteristics suggestive of COVID-19 on a chest CT scan and had a complete medical record in the study period were included.

Results

The participants in this study were 418 confirmed COVID-19 cases with a median age of 66.313 years. There were 279 men (66.7%) among the patients. The most prevalent comorbidities were hypertension (n = 195; 46.7%) and diabetes (n = 187; 44.7%). Fever (n = 303; 72.5%), cough (n = 278; 66.5%), and dyspnea (n = 256; 61.2%) were the most prevalent symptoms at the onset of COVID-19. The overall mortality rate (n = 148) was 35.4%. Patients with severe illness had a mortality rate of 42.3% (n = 118). Older age, anemia, neutrophilia, and lymphocytopenia, as well as higher glucose, HbA1c, and creatinine levels, were all linked to severe COVID-19, according to the chi-square test and analysis of variance analysis.

Conclusion

Sixteen variables were found to be associated with COVID-19 severity. These patients are more prone to go through a serious infection and as a result have a greater death rate than those who do not have these characteristics.

Explainable Machine Learning for COVID-19 Pneumonia Classification With Texture-Based Features Extraction in Chest Radiography

Both reverse transcription-PCR (RT-PCR) and chest X-rays are used for the diagnosis of the coronavirus disease-2019 (COVID-19). However, COVID-19 pneumonia does not have a defined set of radiological findings. Our work aims to investigate radiomic features and classification models to differentiate chest X-ray images of COVID-19-based pneumonia and other types of lung patterns. The goal is to provide grounds for understanding the distinctive COVID-19 radiographic texture features using supervised ensemble machine learning methods based on trees through the interpretable Shapley Additive Explanations (SHAP) approach. We use 2,611 COVID-19 chest X-ray images and 2,611 non-COVID-19 chest X-rays. After segmenting the lung in three zones and laterally, a histogram normalization is applied, and radiomic features are extracted. SHAP recursive feature elimination with cross-validation is used to select features. Hyperparameter optimization of XGBoost and Random Forest ensemble tree models is applied using random search. The best classification model was XGBoost, with an accuracy of 0.82 and a sensitivity of 0.82. The explainable model showed the importance of the middle left and superior right lung zones in classifying COVID-19 pneumonia from other lung patterns.

The journey of SARS-CoV-2 in human hosts: a review of immune responses, immunosuppression, and their consequences

Coronavirus disease 2019 (COVID-19) is a highly infectious viral disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Laboratory findings from a significant number of patients with COVID-19 indicate the occurrence of leukocytopenia, specifically lymphocytopenia. Moreover, infected patients can experience contrasting outcomes depending on lymphocytopenia status. Patients with resolved lymphocytopenia are more likely to recover, whereas critically ill patients with signs of unresolved lymphocytopenia develop severe complications, sometimes culminating in death. Why immunodepression manifests in patients with COVID-19 remains unclear. Therefore, the evaluation of clinical symptoms and laboratory findings from infected patients is critical for understanding the disease course and its consequences. In this review, we take a logical approach to unravel the reasons for immunodepression in patients with COVID-19. Following the footprints of the virus within host tissues, from entry to exit, we extrapolate the mechanisms underlying the phenomenon of immunodepression.

CRP, SAA, LDH, and DD predict poor prognosis of coronavirus disease (COVID-19): a meta-analysis from 7739 patients

Understanding factors associated with disease severity and mortality from coronavirus disease (COVID-19) was critical for effective risk stratification. We aimed to investigate the association between biomarkers of clinical laboratory tests, including serum C-reactive protein (CRP), serum amyloid protein (SAA), lactate dehydrogenase (LDH), and D-dimer (DD) and poor prognosis of COVID-19. We have searched many studies on COVID-19 on PubMed (Medline), Web of Science and Cochrane until 1 March 2021. The interest of this study was original articles reporting on laboratory testing projects and outcome of patients with COVID-19 that comprises mortality, acute respiratory distress syndrome (ARDS), need for care in an intensive care unit (ICU), and severe COVID-19. After synthesizing all data, we performed meta-analysis of random effects, and determined mean difference (MD) and standard mean difference at the biomarker level for different disease severity. A total of 7,739 patients with COVID-19 were pooled from 32 studies. CRP was significantly associated with poor prognosis of COVID-19 (SMD = 0.98, 95% CI = (0.85, 1.11), p < .001). Elevated SAA was associated with an increased composite poor outcome in COVID-19 (SMD = 1.06, 95% CI = (0.39, 1.72), p = .002). An elevated LDH was associated with a composite poor outcome (SMD = 1.18, 95% CI = (1.00, 1.36), p < .001). Patients with a composite poor outcome had a higher DD level (SMD = 0.91, 95% CI = (0.79, 1.02), p < .001). This meta-analysis showed that elevated serum CRP, SAA, LDH, and DD were associated with a poor outcome in COVID-19.

Chronic Diseases as a Predictor for Severity and Mortality of COVID-19: A Systematic Review With Cumulative Meta-Analysis

Introduction: Given the ongoing coronavirus disease 2019 (COVID-19) pandemic and the consequent global healthcare crisis, there is an urgent need to better understand risk factors for symptom deterioration and mortality among patients with COVID-19. This systematic review aimed to meet the need by determining the predictive value of chronic diseases for COVID-19 severity and mortality.

Methods: We searched PubMed, Embase, Web of Science, and Cumulative Index to Nursing and Allied Health Complete to identify studies published between December 1, 2019, and December 31, 2020. Two hundred and seventeen observational studies from 26 countries involving 624,986 patients were included. We assessed the risk of bias of the included studies and performed a cumulative meta-analysis.

Results: We found that among COVID-19 patients, hypertension was a very common condition and was associated with higher severity, intensive care unit (ICU) admission, acute respiratory distress syndrome, and mortality. Chronic obstructive pulmonary disease was the strongest predictor for COVID-19 severity, admission to ICU, and mortality, while asthma was associated with a reduced risk of COVID-19 mortality. Patients with obesity were at a higher risk of experiencing severe symptoms of COVID-19 rather than mortality. Patients with cerebrovascular disease, chronic liver disease, chronic renal disease, or cancer were more likely to become severe COVID-19 cases and had a greater probability of mortality.

Conclusions: COVID-19 patients with chronic diseases were more likely to experience severe symptoms and ICU admission and faced a higher risk of mortality. Aggressive strategies to combat the COVID-19 pandemic should target patients with chronic diseases as a priority.

Clinical Characteristics and the Long-Term Post-recovery Manifestations of the COVID-19 Patients-A Prospective Multicenter Cross-Sectional Study

Objective: Coronavirus disease 2019 (COVID-19) or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a global issue. In addition to managing acute cases, post-COVID-19 persisting symptoms/complaints and different hematological values are of great concern. These have an impact on the patient's well-being and are yet to be evaluated. Therefore, clinical and primary diagnosis based on routine laboratory findings bears high importance during the initial period of COVID-19, especially in regions with fewer diagnostic facilities.

Methods: Clinical information and associated complaints of the COVID-19 illness confirmed by reverse transcription-polymerase chain reaction (RT-PCR) were collected directly from the patients. Regular follow-ups were obtained on the phone every 2 weeks following recovery for 20 weeks. Initial hematological and radiology findings of the hospitalized patients except for intensive care unit (ICU) and high dependency units (HDUs) and a follow-up evaluation after 4 weeks following recovery were analyzed.

Results: The post-COVID-19 persisting symptoms/complaints were found among 21.4% of symptomatic patients, which persisted for ≥20 weeks and had a significant relationship with the duration of COVID-19 illness and the existing comorbidity (p < 0.05). Post-COVID-19 primary type 2 diabetes mellitus (DM, 0.64%) and hypertension (HTN, 1.28%) and unstable DM (54.55%) and HTN (34.78%) to the pre-existing diabetic and hypertensive patients were observed. Post-recovery remarkable changes in the laboratory values included leukocytosis (16.1%), lymphocytosis (14.5%), and an increased prothrombin time (PT, 25.8%). Abnormalities in the D-dimer, serum ferritin, hemoglobin, and erythrocyte sedimentation rate (ESR) levels were present to an extent. Laboratory findings like chest X-ray, ESR, white blood cell (WBC) count, lymphocyte count, C-reactive protein (CRP), serum glutamic pyruvic transaminase (SGPT), serum ferritin, PT, D-dimer, and serum creatinine are important markers for the diagnosis and prognosis of COVID-19 illness (p < 0.05).

Conclusion: Post-COVID-19 persisting symptoms and the changes in the laboratory values need to be considered with importance and as a routine clinical measure. Post-COVID-19 periodic follow-up for evaluating the patient's physical condition and the biochemical values should be scheduled with care and managed accordingly to prevent future comorbidity in patients with the post-COVID-19 syndrome.

COVID-19 disease in hospitalized young adults in India and China: Evaluation of risk factors predicting progression across two major ethnic groups

Data pertaining to risk factor analysis in coronavirus disease 2019 (COVID-19) is confounded by the lack of data from an ethnically diverse population. In addition, there is a lack of data for young adults. This study was conducted to assess risk factors predicting COVID-19 severity and mortality in hospitalized young adults. A retrospective observational study was conducted at two centers from China and India on COVID-19 patients aged 20-50 years. Regression analysis to predict adverse outcomes was performed using parameters including age, sex, country of origin, hospitalization duration, comorbidities, lymphocyte count, and National Early Warning Score 2 (NEWS2) score at admission. A total of 420 patients (172 East Asians and 248 South Asians) were included. The predictive model for intensive care unit (ICU) admission with variables NEWS2 Category II and higher, diabetes mellitus, liver dysfunction, and low lymphocyte counts had an area under the curve (AUC) value of 0.930 with a sensitivity of 0.931 and a specificity of 0.784. The predictive model for mortality with NEWS2 Category III, cancer, and decreasing lymphocyte count had an AUC value of 0.883 with a sensitivity of 0.903 and a specificity of 0.701. A combined predictive model with bronchial asthma and low lymphocyte count, in contrast, had an AUC value of 0.768 with a sensitivity of 0.828 and a specificity of 0.719 for NEWS2 score (5 or above) at presentation. NEWS2 supplemented with comorbidity profile and lymphocyte count could help identify hospitalized young adults at risk of adverse COVID-19 outcomes.

Clinical Outcome Prediction in COVID-19 Patients by Lymphocyte Subsets Analysis and Monocytes' iTNF-α Expression

In December 2019, a novel coronavirus, "SARS-CoV-2", was recognized as the cause of coronavirus disease 2019 (COVID-19). Several studies have explored the changes and the role of inflammatory cells and cytokines in the immunopathogenesis of the disease, but until today, the results have been controversial. Based on these premises, we conducted a retrospective assessment of monocyte intracellular TNF-α expression (iTNF-α) and on the frequencies of lymphocyte sub-populations in twenty-five patients with moderate/severe COVID-19. We found lymphopenia in all COVID-19 infected subjects compared to healthy subjects. On initial observation, in patients with favorable outcomes, we detected a high absolute eosinophil count and a high CD4+/CD8+ T lymphocytes ratio, while in the Exitus Group, we observed high neutrophil and CD8+ T lymphocyte counts. During infection, in patients with favorable outcomes, we observed a rise in the lymphocyte count, in the monocyte and in Treg lymphocyte counts, and in the CD4+ and in CD8+ T lymphocytes count but a reduction in the CD4+/CD8+ T lymphocyte ratio. Instead, in the Exitus Group, we observed a reduction in the Treg lymphocyte counts and a decrease in iTNF-α expression. Our preliminary findings point to a modulation of the different cellular mediators of the immune system, which probably play a key role in the outcomes of COVID-19.

Biomarkers of cytokine storm as red flags for severe and fatal COVID-19 cases: A living systematic review and meta-analysis

OBJECTIVE

To describe the laboratory parameters and biomarkers of the cytokine storm syndrome associated with severe and fatal COVID-19 cases.

METHODS

A search with standardized descriptors and synonyms was performed on November 28th, 2020 of the MEDLINE, EMBASE, Cochrane Central Register of Controlled Trials, ClinicalTrials.gov, LILACS, and IBECS to identify studies of interest. Grey literature searches and snowballing techniques were additionally utilized to identify yet-unpublished works and related citations. Two review authors independently screened the retrieved titles and abstracts, selected eligible studies for inclusion, extracted data from the included studies, and then assessed the risk of bias using the Newcastle-Ottawa Scale. Eligible studies were those including laboratory parameters-including serum interleukin-6 levels-from mild, moderate, or severe COVID-19 cases. Laboratory parameters, such as interleukin-6, ferritin, hematology, C-Reactive Protein, procalcitonin, lactate dehydrogenase, aspartate aminotransferase, creatinine, and D-dimer, were extracted from the studies. Meta-analyses were conducted using the laboratory data to estimate mean differences with associated 95% confidence intervals.

DATA SYNTHESIS

The database search yielded 9,620 records; 40 studies (containing a total of 9,542 patients) were included in the final analysis. Twenty-one studies (n = 4,313) assessed laboratory data related to severe COVID-19 cases, eighteen studies (n = 4,681) assessed predictors for fatal COVID-19 cases and one study (n = 548) assessed laboratory biomarkers related to severe and fatal COVID-19 cases. Lymphopenia, thrombocytopenia, and elevated levels of interleukin-6, ferritin, D-dimer, aspartate aminotransferase, C-Reactive-Protein, procalcitonin, creatinine, neutrophils and leucocytes were associated with severe and fatal COVID-19 cases.

CONCLUSIONS

This review points to interleukin-6, ferritin, leukocytes, neutrophils, lymphocytes, platelets, C-Reactive Protein, procalcitonin, lactate dehydrogenase, aspartate aminotransferase, creatinine, and D-dimer as important biomarkers of cytokine storm syndrome. Elevated levels of interleukin-6 and hyperferritinemia should be considered as red flags of systemic inflammation and poor prognosis in COVID-19.

Serum Complement C3 and C4 and COVID-19 Severity and Mortality: A Systematic Review and Meta-Analysis With Meta-Regression

Activation of the complement system has been observed in coronavirus disease 19 (COVID-19). We conducted a systematic review and meta-analysis with meta-regression to investigate possible differences in the serum concentrations of two routinely measured complement components, C3 and C4, in COVID-19 patients with different severity and survival status. We searched PubMed, Web of Science and Scopus, between January 2020 and February 2021, for studies reporting serum complement C3 and C4, measures of COVID-19 severity, and survival. Eligibility criteria were a) reporting continuous data on serum C3 and C4 concentrations in COVID-19 patients, -b) investigating COVID-19 patients with different disease severity and/or survival status, c) adult patients, d) English language, e) ≥10 patients, and f) full-text available. Using a random-effects model, standardized mean differences (SMD) with 95% confidence intervals (CIs) were calculated to evaluate differences in serum C3 and C4 concentrations between COVID-19 patients with low vs. high severity or survivor vs. non-survivor status. Risk of bias was assessed using the Newcastle-Ottawa scale whereas publication bias was assessed with the Begg’s and Egger’s tests. Certainty of evidence was assessed using GRADE. Nineteen studies in 3,764 COVID-19 patients were included in the meta-analysis. Both C3 and C4 concentrations were significantly lower in patients with high disease severity or non-survivor status than patients with low severity or survivor status (C3 SMD=-0.40, 95% CI -0.60 to -0.21, p<0.001; C4 SMD=-0.29, 95% CI -0.49 to -0.09, p=0.005; moderate certainty of evidence). Extreme between-study heterogeneity was observed (C3, I² = 82.1%; C4, I² = 84.4%). Sensitivity analysis, performed by sequentially removing each study and re-assessing the pooled estimates, showed that the magnitude and direction of the effect size was not modified. There was no publication bias. In meta-regression, the SMD of C3 was significantly associated with white blood cell count, C-reactive protein (CRP), and pro-thrombin time, whereas the SMD of C4 was significantly associated with CRP, pro-thrombin time, D-dimer, and albumin. In conclusion, lower concentrations of C3 and C4, indicating complement activation, were significantly associated with higher COVID-19 severity and mortality. C3 and C4 might be useful to predict adverse clinical consequences in these patients.

Systematic Review Registration: PROSPERO, Registration number: CRD42021239634.

Role of leukotriene pathway and montelukast in pulmonary and extrapulmonary manifestations of Covid-19: The enigmatic entity

Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), the responsible agent for the coronavirus disease 2019 (Covid-19), has its entry point through interaction with angiotensin converting enzyme 2 (ACE2) receptors, highly expressed in lung type II alveolar cells and other tissues, like heart, pancreas, brain, and vascular endothelium. This review aimed to elucidate the potential role of leukotrienes (LTs) in the pathogenesis and clinical presentation of SARS-CoV-2 infection, and to reveal the critical role of LT pathway receptor antagonists and inhibitors in Covid-19 management. A literature search was done in PubMed, Scopus, Web of Science and Google Scholar databases to find the potential role of montelukast and other LT inhibitors in the management of pulmonary and extra-pulmonary manifestations triggered by SARS-CoV-2. Data obtained so far underline that pulmonary and extra-pulmonary manifestations in Covid-19 are attributed to a direct effect of SARS-CoV-2 in expressed ACE2 receptors or indirectly through NF-κB dependent induction of a cytokine storm. Montelukast can ameliorate extra-pulmonary manifestations in Covid-19 either directly through blocking of Cys-LTRs in different organs or indirectly through inhibition of the NF-κB signaling pathway.

CD4+ T Cells of Prostate Cancer Patients Have Decreased Immune Responses to Antigens Derived From SARS-CoV-2 Spike Glycoprotein

The adaptive immune response to severe acute respiratory coronavirus 2 (SARS-CoV-2) is important for vaccine development and in the recovery from coronavirus disease 2019 (COVID-19). Men and cancer patients have been reported to be at higher risks of contracting the virus and developing the more severe forms of COVID-19. Prostate cancer (PCa) may be associated with both of these risks. We show that CD4⁺ T cells of SARS-CoV-2-unexposed patients with hormone-refractory (HR) metastatic PCa had decreased CD4⁺ T cell immune responses to antigens from SARS-CoV-2 spike glycoprotein but not from the spiked glycoprotein of the ‘common cold’-associated human coronavirus 229E (HCoV-229E) as compared with healthy male volunteers who responded comparably to both HCoV-229E- and SARS-CoV-2-derived antigens. Moreover, the HCoV-229E spike glycoprotein antigen-elicited CD4⁺ T cell immune responses cross-reacted with the SARS-CoV-2 spiked glycoprotein antigens. PCa patients may have impaired responses to the vaccination, and the cross-reactivity can mediate antibody-dependent enhancement (ADE) of COVID-19. These findings highlight the potential for increased vulnerability of PCa patients to COVID-19.

Radiological and clinical spectrum of COVID-19: A major concern for public health

The pandemic of novel coronavirus disease 2019 (COVID-19) is an infectious disease caused by +ve strand RNA virus (SARS-CoV-2, severe acute respiratory syndrome coronavirus 2) that belongs to the corona viridae family. In March, the World Health Organization declared the outbreak of novel coronavirus for the public health emergency. Although SARS-CoV-2 infection presents with respiratory symptoms, it affects other organs such as the kidneys, liver, heart and brain. Early-stage laboratory disease testing shows many false positive or negative outcomes such as less white blood cell count and a low number of lymphocyte count. However, radiological examination and diagnosis are among the main components of the diagnosis and treatment of COVID-19. In particular, for COVID-19, chest computed tomography developed vigorous initial diagnosis and disease progression assessment. However, the accuracy is limited. Although real-time reverse transcription-polymerase chain reaction is the gold standard method for the diagnosis of COVID-19, sometimes it may give false-negative results. Due to the consequences of the missing diagnosis. This resulted in a discrepancy between the two means of examination. Conversely, based on currently available evidence, we summarized the possible understanding of the various patho-physiology, radio diagnostic methods in severe COVID-19 patients. As the information on COVID-19 evolves rapidly, this review will provide vital information for scientists and clinicians to consider novel perceptions for the comprehensive knowledge of the diagnostic approaches based on current experience.

Potential Effects of COVID-19 on Cytochrome P450-Mediated Drug Metabolism and Disposition in Infected Patients

Coronavirus Disease 2019 (COVID-19) has been a global health crisis since it was first identified in December 2019. In addition to fever, cough, headache, and shortness of breath, an intense increase in immune response-based inflammation has been the hallmark of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) virus infection. This narrative review summarizes and critiques pathophysiology of COVID-19 and its plausible effects on drug metabolism and disposition. The release of inflammatory cytokines (e.g., interleukins, tumor necrosis factor α), also known as ‘cytokine storm’, leads to altered molecular pathophysiology and eventually organ damage in the lung, heart, and liver. The laboratory values for various liver function tests (e.g., alanine aminotransferase, aspartate aminotransferase, total bilirubin, albumin) have indicated potential hepatocellular injury in COVID-19 patients. Since the liver is the powerhouse of protein synthesis and the primary site of cytochrome P450 (CYP)-mediated drug metabolism, even a minor change in the liver function status has the potential to affect the hepatic clearance of xenobiotics. It has now been well established that extreme increases in cytokine levels are common in COVID-19 patients, and previous studies with patients infected with non-SARS-CoV-2 virus have shown that CYP enzymes can be suppressed by an infection-related cytokine increase and inflammation. Alongside the investigational COVID-19 drugs, the patients may also be on therapeutics for comorbidities; especially epidemiological studies have indicated that individuals with hypertension, hyperglycemia, and obesity are more vulnerable to COVID-19 than the average population. This complicates the drug-disease interaction profile of the patients as both the investigational drugs (e.g., remdesivir, dexamethasone) and the agents for comorbidities can be affected by compromised CYP-mediated hepatic metabolism. Overall, it is imperative that healthcare professionals pay attention to the COVID-19 and CYP-driven drug metabolism interactions with the goal to adjust the dose or discontinue the affected drugs as appropriate.

Predictors of Hospitalization Among Older Adults with COVID-19 in Saudi Arabia: A Cross-Sectional Study of a Nationally Representative Sample

Background

The aim of this study was to identify the predictors of hospitalization in older (≥60 years) patients with coronavirus disease-19 (COVID-19) in Saudi Arabia.

Methods

Patients were randomly selected from a COVID-19 database maintained by the Ministry of Health, Saudi Arabia. All patients were aged ≥60 years, had reverse transcriptase-polymerase chain reaction (RT-PCR)-confirmed COVID-19, and were registered in the database during March 2020 to July 2020. Medical and sociodemographic characteristics were retrieved from the database. Additional data were collected by telephone interviews conducted by trained health professionals. Descriptive statistics and multiple logistic regression analyses were used to analyze the relationship between patient characteristics and the risk of hospitalization.

Results

Of the 613 included patients (51.1% females), more than half (57.3%) were between 60 to 69 years of age, and 53% (324/613) had been hospitalized. The independent predictors of hospitalization included age ≥65 years (OR = 2.35, 95% CI: 1.66–3.33, P < 0.001), having more than one comorbidity (OR = 1.55, 95% CI: 1.09–2.20, P = 0.01), diabetes mellitus (OR = 1.52, 95% CI: 1.09–2.11, P = 0.01), hypertension (OR = 1.40, 95% CI: 1.007–1.97, P = 0.04), chronic kidney disease (OR = 3.87, 95% CI: 1.41–10.58, P = 0.008), and history of hospital admission within the preceding year (OR = 1.69, 95% CI: 1.11–2.55, P = 0.013). Risk of hospitalization was lower in males (OR = 0.65, 95% CI: 0.43–0.90, P = 0.01) and in patients co-living with health care workers (OR = 0.64, 95% CI: 0.43–0.96, P = 0.03).

Conclusion

Factors associated with higher risk of COVID-19-associated hospitalization should be used in prioritizing older adults’ admission. Future studies with more robust designs should be conducted to examine the risk of COVID-19-associated illness severity and mortality.

Evidence of central nervous system infection and neuroinvasive routes, as well as neurological involvement, in the lethality of SARS-CoV-2 infection

The outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has become a significant and urgent threat to global health. This review provided strong support for central nervous system (CNS) infection with SARS-CoV-2 and shed light on the neurological mechanism underlying the lethality of SARS-CoV-2 infection. Among the published data, only 1.28% COVID-19 patients who underwent cerebrospinal fluid (CSF) tests were positive for SARS-CoV-2 in CSF. However, this does not mean the absence of CNS infection in most COVID-19 patients because postmortem studies revealed that some patients with CNS infection showed negative results in CSF tests for SARS-CoV-2. Among 20 neuropathological studies reported so far, SARS-CoV-2 was detected in the brain of 58 cases in nine studies, and three studies have provided sufficient details on the CNS infection in COVID-19 patients. Almost all in vitro and in vivo experiments support the neuroinvasive potential of SARS-CoV-2. In infected animals, SARS-CoV-2 was found within neurons in different brain areas with a wide spectrum of neuropathology, consistent with the reported clinical symptoms in COVID-19 patients. Several lines of evidence indicate that SARS-CoV-2 used the hematopoietic route to enter the CNS. But more evidence supports the trans-neuronal hypothesis. SARS-CoV-2 has been found to invade the brain via the olfactory, gustatory, and trigeminal pathways, especially at the early stage of infection. Severe COVID-19 patients with neurological deficits are at a higher risk of mortality, and only the infected animals showing neurological symptoms became dead, suggesting that neurological involvement may be one cause of death.

Comorbidities in SARS-CoV-2 Patients: a Systematic Review and Meta-Analysis

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread across the globe at unprecedented speed and is showing no signs of slowing down. The outbreak of coronavirus disease 2019 (COVID-19) has led to significant health burden in infected patients especially in those with underlying comorbidities. The aim of this study was to evaluate the correlation between comorbidities and their role in the exacerbation of disease in COVID-19 patients leading to fatal outcomes. A systematic review was conducted using data from MEDLINE, Scopus, Web of Science, and EMBASE databases published from 1 December 2019 to 15 September 2020. Fifty-three articles were included in the systematic review. Of those 53 articles, 8 articles were eligible for meta-analysis. Hypertension, obesity, and diabetes mellitus were identified to be the most prevalent comorbidities in COVID-19 patients. Our meta-analysis showed that cancer, chronic kidney diseases, diabetes mellitus, and hypertension were independently associated with mortality in COVID-19 patients. Chronic kidney disease was statistically the most prominent comorbidity leading to death. However, despite having high prevalence, obesity was not associated with mortality in COVID-19 patients.IMPORTANCE COVID-19 has plagued the world since it was first identified in December 2019. Previous systematic reviews and meta-analysis were limited by various factors such as the usage of non-peer reviewed data and were also limited by the lack of clinical data on a global scale. Comorbidities are frequently cited as risk factors for severe COVID-19 outcomes. However, the degree to which specific comorbidities impact the disease is debatable. Our study selection involves a global reach and covers all comorbidities that were reported to be involved in the exacerbation of COVID-19 leading to fatal outcomes, which allows us to identify the specific comorbidities that have higher risk in patients. The study highlights COVID-19 high-risk groups. However, further research should focus on the status of comorbidities and prognosis in COVID-19 patients.

Immune Response to SARS-CoV-2 Infection in Obesity and T2D: Literature Review

In December 2019, a novel coronavirus known as SARS-CoV-2 was first detected in Wuhan, China, causing outbreaks of the coronavirus disease COVID-19 that has now spread globally. For this reason, The World Health Organization (WHO) declared COVID-19 a public health emergency in March 2020. People living with pre-existing conditions such as obesity, cardiovascular diseases, type 2 diabetes (T2D), and chronic kidney and lung diseases, are prone to develop severe forms of disease with fatal outcomes. Metabolic diseases such as obesity and T2D alter the balance of innate and adaptive responses. Both diseases share common features characterized by augmented adiposity associated with a chronic systemic low-grade inflammation, senescence, immunoglobulin glycation, and abnormalities in the number and function of adaptive immune cells. In obese and T2D patients infected by SARS-CoV-2, where immune cells are already hampered, this response appears to be stronger. In this review, we describe the abnormalities of the immune system, and summarize clinical findings of COVID-19 patients with pre-existing conditions such as obesity and T2D as this group is at greater risk of suffering severe and fatal clinical outcomes.

Acute Functional Outcomes in Critically Ill COVID-19 Patients

Background: COVID-19 (Coronavirus Disease 2019) is a global cause of morbidity and mortality currently. We aim to describe the acute functional outcomes of critically ill coronavirus disease 2019 (COVID-19) patients after transferring out of the intensive care unit (ICU).

Methods: 51 consecutive critically ill COVID-19 patients at a national designated center for COVID-19 were included in this exploratory, retrospective observational cohort study from January 1 to May 31, 2020. Demographic and clinical data were collected and analyzed. Functional outcomes were measured primarily with the Functional Ambulation Category (FAC), and divided into 2 categories: dependent ambulators (FAC 0–3) and independent ambulators (FAC 4–5). Multivariate analysis was performed to determine associations.

Results: Many patients were dependent ambulators (47.1%) upon transferring out of ICU, although 92.2% regained independent ambulation at discharge. On multivariate analysis, we found that a Charlson Comorbidity Index of 1 or more (odds ratio 14.02, 95% CI 1.15–171.28, P = 0.039) and a longer length of ICU stay (odds ratio 1.50, 95% CI 1.04–2.16, P = 0.029) were associated with dependent ambulation upon discharge from ICU.

Conclusions: Critically ill COVID-19 survivors have a high level of impairment following discharge from ICU. Such patients should be screened for impairment and managed appropriately by rehabilitation professionals, so as to achieve good functional outcomes on discharge.

COVID-19 and Diabetes: Understanding the Interrelationship and Risks for a Severe Course

The relationship between COVID-19 and diabetes mellitus is complicated and bidirectional. On the one hand, diabetes mellitus is considered one of the most important risk factors for a severe course of COVID-19. Several factors that are often present in diabetes mellitus are likely to contribute to this risk, such as older age, a proinflammatory and hypercoagulable state, hyperglycemia and underlying comorbidities (hypertension, cardiovascular disease, chronic kidney disease and obesity). On the other hand, a severe COVID-19 infection, and its treatment with steroids, can have a specific negative impact on diabetes itself, leading to worsening of hyperglycemia through increased insulin resistance and reduced β-cell secretory function. Worsening hyperglycemia can, in turn, adversely affect the course of COVID-19. Although more knowledge gradually surfaces as the pandemic progresses, challenges in understanding the interrelationship between COVID-19 and diabetes remain.

The potential role of neopterin in Covid-19: a new perspective

Neopterin (NPT) is a member of pteridines group, synthesized by macrophages when stimulated by interferon gamma (INF-γ). NPT is regarded as a macrophage stimulation indicator, marker of cellular immune activation and T helper 1 (Th1) type 1 immune response. Here, we aimed to provide a view point on the NPT features and role in Covid-19. Serum NPT level is regarded as an independent prognostic factor for Covid-19 severity, with levels starting to increase from the 3rd day of SARS-CoV-2 infection, being associated with severe dyspnea, longer hospitalization period and complications. Also, early raise of NPT reflects monocytes/macrophages activation before antibody immune response, despite the NPT level may also remain high in Covid-19 patients or at the end of incubation period before the onset of clinical symptoms. On the other hand, NPT attenuates the activity of macrophage foam cells and is linked to endothelial inflammation through inhibition of adhesion molecules and monocytes migration. However, NPT also exerts anti-inflammatory and antioxidant effects by suppressing NF-κB signaling and NLRP3 inflammasomes. NPT can be viewed as a protective compensatory mechanism to counterpoise hyper-inflammation, oxidative stress, and associated organ damage.

Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia

BACKGROUND

Recently, SARS-CoV-2 virus with the D614G mutation has become a public concern due to rapid dissemination of this variant across many countries. Our study aims were (1) to report full-length genome sequences of SARS-CoV-2 collected from four COVID-19 patients in the Special Region of Yogyakarta and Central Java provinces, Indonesia; (2) to compare the clade distribution of full-length genome sequences from Indonesia (n = 60) from March to September 2020 and (3) to perform phylogenetic analysis of SARS-CoV-2 complete genomes from different countries, including Indonesia.

METHODS

Whole genome sequencing (WGS) was performed using next-generation sequencing (NGS) applied in the Illumina MiSeq instrument. Full-length virus genomes were annotated using the reference genome of hCoV-19/Wuhan/Hu-1/2019 (NC_045512.2) and then visualized in UGENE v. 1.30. For phylogenetic analysis, a dataset of 88 available SARS-CoV-2 complete genomes from different countries, including Indonesia, was retrieved from GISAID.

RESULTS

All patients were hospitalized with various severities of COVID-19. Phylogenetic analysis revealed that one and three virus samples belong to clade L and GH. These three clade GH virus samples (EPI_ISL_525492, EPI_ISL_516800 and EPI_ISL_516829) were not only located in a cluster with SARS-CoV-2 genomes from Asia but also those from Europe, whereas the clade L virus sample (EPI_ISL_516806) was located amongst SARS-CoV-2 genomes from Asia. Using full-length sequences available in the GISAID EpiCoV Database, 39 of 60 SARS-CoV-2 (65%) from Indonesia harbor the D614G mutation.

CONCLUSION

These findings indicate that SARS-CoV-2 with the D614G mutation appears to become the major circulating virus in Indonesia, concurrent with the COVID-19 situation worldwide.

COVID-19 Transmission: Bangladesh Perspective

The sudden emergence of the COVID-19 pandemic has tested the strength of the public health system of the most developed nations and created a “new normal”. Many nations are struggling to curb the epidemic in spite of expanding testing facilities. In this study, we consider the case of Bangladesh, and fit a simple compartmental model holding a feature to distinguish between identified infected and infectious with time series data using least square fitting as well as the likelihood approach; prior to which, dynamics of the model were analyzed mathematically and the identifiability of the parameters has also been confirmed. The performance of the likelihood approach was found to be more promising and was used for further analysis. We performed fitting for different lengths of time intervals starting from the beginning of the outbreak, and examined the evolution of the key parameters from Bangladesh’s perspective. In addition, we deduced profile likelihood and 95% confidence interval for each of the estimated parameters. Our study demonstrates that the parameters defining the infectious and quarantine rates change with time as a consequence of the change in lock-down strategies and expansion of testing facilities. As a result, the value of the basic reproduction number R0 was shown to be between 1.5 and 12. The analysis reveals that the projected time and amplitude of the peak vary following the change in infectious and quarantine rates obtained through different lock-down strategies and expansion of testing facilities. The identification rate determines whether the observed peak shows the true prevalence. We find that by restricting the spread through quick identification and quarantine, or by implementing lock-down to reduce overall contact rate, the peak could be delayed, and the amplitude of the peak could be reduced. Another novelty of this study is that the model presented here can infer the unidentified COVID cases besides estimating the officially confirmed COVID cases.