Association of viral load with serum biomakers among COVID-19 cases

Prognostic value of serum amyloid A protein as a biomarker in the diagnosis of 2019 novel coronavirus disease (COVID-19)

BACKGROUND

The current study aimed to evaluate the prognostic value of serum amyloid A protein)SAA(protein as a biomarker in diagnosing 2019 novel coronavirus disease)COVID-19(infection.

METHODS

The study was conducted on 123 patients with definitive COVID-19 infection referred to Shahid Beheshti and Sina hospitals in Hamedan province, Iran. Five-milliliter blood samples were taken from all included patients and serum was isolated using a centrifuge at 10,000 rpm for 10 min. Laboratory tests were conducted, including c-reactive protein (CRP), Erythrocyte Sedimentation Rate (ESR), potassium level, sodium blood test, platelets (PLT), complete blood count (CBC), lymphocyte count, and neutrophil count. The SAA enzyme-linked immunosorbent assay (ELISA) Kit was applied to measure the SAA level in serum samples.

RESULTS

123 patients included 73 males and 50 females, age ±50. Sixty-six (53.7 %) patients had negative CRP while 80 (65 %) patients had normal ESR. Potassium levels were not normal among 111 (94.9 %) patients. Seventy-seven (63.1 %) patients had normal CBC, while 108 (87.8 %) patients had neutrophils above the normal range. 94 (97.9 %) patients over the age of 50 were positive for SAA. In terms of gender, men were the most frequent patients with SAA. There was a statistically significant relationship between the serum level of SAA and outcomes of patients with COVID-19 (p = 0.0001). 94 % of patients with SAA ≤50 were recovered from COVID-19 infection. The sensitivity rate of SAA compared to polymerase chain reaction (PCR) and computed tomography scan (CT scan) tests was 93 % and 99 %, respectively. Moreover, the accuracy of SAA compared to PCR and CT scan tests was 52 % and 96 %, respectively.

CONCLUSION

Results indicate the SAA is a sensitive, but not specific biomarker in the early detection of COVID-19. The quantitative levels of SAA can be useful in predicting treatment outcomes among patients with COVID-19.

A closer look at the link between cycle threshold, clinical features and biomarkers: An observational study in COVID-19 patients

Background

Symptoms for severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) appear 2-3 days after exposure to the virus. Being a virus, detection is primarily by polymerase chain reaction as this offers superior sensitivity and specificity. There was a misconception that patients with low cycle threshold (Ct) have severe coronavirus disease (COVID), and for individuals with higher Ct, it is the other way around. The prognosis for COVID was derived from various biomarkers and physicians heavily relied on them.

Materials and Methods

A cross-sectional study spanning a duration of 2 years was conducted at a tertiary care centre in western India. A total of 201 individuals were included and the correlation between Ct, clinical features and biomarkers was studied.

Results

In the E-gene, 43.28% had lower Ct values and 40.79% had low Ct values in the RdRp gene. 50% of all patients had diabetes, with 60% being between the ages of 61 and 80. 54.1% of hypertension patients belonged to ages between 61 and 80. 90.54% of COVID-positive individuals had lactose dehydrogenase levels ranging from 440 to 760. 79% of patients had a procalcitonin value of more than one but less than six. 79.1% of patients had an erythrocyte sedimentation rate between 36 and 90.

Conclusion

Ct value though has a research value; it is a poor prognostic marker when compared to the various biomarkers that have been studied earlier. We cannot conclusively state that all our findings are accurate due to a lack of data but further research into the prognostic value of Ct should be conducted which will help in the ongoing scenario.

Epidemiological and laboratory characteristics of Omicron infection in a general hospital in Guangzhou: a retrospective study

The COVID-19 pandemic caused by SARS-CoV-2 has emerged as a major global public health concern. In November 2022, Guangzhou experienced a significant outbreak of Omicron. This study presents detailed epidemiological and laboratory data on Omicron infection in a general hospital in Guangzhou between December 1, 2022, and January 31, 2023. Out of the 55,296 individuals tested, 12,346 were found to be positive for Omicron. The highest prevalence of positive cases was observed in the 20 to 39 age group (24.6%), while the lowest was in children aged 0 to 9 years (1.42%). Females had a higher incidence of infection than males, accounting for 56.6% of cases. The peak time of Omicron infection varied across different populations. The viral load was higher in older adults and children infected with Omicron, indicating age-related differences. Spearman's rank correlation analysis revealed positive correlations between Ct values and laboratory parameters in hospitalized patients with Omicron infection. These parameters included CRP (rs = 0.059, p = 0.009), PT (rs = 0.057, p = 0.009), INR (rs = 0.055, p = 0.013), AST (rs = 0.067, p = 0.002), LDH (rs = 0.078, p = 0.001), and BNP (rs = 0.063, p = 0.014). However, EO (Eosinophil, rs = -0.118, p < 0.001), BASO (basophil, rs = -0.093, p < 0.001), and LY (lymphocyte, rs = -0.069, p = 0.001) counts showed negative correlations with Ct values. Although statistically significant, the correlation coefficients between Ct values and these laboratory indices were very low. These findings provide valuable insights into the epidemiology of Omicron infection, including variations in Ct values across gender and age groups. However, caution should be exercised when utilizing Ct values in clinical settings for evaluating Omicron infection.

Clinical characteristics and prognostic nomograms of 12555 non-severe COVID-19 cases with Omicron infection in Shanghai

BACKGROUND

Omicron variant of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has rapidly become a global threat to public health. Numerous asymptomatic and mild cases had been admitted in shelter hospitals to quickly win the fight against Omicron pandemic in Shanghai. However, little is known about influencing factors for deterioration and length of stay (LOS) in hospitals among these non-severe cases.

METHODS

This study included 12,555 non-severe cases with COVID-19 in largest shelter hospital of Shanghai, aiming to explore prognostic factors and build effective models for prediction of LOS.

RESULTS

Data showed that 75.0% of participants were initially asymptomatic. In addition, 94.6% were discharged within 10 days, only 0.3% with deterioration in hospitals. The multivariate analysis indicated that less comorbidities (OR = 1.792, P = 0.012) and booster vaccination (OR = 0.255, P = 0.015) was associated with the decreased risk of deterioration. Moreover, age (HR = 0.991, P < 0.001), number of symptoms (HR = 0.969, P = 0.005), time from diagnosis to admission (HR = 1.013, P = 0.001) and Cycle threshold (CT) values of N gene (HR = 1.081, P < 0.001) were significant factors associated with LOS. Based on these factors, a concise nomogram model for predicting patients discharged within 3 days or more than 10 days was built in the development cohort. In validation cohort, 0.75 and 0.73 of Areas under the curve (AUC) in nomograms, similar with AUC in models of simple machine learning, showed good performance in estimating LOS.

CONCLUSION

Collectively, this study not only provides important evidence to deeply understand clinical characteristics and risk factors of short-term prognosis in Shanghai Omicron outbreaks, but also offers a concise and effective nomogram model to predict LOS. Our findings will play critical roles in screening high-risk groups, providing advice on duration of quarantine and helping decision-makers with better preparation in outbreak of COVID-19.

Delayed intubation associated with in-hospital mortality in patients with COVID-19 respiratory failure who fail heated and humified high flow nasal canula

BACKGROUND

Advanced respiratory support modalities such as non-invasive positive pressure ventilation (NiPPV) and heated and humidified high flow nasal canula (HFNC) served as useful alternatives to invasive mechanical ventilatory support for acute respiratory failure (ARF) during the peak of the SARS-CoV-2/COVID-19 pandemic. Unlike NiPPV, HFNC is a newer modality and its role in the treatment of patients with severe ARF is not yet clearly defined. Furthermore, the characteristics of responders versus non-responders to HFNC have not been determined. Although recent evidence indicates that many patients with ARF treated with HFNC survive without needing intubation, those who fail and are subsequently intubated have worse outcomes. Given that prolonged use of HFNC in patients with ARF might exacerbate patient self-inflicted lung injury, we hypothesized that among those patients with ARF due to COVID-19 pneumonia, prolonged HFNC beyond 24 h before intubation would be associated with increased in-hospital mortality.

METHODS

This was a retrospective, multicenter, observational cohort study of 2720 patients treated for ARF secondary to SARS-CoV-2/COVID-19 pneumonia and initially managed with HFNC within the Banner Health system during the period from March 1st, 2020, to July 31st, 2021. In the subgroup of patients for went from HFNC to IMV, we assessed the effect of the duration of HFNC prior to intubation on mortality.

RESULTS

1392 (51%) were successfully treated with HFNC alone and 1328 (49%) failed HFNC and were intubated (HFNC to IMV). When adjusted for the covariates, HFNC duration less than 24 h prior to intubation was significantly associated with reduced mortality.

CONCLUSIONS

Among patients with ARF due to COVID-19 pneumonia who fail HFNC, delay of intubation beyond 24 h is associated with increased mortality.

Study of some immunological signatures and their association with COVID-19 in a sample of recovered Iraqi patients

Since its emergence about two years ago, the novel coronavirus has continued to be a challenge and threat to public health, struck most parts of the world, leaving more than half a billion cases of infection and more than five million deaths. Immune response abnormalities post-infection with SARS-CoV-2 have been reported, and the mechanisms that lead to them are still ambiguous. This study was conducted to evaluate some immunological markers in the serum samples of COVID-19 convalescent patients and investigate the association of these immunological signatures with their age and sex. The serum levels of immunoglobulin G, interleukin-1 beta, and interferon lambda-1 of 75 patients and 50 healthy control group members were measured, with 55 % males and 45 % females participating and ages ranging from 20 to 80 years. The measurement of the immunological signatures was performed using the enzyme-linked immunosorbent assay (ELISA). The result revealed highly significant elevated levels of the serum immunological signatures of the convalescent group in comparison to the control group, with P-values of 0.00001 for each signature. Moreover, age was observed to have an association with an elevated level of the immunological signatures as it increased in the elderly, whereas no association with sex was detected. The findings strongly suggest that COVID-19 infection results in a persistent inflammatory response, which leads to prolonged post-recovery symptoms. Post-COVID-19 syndrome necessitates additional research to clarify its pathophysiology, pathogenesis, and long-term implications.

Serum cystatin C and CRP are early predictive biomarkers for emergence of hypoxia in COVID-19

BACKGROUND

In Japan, during the coronavirus disease 2019 (COVID-19) pandemic, patients with non-hypoxia are recommended to recuperate at home or in pre-hospital facilities. However, it was observed that unexpected hypoxia may occur and become severe subsequently in patients whose symptoms were initially expected to improve naturally. The aim of this study is to validate biomarkers that can predict at an early stage the emergence of hypoxia in COVID-19 patients without hypoxia.

METHODS

We retrospectively enrolled 193 patients with COVID-19, excluding patients with hypoxia and severe disease from the onset. Participants were classified into two groups according to the emergence of hypoxia during the clinical course, and the laboratory data were compared to identify biomarkers that could predict early the emergence of hypoxia.

RESULTS

The areas under the curve for serum cystatin C (CysC) and C-reactive protein (CRP) levels for the emergence of hypoxia during the clinical course were higher than those for other biomarkers (CysC, 0.84 and CRP, 0.83). Multivariate analysis showed that high serum CysC and CRP levels were associated with the emergence of hypoxia during the clinical course.

CONCLUSIONS

Elevated serum CysC and CRP levels were associated with the emergence of hypoxia during the clinical course in COVID-19 patients without hypoxia. These findings may help determine the need for hospitalization in initially non-hypoxic COVID-19 patients.

A Four-Channel Surface Plasmon Resonance Sensor Functionalized Online for Simultaneous Detections of Anti-SARS-CoV-2 Antibody, Free Viral Particles, and Neutralized Viral Particles

Current tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detect either the constituent nucleic acids/proteins of the viral particles or antibodies specific to the virus, but cannot provide information about viral neutralization by an antibody and the efficacy of an antibody. Such information is important about individuals' vulnerability to severe symptoms or their likelihood of showing no symptoms. We immobilized online SARS-CoV-2 spike (S1) protein and angiotensin-converting enzyme 2 (ACE2) into separate surface plasmon resonance (SPR) channels of a tris-nitrilotriacetic acid (tris-NTA) chip to simultaneously detect the anti-S1 antibody and viral particles in serum samples. In addition, with a high-molecular-weight-cutoff filter, we separated the neutralized viral particles from the free antibody molecules and used a sensing channel immobilized with Protein G to determine antibody-neutralized viral particles. The optimal density of probe molecules in each fluidic channel can be precisely controlled through the closure and opening of the specific ports. By utilizing the high surface density of ACE2, multiple assays can be carried out without regenerations. These three species can be determined with a short analysis time (<12 min per assay) and excellent sensor-to-sensor/cycle-to-cycle reproducibility (RSD < 5%). When coupled with an autosampler, continuous assays can be performed in an unattended manner at a single chip for up to 6 days. Such a sensor capable of assaying serum samples containing the three species at different levels provides additional insights into the disease status and immunity of persons being tested, which should be helpful for containing the SARS-CoV-2 spread during the era of incessant viral mutations.

Role of Serum Amyloid A as a Biomarker for Predicting the Severity and Prognosis of COVID-19

OBJECTIVE

To detect biomarkers that can be used to predict COVID-19 severity to identify patients with high probability of disease progression and poor prognosis.

METHODS

Of the 102 patients with confirmed COVID-19 who were admitted to King Fahd General Hospital, Jeddah City, Saudi Arabia, from July 1, 2021 to August 5, 2021, 50 were included in this cross-sectional study to investigate the influence of serum amyloid A (SAA) on disease severity and survival outcomes of COVID-19 patients. Dynamic shifts in SAA, C-reactive protein (CRP), white blood cell (WBC), lymphocytes, neutrophils, biochemical markers, and disease progression were examined. At admission, and at three, five, and seven days after treatment, at least four data samples were collected from all patients, and they underwent clinical status assessments.

RESULTS

Critically ill patients showed higher SAA and CRP levels and WBC and neutrophil counts and significantly lower lymphocyte and eosinophil counts compared to the moderately/severely ill patients, especially with regard to disease progression. Similarly, nonsurvivors had higher SAA levels than survivors. The moderately/severely ill patients and the survivors had significantly higher dynamic changes in SAA compared to the critically ill patients and nonsurvivors, respectively, with differences clearly noticed on the fifth and seventh day of treatment. ROC curve analysis revealed that the combination of SAA and CRP was valuable in evaluating the disease progression and prognosis of COVID-19 patients at different time points; however, a combination of SAA and lymphocyte counts was more sensitive for disease severity prediction on admission. The most sensitive parameters for predicting survival on admission were the combination of SAA/WBC and SAA/neutrophil count.

CONCLUSIONS

The study findings indicate that SAA can be used as a sensitive indicator to assess the degree of disease severity and survival outcomes of COVID-19 patients.

A comprehensive review of BBV152 vaccine development, effectiveness, safety, challenges, and prospects

The world has responded to the COVID-19 pandemic with unprecedented speed and vigor in the mass vaccination campaigns, targeted to reduce COVID-19 severity and mortality, reduce the pressure on the healthcare system, re-open society, and reduction in disease mortality and morbidity. Here we review the preclinical and clinical development of BBV152, a whole virus inactivated vaccine and an important tool in the fight to control this pandemic. BBV152, formulated with a TLR7/8 agonist adjuvant generates a Th1-biased immune response that induces high neutralization efficacy against different SARS-CoV-2 variants of concern and robust long-term memory B- and T-cell responses. With seroconversion rates as high as 98.3% in vaccinated individuals, BBV152 shows 77.8% and 93.4% protection from symptomatic COVID-19 disease and severe symptomatic COVID-19 disease respectively. Studies in pediatric populations show superior immunogenicity (geometric mean titer ratio of 1.76 compared to an adult) with a seroconversion rate of >95%. The reactogenicity and safety profiles were comparable across all pediatric age groups between 2-18 yrs. as in adults. Like most approved vaccines, the BBV152 booster given 6 months after full vaccination, reverses a waning immunity, restores the neutralization efficacy, and shows synergy in a heterologous prime-boost study with about 3-fold or 300% increase in neutralization titers against multiple SARS-CoV-2 variants of concern. Based on the interim Phase III data, BBV152 received full authorization for adults and emergency use authorization for children from ages 6 to 18 years in India. It is also licensed for emergency use in 14 countries globally. Over 313 million vaccine doses have already been administered in India alone by April 18th, 2022.

Initial viral cycle threshold values in patients with COVID-19 and their clinical significance

BACKGROUND

The connection between initial viral cycle threshold (Ct) values of the SARS-CoV-2 with symptoms and hospital course is not clearly studied.

METHODS

This is a retrospective study of hospitalized COVID-19 patients from Jun 1st 2020 to March 30th, 2021 examining the relationship between initial viral cycle threshold (Ct) values of SARS-CoV-2 as obtained from nasopharyngeal samples. The clinical presentations and outcomes were analyzed in relation to the initial Ct values.

RESULTS

The study included 202 hospitalized COVID-19 patients with a mean age (± SD) of 54.75 (± 15.93) and 123 (60.9%) males and 79 (39.1%) females. Of all the patients, the most frequent comorbidity was diabetes mellitus (95; 47%) and the most frequent symptoms were fever (148; 73.3%) and cough (141; 69.8%). There was no significant difference in relation to underlying conditions, clinical presentation, radiographic and laboratory data among those with low, medium and high Ct values. The mean Ct values showed no statistical change over the 10-month study period.

CONCLUSIONS

Initial SARS-CoV-2 Ct values did not show any association with clinical symptoms and did not predict the need for mechanical intubation or death.

Co-relation of SARS-CoV-2 related 30-d mortality with HRCT score and RT-PCR Ct value-based viral load in patients with solid malignancy

BACKGROUND

Coronavirus disease 2019 (COVID-19) patients with malignancy are published worldwide but are lacking in data from India.

AIM

To characterize COVID-19 related mortality outcomes within 30 d of diagnosis with HRCT score and RT-PCR Ct value-based viral load in various solid malignancies.

METHODS

Patients included in this study were with an active or previous malignancy and with confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection from the institute database. We collected data on demographic details, baseline clinical conditions, medications, cancer diagnosis, treatment and the COVID-19 disease course. The primary endpoint was the association between the mortality outcome and the potential prognostic variables, specially, HRCT score, RT-PCR Ct value-based viral load, etc. using logistic regression analyses treatment received in 30 d.

RESULTS

Out of 131 patients, 123 met inclusion criteria for our analysis. The median age was 57 years (interquartile range = 19-82) while 7 (5.7%) were aged 75 years or older. The most prevalent malignancies were of GUT origin 49 (39.8%), hepatopancreatobiliary (HPB) 40 (32.5%). 109 (88.6%) patients were on active anticancer treatment, 115 (93.5%) had active (measurable) cancer. At analysis on May 20, 2021, 26 (21.1%) patients had died. In logistic regression analysis, independent factors associated with an increased 30-d mortality were in patients with the symptomatic presentation. Chemotherapy in the last 4 wk, number of comorbidities (≥ 2 vs none: 3.43, 1.08-8.56). The univariate analysis showed that the risk of death was significantly associated with the HRCT score: for moderate (8-15) [odds ratio (OR): 3.44; 95% confidence interval (CI): 1.3-9.12; P = 0.0132], severe (> 15) (OR: 7.44; 95%CI: 1.58-35.1; P = 0.0112).

CONCLUSION

To the best of our knowledge, this is the first study from India reporting the association of HRCT score and RT-PCR Ct value-based 30-d mortality outcomes in SARS-CoV-2 infected cancer patients.

SARS-CoV-2 RT-qPCR Test Detection Rates Are Associated with Patient Age, Sex, and Time since Diagnosis

Quantifying the detection rate of the widely used quantitative RT-PCR (RT-qPCR) test for severe acute respiratory syndrome coronavirus 2 and its dependence on patient demographic characteristics and disease progression is key in designing epidemiologic strategies. Analyzing 843,917 test results of 521,696 patients, a "positive period" was defined for each patient between diagnosis of coronavirus disease 2019 and the last positive test result. The fraction of positive test results within this period was then used to estimate detection rate. Regression analyses were used to determine associations of detection with time of sampling after diagnosis, patient demographic characteristics, and viral RNA copy number based on RT-qPCR cycle threshold values of the next positive test result. The overall detection rate in tests performed within 14 days after diagnosis was 83.1%. This rate was higher at days 0 to 5 after diagnosis (89.3%). Furthermore, detection rate was strongly associated with age and sex. Finally, the detection rate with the Allplex 2019-nCoV RT-qPCR kit was associated, at the single-patient level, with viral RNA copy number (P < 10-9). These results show that the reliability of the test result is reduced in later days as well as for women and younger patients, in whom the viral loads are typically lower.

Viral Load in COVID-19 Patients: Implications for Prognosis and Vaccine Efficacy in the Context of Emerging SARS-CoV-2 Variants

The worldwide spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused an unprecedented public health crisis in the 21st century. As the pandemic evolves, the emergence of SARS-CoV-2 has been characterized by the emergence of new variants of concern (VOCs), which resulted in a catastrophic impact on SARS-CoV-2 infection. In light of this, research groups around the world are unraveling key aspects of the associated illness, coronavirus disease 2019 (COVID-19). A cumulative body of data has indicated that the SARS-CoV-2 viral load may be a determinant of the COVID-19 severity. Here we summarize the main characteristics of the emerging variants of SARS-CoV-2, discussing their impact on viral transmissibility, viral load, disease severity, vaccine breakthrough, and lethality among COVID-19 patients. We also provide a rundown of the rapidly expanding scientific evidence from clinical studies and animal models that indicate how viral load could be linked to COVID-19 prognosis and vaccine efficacy among vaccinated individuals, highlighting the differences compared to unvaccinated individuals.

Movable Layer Device for Rapid Detection of Influenza a H1N1 Virus Using Highly Bright Multi-Quantum Dot-Embedded Particles and Magnetic Beads

Preventing the rapid spread of viral infectious diseases has become a major concern for global health. In this study, we present a microfluidic platform that performs an immunoassay of viral antigens in a simple, automated, yet highly sensitive manner. The device uses silica particles embedded with highly bright quantum dots (QD2) and performs the immunoassay with a vertically movable top layer and a rotating bottom layer. Through the motion of the layers and the surface tension in the liquids, reagents move from top chambers to bottom chambers and mix homogeneously. A tip in the top layer with a mobile permanent magnet moves the immune complexes comprising the magnetic beads, virus particles, and QD2 between the bottom chambers. In this way, our automated device achieves a highly sensitive magnetic bead-based sandwich immunoassay for the influenza A H1N1 virus within 32.5 min. The detection limit of our method is 5.1 × 10-4 hemagglutination units, which is 2 × 103 times more sensitive than that of the conventional hemagglutination method and is comparable to PCR. Our device is useful for the rapid and sensitive detection of infectious diseases in point-of-care applications and resource-limited environments.

Adjuvant Therapy System of COVID-19 Patient: Integrating Warning, Therapy, Post-Therapy Psychological Intervention

The 2019 novel coronavirus(COVID-19) spreads rapidly, and the large-scale infection leads to the lack of medical resources. For the purpose of providing more reasonable medical service to COVID-19 patients, we designed an novel adjuvant therapy system integrating warning, therapy, and post-therapy psychological intervention. The system combines data analysis, communication networks and artificial intelligence(AI) to design a guidance framework for the treatment of COVID-19 patients. Specifically, in this system, we first can use blood characteristic data to help make a definite diagnosis and classify the patients. Then, the classification results, together with the blood characteristics and underlying diseases disease characteristics of the patient, can be used to assist the doctor in treat treating the patient according to AI algorithms. Moreover, after the patient is discharged from the hospital, the system can monitor the psychological and physiological state at the data collection layer. And in the data feedback layer, this system can analyze the data and report the abnormalities of the patient to the doctor through communication network. Experiments show the effectiveness of our proposed system.

Contact tracing period and epidemiological characteristics of an outbreak by SARS-CoV-2 Delta variant in Guangzhou

Objectives

An outbreak of the SARS-CoV-2 Delta variant occurred in Guangzhou in 2021. This study aimed to identify the transmission dynamics and epidemiological characteristics of the Delta variant outbreak to formulate an effective prevention strategy.

Methods

A total of 13102 close contacts and 69 index cases were collected. The incubation period, serial interval, and time interval from the exposure of close contacts to the symptom onset of cases were estimated. Transmission risks based on the exposure time and various characteristics were also assessed.

Results

The mean time from exposure to symptom onset among non-household presymptomatic transmission was 3.83 ± 2.29 days, the incubation period was 5 days, and the serial interval was 3 days. The secondary attack rate was high within 4 days before onset and 4–10 days after symptom onset. Compared with other contact types, household contact had a higher transmission risk. The transmission risk increased with the number and frequency of contact with index cases. Cycle threshold (Ct) values were associated with lower transmission risk (adjusted odds ratio [OR] 0.93 [95% CI 0.88–0.99] for ORF 1ab gene; adjusted OR 0.91 [95% CI 0.86–0.97] for N gene).

Conclusion

The contact tracing period may need to be extended to 4 days before symptom onset. The low Ct value of index cases, the high number and frequency of contact with index cases, and household contacts were associated with a higher transmission risk of SARS-CoV-2 Delta.

Can systemic immune inflammation index at admission predict in-hospital mortality in chronic kidney disease patients with SARS-CoV-2 infection?

BACKGROUND AND AIM

Patients with chronic kidney disease (CKD) are susceptible to SARS-CoV-2 infection and more prone to develop severe disease. It is important to know predictors of poor outcomes to optimize the strategies of care.

METHODS

93 patients with CKD and 93 age-sex matched patients without CKD were included in the study. Data on demographic, clinical features, hematological indices and outcomes were noted and compared between the groups. Neutrophile to lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), systemic immune inflammation index (SII) (platelet counts×neutrophil counts/lymphocyte counts) and lymphocyte-to-CRP ratio (LCR) were calculated on admission and the association of these markers with disease mortality in CKD patients was identified.

RESULTS

CKD patients had higher risk of severe disease, and mortality compared to non-CKD patients (72% vs 50.5%, p=0.003, 36.6% vs 10.8%, p<0.001, respectively) and were more likely to have higher values of immuno-inflammatory indices (leukocyte count, neutrophil, NLR, SII and C-reactive protein, etc.) and lower level of lymphocyte and LCR. Also, higher levels of NLR, SII, PLR and lower level of LCR were seen in CKD patients who died compared to those recovered. In a receiver operating characteristic curve analysis, NLR, SII, PLR and LCR area under the curve for in-hospital mortality of CKD patients were 0.830, 0.811, 0.664 and 0.712, respectively. Among all parameters, NLR and SII gave us the best ability to distinguish patients with higher risk of death. Based on the cut-off value of 1180.5, the sensitivity and specificity of the SII for predicting in-hospital mortality were found to be 67.5% and 79.6%, respectively. The corresponding sensitivity and specificity of the NLR were 85.2% and 66.1%, respectively, at the cut-off value of 5.1. Forward stepwise logistic regression analysis showed that NLR (≥5.1), SII (≥1180.5) and LCR (≤9) were predictors for in-hospital mortality.

CONCLUSION

We report for the first time that SII is able to distinguish COVID-19 infected CKD patients of worse survival and it is as powerful as NLR in this regard. As SII is easily quantified from blood sample data, it may assist for early identification and timely management of CKD patients with worse survival.

Changes of Routine Hematological Parameters in COVID-19 Patients: Correlation with Imaging Findings, RT-PCR and Outcome

BACKGROUND & OBJECTIVE

Coronavirus disease 2019 (COVID-19) is progressively spreading, and many researchers have focused on the prognostic value of laboratory analyses. This study reviewed routine blood parameters, upper respiratory viral load, and chest imaging in recovered and expired COVID-19 patients and evaluated possible correlations.

METHODS

In this retrograde study, 138 COVID-19 cases were enrolled. Chest tomography scores of patients, routine hematologic and biochemical parameters, and respiratory viral loads were measured. Furthermore, their correlation with severity of disease and the outcome was investigated during a week of admission.

RESULTS

The mean age of participants was 58.6±16; 36.2% of whom were diagnosed as critical, 8.7% expired, and 46% showed less than 50% lung opacity. The expiring rate was only correlated to the severity of illness and viral load. During admission, hemoglobin concentration was decreased in critical patients (from 11.49±0.27 to 10.59±0.36, P=0.042) and also among CT-scan scoring groups (P=0.000), while neutrophils (P=0.04), WBC (P=0.03), and platelets (P=0.000) count were increased. In patients with more than 50% lung opacity, leukocyte counts were decreased, but neutrophil and platelets counts showed raise (all P<0.05), while other hematologic parameters did not change. CRP and LDH demonstrated no increase based on the severity of the illness, RT-PCR viral loads and/or outcome. However, both CRP and LDH were increased in patients with more than 50% lobal opacity (CRP: 69.3±9.9 to 1021.1±7.5 and LDH:589.5±93.2 to 1128.6±15.81, P<0.05).

CONCLUSION

We found that hemoglobin, white blood cells, neutrophil, lymphocytes, and platelets count together with chest tomography score might be beneficial for expedition the diagnosis, assessmen the severity of the disease, and outcome in the hospitalized cases, while CRP and LDH might be considered as the consequence of lung involvement.

A comparison between virus- versus patients-centred therapeutic attempts to reduce COVID-19 mortality

Since December 2019, coronavirus disease 2019 (COVID-19), caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has changed our lives. Elderly and those with comorbidities represent the vast majority of patients hospitalized with severe COVID-19 symptoms, including acute respiratory disease syndrome and cardiac dysfunction. Despite a huge effort of the scientific community, improved treatment modalities limiting the severity and mortality of hospitalized COVID-19 patients are still required. Here, we compare the effectiveness of virus- and patients-centred strategies to reduce COVID-19 mortality. We also discuss the therapeutic options that might further reduce death rates associated with the disease in the future. Unexpectedly, extensive review of the literature suggests that SARS-CoV-2 viral load seems to be associated neither with the severity of symptoms nor with mortality of hospitalized patients with COVID-19. This may explain why, so far, virus-centred strategies using antivirals aiming to inhibit the viral replicative machinery have failed to reduce COVID-19 mortality in patients with respiratory failure. By contrast, anti-inflammatory treatments without antiviral capacities but centred on patients, such as dexamethasone or Tocilizumab®, reduce COVID-19 mortality. Finally, since the spike protein of SARS-CoV-2 binds to angiotensin converting enzyme 2 and inhibits its function, we explore the different treatment options focussing on rebalancing the renin-angiotensin system. This new therapeutic strategy could hopefully further reduce the severity of respiratory failure and limit COVID-19 mortality in elderly patients.

Features of Pathobiology and Clinical Translation of Approved Treatments for Coronavirus Disease 2019

BACKGROUND

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is currently the most important etiological agent of acute respiratory distress syndrome (ARDS) with millions of infections and deaths in the last 2 years worldwide. Several reasons and parameters are responsible for the difficult management of coronavirus disease-2019 (COVID-19) patients; the first is virus behavioral factors such as high transmission rate, and the different molecular and cellular mechanisms of pathogenesis remain a matter of controversy, which is another factor.

SUMMARY

In the present review, we attempted to explain about features of SARS-COV-2, particularly focusing on the various aspects of pathogenesis and treatment strategies.

KEY MESSAGES

We note evidence for the understanding of the precise molecular and cellular mechanisms of SARS-CoV-2 pathogenesis, which can help design the appropriate drug or vaccine. Additionally, and importantly, we reported the updated issues associated with the history and development of treatment strategies such as, drugs, vaccines, and other medications that have been approved or under consideration in clinics and markets worldwide.

Epidemiological Risk Factors for Acquiring Severe COVID-19: Prospective Cohort Study

Objectives

We aimed to determine epidemiological risk factors associated with acquiring severe coronavirus disease 2019 (COVID-19) in patients requiring hospitalization.

Methods

A prospective cohort study was conducted using a questionnaire comprised of six closed-ended questions to identify potential risk factors for severe COVID-19. Using COVID-19 associated illnesses and complications (pneumonia, acute respiratory distress syndrome, need for mechanical ventilation, acute kidney failure, cardiac failure, and thromboembolic events), we derived an index variable to measure the severity of COVID-19 in patients.

Results

We included 143 adult patients with confirmed COVID-19 of whom 62.2% (n = 89) were male and 37.8% (n = 54) were female. The average age of the cohort was 50.6±16.5 years. Our study found that being a female, working at the health care facility, being a healthcare worker, attending a mass gathering within the last 14 days, attending a gathering with 10 persons or less, and being admitted to a hospital were associated with increased risk of developing severe COVID-19. The only risk factor associated with severe COVID-19 was working at a health care facility (odds ratio = 33.42, p =0.029).

Conclusions

Intervention directed to control risk factors associated with acquiring severe COVID-19 should be a core priority for all countries, especially among high-risk occupations and workplaces, including working at a health care facility. A risk-based approach to prioritize vaccination among these high-risk individuals should be supported to strengthen the implementation of non-pharmaceutical interventions.

Venous Thromboembolism in Hospitalized COVID-19 Patients Treated in a Single Academic Center in Mexico: A Case Series Study

BACKGROUND

The increasing prevalence of venous thromboembolism (VTE) among patients with coronavirus disease 2019 (COVID-19) is a matter of concern as it contributes significantly to patients' morbidity and mortality. Data regarding the optimal anticoagulation regimen for VTE prevention and treatment remain scarce. This study describes the characteristics, treatment, and outcomes of COVID-19 patients with VTE treated in a single academic center in Mexico.

METHODS

We conducted a retrospective study of all patients with a positive PCR test for SARS-CoV-2 hospitalized in a single academic center in Monterrey, Mexico, between March 2020 and February 2021, with a radiologically confirmed VTE, including deep venous thrombosis (DVT) and pulmonary embolism (PE). Informed consent was obtained from each patient before reviewing their medical records.

RESULTS

Of the 2000 COVID-19 hospitalized patients, 36 (1.8%) developed VTE and were included in the analysis. The median age was 60 years (range 32-88 years), and up to 78% (n = 28) were males. Most patients (n = 34, 94%) had an underlying comorbidity and 47% (n = 17) had a BMI ≥ 30 kg/m2. In most cases (n=28, 78%), VTE presented as a PE, whereas the remaining 22% (n = 8) had a DVT. The median time between hospital admission and VTE was 8 days (range 0-33 days). Regarding the thromboprophylaxis regimen, 35/36 patients received low molecular weight heparin enoxaparin on admission, most commonly at a dose of 60 mg daily (n = 19, 53%). Other complications presented were superinfection (n = 19, 53%), acute kidney injury (n = 11, 31%), and septic shock (n = 5, 14%). A total of 69% of patients (n = 25) required intensive care unit admission, and patients' overall mortality was 55.6%.

CONCLUSION

VTE remains a significant cause of increased morbidity and mortality among patients with COVID-19. The strikingly high mortality among patients with VTE highlights the need for further investigation regarding the best preventive, diagnostic, and treatment approaches.

[Can systemic immune inflammation index at admission predict in-hospital mortality in chronic kidney disease patients with SARS-CoV-2 infection]

BACKGROUND AND AIM

Patients with chronic kidney disease (CKD) are susceptible to SARS-CoV-2 infection and more prone to develop severe disease. It is important to know predictors of poor outcomes to optimize the strategies of care.

METHODS

93 patients with CKD and 93 age-sex matched patients without CKD were included in the study. Data on demographic, clinical features, hematological indices and outcomes were noted and compared between the groups. Neutrophile to lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), systemic immune inflammation index (SII) (platelet counts × neutrophil counts / lymphocyte counts) and lymphocyte-to-CRP ratio (LCR) were calculated on admission and the association of these markers with disease mortality in CKD patients was identified.

RESULTS

CKD patients had higher risk of severe disease, and mortality compared to non-CKD patients (72% vs 50.5%, p=0.003, 36,6% vs 10.8%, p<0.001, respectively) and were more likely to have higher values of immuno-inflammatory indices (leucocyte count, neutrophil, NLR, SII and C-reactive protein etc.) and lower level of lymphocyte and LCR. Also, higher levels of NLR, SII, PLR and lower level of LCR were seen in CKD patients who died compared to those recovered. In a receiver operating characteristic curve analysis, NLR, SII, PLR and LCR area under the curve for in-hospital mortality of CKD patients were 0.830, 0.811, 0.664 and 0.712, respectively. Among all parameters, NLR and SII gave us the best ability to distinguish patients with higher risk of death. Based on the cut-off value of 1180.5, the sensitivity and specificity of the SII for predicting in-hospital mortality were found to be 67.5% and 79.6%, respectively. The corresponding sensitivity and specificity of the NLR were 85.2% and 66.1%, respectively, at the cut-off value of 5.1. Forward stepwise logistic regression analysis showed that NLR (≥5.1), SII (≥1180.5) and LCR (≤9) were predictors for in-hospital mortality.

CONCLUSION

We report for the first time that SII is able to distinguish COVID-19 infected CKD patients of worse survival and it is as powerful as NLR in this regard. As SII is easily quantified from blood sample data, it may assist for early identification and timely management of CKD patients with worse survival.

Association of cycle threshold values of CBNAAT with severity and outcome in COVID-19

Determination of viral load through cycle threshold (Ct) values may act as a predictor of severity and outcomes in patients with corona virus disease 2019 (COVID-19). However, variable literature is available regarding this relationship. Our study attempted to explore this association and the effect of various socio-demographic and clinical parameters on severity and outcome of COVID-19. Retrospective analysis of records of 731 patients whose nasopharyngeal/oropharyngeal swabs were subjected to cartridge based nucleic acid amplification (CBNAAT) on Cepheid Xpert Xpress SARS-CoV-2 was done. Ct values of N2 and E genes were studied in relation to severity and outcome of COVID-19. The viral load as determined by Ct values was classified as high (<25), medium (25.1-32) and low (>32). Association of socio-demographic and clinical parameters with respect to severity and outcome was also studied. Severity and mortality were significantly more in elder individuals, those belonging to the rural background, those with symptoms >7 days in duration before presentation and those with increasing number of co-morbidities (severity: p<0.001; mortality: p<0.001, 0.005, 0.006 and <0.001, respectively). The Ct values of gene N2 and E inversely correlated with severity and mortality from the disease (N2 gene: p=0.001 for both severity and mortality, E gene: severity: p<0.001, mortality: p=0.016, respectively). The severity of the illness and chances of mortality were significantly lesser when the CT value of N2 gene was >32, in comparison when it was upto 25, and when between 25.1 and 32 (severity: p=0.032 and 0.003, respectively; mortality: p=0.018 and <0.001, respectively). Almost similar trends were seen with respect to E gene (severity: p<0.001 and 0.067, respectively; mortality p=0.175 and 0.005, respectively). Viral load as determined by Ct values of N2 and E genes can act as surrogate markers for prediction of severity and disease outcomes in COVID-19.

SARS-CoV-2 (COVID-19), viral load and clinical outcomes; lessons learned one year into the pandemic: A systematic review

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is diagnosed via real time reverse transcriptase polymerase chain reaction (RT-PCR) and reported as a binary assessment of the test being positive or negative. High SARS-CoV-2 viral load is an independent predictor of disease severity and mortality. Quantitative RT-PCR may be useful in predicting the clinical course and prognosis of patients diagnosed with coronavirus disease 2019 (COVID-19).

AIM

To identify whether quantitative SARS-CoV-2 viral load assay correlates with clinical outcome in COVID-19 infections.

METHODS

A systematic literature search was undertaken for a period between December 30, 2019 to December 31, 2020 in PubMed/MEDLINE using combination of terms "COVID-19, SARS-CoV-2, Ct values, Log10 copies, quantitative viral load, viral dynamics, kinetics, association with severity, sepsis, mortality and infectiousness''. After screening 990 manuscripts, a total of 60 manuscripts which met the inclusion criteria were identified. Data on age, number of patients, sample sites, RT-PCR targets, disease severity, intensive care unit admission, mortality and conclusions of the studies was extracted, organized and is analyzed.

RESULTS

At present there is no Food and Drug Administration Emergency Use Authorization for quantitative viral load assay in the current pandemic. The intent of this research is to identify whether quantitative SARS-CoV-2 viral load assay correlates with severity of infection and mortality? High SARS-CoV-2 viral load was found to be an independent predictor of disease severity and mortality in majority of studies, and may be useful in COVID-19 infection in susceptible individuals such as elderly, patients with co-existing medical illness such as diabetes, heart diseases and immunosuppressed. High viral load is also associated with elevated levels of TNF-α, IFN-γ, IL-2, IL-4, IL-6, IL-10 and C reactive protein contributing to a hyper-inflammatory state and severe infection. However there is a wide heterogeneity in fluid samples and different phases of the disease and these data should be interpreted with caution and considered only as trends.

CONCLUSION

Our observations support the hypothesis of reporting quantitative RT-PCR in SARS-CoV-2 infection. It may serve as a guiding principle for therapy and infection control policies for current and future pandemics.

Diagnostic performance of COVID-19 serological assays during early infection: A systematic review and meta-analysis of 11 516 samples

OBJECTIVE

The use of coronavirus disease 2019 (COVID-19) serological testing to diagnose acute infection or determine population seroprevalence relies on understanding assay accuracy during early infection. We aimed to evaluate the diagnostic performance of serological testing in COVID-19 by providing summary sensitivity and specificity estimates with time from symptom onset.

METHODS

A systematic search of Ovid MEDLINE, Embase, Cochrane Central Register of Controlled Trials (CENTRAL) and PubMed was performed up to May 13, 2020. All English language, original peer-reviewed publications reporting the diagnostic performance of serological testing vis-à-vis virologically confirmed SARS-CoV-2 infection were included.

RESULTS

Our search yielded 599 unique publications. A total of 39 publications reporting 11 516 samples from 8872 human participants met eligibility criteria for inclusion in our study. Pooled percentages of IgM and IgG seroconversion by Day 7, 14, 21, 28 and after Day 28 were 37.5%, 73.3%, 81.3%, 72.3% and 73.3%, and 35.4%, 80.6%, 93.3%, 84.4% and 98.9%, respectively. By Day 21, summary estimate of IgM sensitivity was 0.872 (95% CI: 0.784-0.928) and specificity 0.973 (95% CI: 0.938-0.988), while IgG sensitivity was 0.913 (95% CI: 0.823-0.959) and specificity 0.960 (95% CI: 0.919-0.980). On meta-regression, IgM and IgG test accuracy was significantly higher at Day 14 using enzyme-linked immunosorbent assay (ELISA) compared to other methods.

CONCLUSIONS

Serological assays offer imperfect sensitivity for the diagnosis of acute SARS-CoV-2 infection. Estimates of population seroprevalence during or shortly after an outbreak will need to adjust for the delay between infection, symptom onset and seroconversion.

SARS-CoV-2 quantitative real time PCR and viral loads analysis among asymptomatic and symptomatic patients: an observational study on an outbreak in two nursing facilities in Campania Region (Southern Italy)

BACKGROUND

In December 2019 an outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 was first observed in Wuhan, China. The virus has spread rapidly throughout the world creating a pandemic scenario. Several risk factors have been identified, such as age, sex, concomitant diseases as well as viral load. A key point is the role of asymptomatic people in spreading SARS-CoV-2. An observational study in Southern Italy was conducted in order to elucidate the possible role of asymptomatic individuals related to their viral loads in the transmission of the virus within two nursing facilities.

METHODS

Oro-nasopharyngeal swabs from 179 nursing health care workers and patients were collected. SARS-CoV-2 RT-qPCR was performed and viral loads were calculated by using standard curve. A statistical correlation between viral loads, the presence/absence of symptoms, age and sex variables was investigated.

RESULTS

SARS-CoV-2 was confirmed in the 50.8 % (n = 91) of the cases. Median age of positive individuals resulted higher than negative ones. Over 65 year as well as female individuals showed higher susceptibility to SARS-CoV-2 infection, OR = 3.93 and 2.86, respectively. Among 91 tested positive, the 70.3 % was symptomatic while the 29.7 % was asymptomatic. Median viral loads of asymptomatic individuals were found statistically significant higher than symptomatic ones (p = 0.001), while no influence was observed in age and sex variables. The presence of comorbidities was 8.9 folds higher in patients who showed and developed symptoms compared to non-symptomatic ones. Moreover, higher viral loads were found in patients who remained asymptomatic than pre-symptomatic (p = 0.022).

CONCLUSIONS

A range from 9.2 to 69 % of confirmed SARS-CoV-2 cases remains asymptomatic, moreover, sporadic transmissions from asymptomatic people are reported, that makes their involvement an important issue to take into account in the spreading control of the virus. An asymptomatic clinical course was observed in the 29.7 % of positive individuals, moreover, median viral loads resulted to be statistically significant when compared to symptomatic ones. Surely, such a relevant frequency should not be ignored in relation to the spread of the disease in an environment which has not only important intrinsic (age, sex, concomitant diseases) but also extrinsic factors such as high population density and close contacts.

SARS-CoV-2 quantitative real time PCR and viral loads analysis among asymptomatic and symptomatic patients: an observational study on an outbreak in two nursing facilities in Campania Region (Southern Italy)

BACKGROUND

In December 2019 an outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 was first observed in Wuhan, China. The virus has spread rapidly throughout the world creating a pandemic scenario. Several risk factors have been identified, such as age, sex, concomitant diseases as well as viral load. A key point is the role of asymptomatic people in spreading SARS-CoV-2. An observational study in Southern Italy was conducted in order to elucidate the possible role of asymptomatic individuals related to their viral loads in the transmission of the virus within two nursing facilities.

METHODS

Oro-nasopharyngeal swabs from 179 nursing health care workers and patients were collected. SARS-CoV-2 RT-qPCR was performed and viral loads were calculated by using standard curve. A statistical correlation between viral loads, the presence/absence of symptoms, age and sex variables was investigated.

RESULTS

SARS-CoV-2 was confirmed in the 50.8 % (n = 91) of the cases. Median age of positive individuals resulted higher than negative ones. Over 65 year as well as female individuals showed higher susceptibility to SARS-CoV-2 infection, OR = 3.93 and 2.86, respectively. Among 91 tested positive, the 70.3 % was symptomatic while the 29.7 % was asymptomatic. Median viral loads of asymptomatic individuals were found statistically significant higher than symptomatic ones (p = 0.001), while no influence was observed in age and sex variables. The presence of comorbidities was 8.9 folds higher in patients who showed and developed symptoms compared to non-symptomatic ones. Moreover, higher viral loads were found in patients who remained asymptomatic than pre-symptomatic (p = 0.022).

CONCLUSIONS

A range from 9.2 to 69 % of confirmed SARS-CoV-2 cases remains asymptomatic, moreover, sporadic transmissions from asymptomatic people are reported, that makes their involvement an important issue to take into account in the spreading control of the virus. An asymptomatic clinical course was observed in the 29.7 % of positive individuals, moreover, median viral loads resulted to be statistically significant when compared to symptomatic ones. Surely, such a relevant frequency should not be ignored in relation to the spread of the disease in an environment which has not only important intrinsic (age, sex, concomitant diseases) but also extrinsic factors such as high population density and close contacts.

Viral Dynamics and Real-Time RT-PCR Ct Values Correlation with Disease Severity in COVID-19

Real-time RT-PCR is considered the gold standard confirmatory test for coronavirus disease 2019 (COVID-19). However, many scientists disagree, and it is essential to understand that several factors and variables can cause a false-negative test. In this context, cycle threshold (Ct) values are being utilized to diagnose or predict SARS-CoV-2 infection. This practice has a significant clinical utility as Ct values can be correlated with the viral load. In addition, Ct values have a strong correlation with multiple haematological and biochemical markers. However, it is essential to consider that Ct values might be affected by pre-analytic, analytic, and post-analytical variables such as collection technique, specimen type, sampling time, viral kinetics, transport and storage conditions, nucleic acid extraction, viral RNA load, primer designing, real-time PCR efficiency, and Ct value determination method. Therefore, understanding the interpretation of Ct values and other influential factors could play a crucial role in interpreting viral load and disease severity. In several clinical studies consisting of small or large sample sizes, several discrepancies exist regarding a significant positive correlation between the Ct value and disease severity in COVID-19. In this context, a revised review of the literature has been conducted to fill the knowledge gaps regarding the correlations between Ct values and severity/fatality rates of patients with COVID-19. Various databases such as PubMed, Science Direct, Medline, Scopus, and Google Scholar were searched up to April 2021 by using keywords including "RT-PCR or viral load", "SARS-CoV-2 and RT-PCR", "Ct value and viral load", "Ct value or COVID-19". Research articles were extracted and selected independently by the authors and included in the present review based on their relevance to the study. The current narrative review explores the correlation of Ct values with mortality, disease progression, severity, and infectivity. We also discuss the factors that can affect these values, such as collection technique, type of swab, sampling method, etc.

Prior immunosuppressive therapy is associated with mortality in COVID-19 patients: A retrospective study of 835 patients

Though it is widely believed that chronic immunosuppressive medications increase the severity of coronavirus disease 2019 (COVID-19) illness, there is little data to support this. We performed a retrospective study of COVID-19 positive patients diagnosed at a single academic medical center between March 10, 2020 and October 13, 2020. A total of 835 patients diagnosed with COVID-19 by polymerase chain reaction were included (median age 64 years; 52% female). Of these, 46 (5.5%) had a prescription for an immunosuppressive therapy before diagnosis, most commonly oral steroids (20, 43%), mycophenolate (12, 26%), or tacrolimus (11, 24%). Patients on immunosuppressive therapy with COVID-19 had increased mortality (30% vs. 17%, p = 0.036; odds ratio 2.1, 95% confidence interval 1.11-4.04), which remained significant (p = 0.040) after performing multivariate logistic regression controlling for gender, age, race, and comorbidity status. Laboratory markers of inflammation were uniformly elevated in both patients on or not on immunosuppressive therapies who died, but lymphocytes and neutrophils were decreased in both COVID-19 patients on immunosuppressive therapies who died and who remained alive. These findings demonstrate that COVID-19 disease is more severe in patients taking prior immunosuppressive medications. This finding emphasizes the need for aggressive monitoring and supportive care for immunosuppressed patients who are diagnosed with COVID-19.

Molecular Docking Study of Antibiotics, Anti-Inflammatory Drugs and [Eu(TTA)3⋅AMX] Complex as COVID-19 Biomarker through Interaction of Its Main Protease (Mpro)

Coronavirus Acute Respiratory Syndrome (SARS-CoV-2) is a very recent viral infection and has generated one of the world’s biggest problems of all time. There is no scientific evidence and clinical trials to indicate that possible therapies have shown results in suspected or confirmed patients other than the use of immunizations. Given the above, some substances are being studied to be applied to contain their spread and further damage. This work aims to perform an in silico study of amoxicillin, widely known as an antibiotic and used to prevent bacterial infections and a possible biomarker made from a complex with Europium (Eu). It was shown to have the ability to interact with the COVID-19 protein in Mpro protease as ligands. The study was conducted using the AutoDock Vina with Lamarckian genetic model algorithm (GA) combined with the estimation of grid-based energy in rigid and flexible conformation. Compared to affinity energy, amoxicillin presented [Formula: see text][Formula: see text]kcal/mol, which was better than its co-crystallized ligand in the study. The Europium complex, where its synthesis was also demonstrated in this work, presented energy of [Formula: see text][Formula: see text]kcal/mol with hydrogen bonds and possible color change when UV light was applied. For the choice of the best poses in the simulation, the neural network parameter, NNScore2, was used. It can be affirmed that this study is still introductory but promising both in the treatment and identification of the virus.

A Well-Structured Follow-Up Program is Required after Recovery from Coronavirus Disease 2019 (COVID-19); Release from Quarantine is Not the End of Treatment

During the Coronavirus Infection Disease-19 (COVID-19) pandemic, the number of patients released from quarantine is exceeding the number of newly diagnosed cases. This study is a retrospective cohort study in which consultation data were collected from a COVID-19 follow-up health consultation program. The studied population was selected from patients who recovered after quarantine and treatment for COVID-19 in Daegu City and in Gyeongsangbukdo province, Korea, from March to June 2020. The healthcare providers comprised 20 family-medicine specialists who consulted and educated the patients through phone calls in accordance with structured guidelines. Physical and mental status before and after recovery were compared among patients who received a single consultation and those who received two or more consultations. A total of 1604 subjects were selected for the final analysis. Of these, 1145 (71.4%) had one consultation and 459 (28.6%) had two or more. The group that had two or more consultations reported significantly more physical symptoms, more psychological symptoms (including depression), and more psychological stress. Multivariate forward selection logistic regression analysis showed that re-confirmed cases of COVID-19, physical symptoms after quarantine, feelings of depression, and psychological stress had a significant effect on the number of consultations received. In conclusion, COVID-19 has various physical and mental sequelae after discharge from quarantine. Therefore, a well-structured follow-up program is needed after recovery.

A tricompartmental model of lung oxygenation disruption to explain pulmonary and systemic pathology in severe COVID-19

The emergent 21st century betacoronaviruses, including SARS-CoV-2, lead to clinicopathological manifestations with unusual features, such as early-onset chest pain, pulmonary infarction, and pulmonary and systemic thromboembolism that is pathologically linked to extensive capillary, arteriolar, and venular thrombosis. Early ground glass opacities detected by CT, which are reminiscent of lung infarcts associated with pulmonary embolism, point to a novel vascular pathology in COVID-19. Under physiological conditions, normal parenchymal oxygenation is maintained by three sources: the alveolus itself and dual oxygen supply from the pulmonary and bronchial artery circulations. We propose a model in which these three components are disrupted in COVID-19 pneumonia, with severe viral alveolitis and concomitant immunothrombotic obstruction of the pulmonary and bronchiolar circulation. Tricompartmental disruption might have two main consequences: systemic clot embolisation from pulmonary vein territory immunothrombosis, and alveolar–capillary barrier disruption with systemic access of thrombogenic viral material. Our model encompasses the known pathological and clinical features of severe COVID-19, and has implications for understanding patient responses to immunomodulatory therapies, which might exert an anti-inflammatory effect within the vascular compartments.

Circulating Calprotectin as a Biomarker of COVID-19 Severity

INTRODUCTION

Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Although demographic and clinical parameters such as sex, age, comorbidities, genetic background and various biomarkers have been identified as risk factors, there is an unmet need to predict the risk and onset of severe inflammatory disease leading to poor clinical outcomes. In addition, very few mechanistic biomarkers are available to inform targeted treatment of severe (auto)-inflammatory conditions associated with COVID-19. Calprotectin, also known as S100A8/S100A9, MRP8/14 (Myeloid-Related Protein) or L1, is a heterodimer involved in neutrophil-related inflammatory processes. In COVID-19 patients, calprotectin levels were reported to be associated with poor clinical outcomes such as significantly reduced survival time, especially in patients with severe pulmonary disease.

AREAS COVERED

Pubmed was searched using the following keywords: Calprotectin + COVID19, S100A8/A9 + COVID19, S100A8 + COVID-19, S100A9 + COVID-19, MRP8/14 + COVID19; L1 + COVID-19 between May 2020 and 8 March 2021. The results summarized in this review provide supporting evidence and propose future directions that define calprotectin as an important biomarker in COVID-19.

EXPERT OPINION

Calprotectin represents a promising serological biomarker for the risk assessment of COVID-19 patients.

Heterogeneity in transmissibility and shedding SARS-CoV-2 via droplets and aerosols

Background

Which virological factors mediate overdispersion in the transmissibility of emerging viruses remains a long-standing question in infectious disease epidemiology.

Methods

Here, we use systematic review to develop a comprehensive dataset of respiratory viral loads (rVLs) of SARS-CoV-2, SARS-CoV-1 and influenza A(H1N1)pdm09. We then comparatively meta-analyze the data and model individual infectiousness by shedding viable virus via respiratory droplets and aerosols.

Results

The analyses indicate heterogeneity in rVL as an intrinsic virological factor facilitating greater overdispersion for SARS-CoV-2 in the COVID-19 pandemic than A(H1N1)pdm09 in the 2009 influenza pandemic. For COVID-19, case heterogeneity remains broad throughout the infectious period, including for pediatric and asymptomatic infections. Hence, many COVID-19 cases inherently present minimal transmission risk, whereas highly infectious individuals shed tens to thousands of SARS-CoV-2 virions/min via droplets and aerosols while breathing, talking and singing. Coughing increases the contagiousness, especially in close contact, of symptomatic cases relative to asymptomatic ones. Infectiousness tends to be elevated between 1 and 5 days post-symptom onset.

Conclusions

Intrinsic case variation in rVL facilitates overdispersion in the transmissibility of emerging respiratory viruses. Our findings present considerations for disease control in the COVID-19 pandemic as well as future outbreaks of novel viruses.

Funding

Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant program, NSERC Senior Industrial Research Chair program and the Toronto COVID-19 Action Fund.

Designing and Interpreting Coronavirus Disease 2019 (COVID-19) Diagnostics: Mathematics, Visual Logistics, and Low Prevalence

CONTEXT.—

Coronavirus infectious disease-19 (COVID-19) diagnostics require understanding of how predictive values depend on sensitivity, specificity, and especially, low prevalence. Clear expectations, high sensitivity and specificity, and manufacturer disclosure will facilitate excellence of tests.

OBJECTIVES.—

To derive mathematical equations for designing and interpreting COVID-19 tests, assess US Food and Drug Administration (FDA) Emergency Use Authorization and Health Canada minimum requirements, establish sensitivity and specificity tiers, and enhance clinical performance in low prevalence settings.

DESIGN.—

PubMed and other sources generated articles on COVID-19 testing and prevalence. EndNote X9.1 consolidated references. Mathematica and open access software helped prove equations, perform recursive calculations, graph multivariate relationships, and visualize patterns, including a new relationship, predictive value geometric mean-squared.

RESULTS.—

Derived equations were used to illustrate shortcomings of COVID-19 diagnostics in low prevalence. Visual logistics helped establish sensitivity/specificity tiers. FDA/Canada's 90% sensitivity, 95% specificity minimum requirements generate excessive false positives at low prevalence. False positives exceed true positives at prevalence lower than 5.3%, or if sensitivity is improved to 100% and specificity to 98%, at prevalence lower than 2%. Recursive testing improves predictive value. Three tiers emerged from these results. With 100% sensitivity, physicians can select desired predictive values, then input local prevalence, to determine suitable specificity.

CONCLUSIONS.—

Understanding low prevalence impact will help health care providers meet COVID-19 needs for effective testing. Laypersons should receive clinical performance disclosure when submitting specimens. Home testing needs to meet the same high standards as other tests. In the long run, it will be more cost-effective to improve COVID-19 point-of-care tests rather than repeat testing multiple times.

The effect of real-time polymerase chain reaction cycle threshold values on perinatal outcomes of pregnant women with COVID-19

OBJECTIVE

To evaluate the effect of cycle threshold (Ct) values on the pregnancy outcomes of women with coronavirus disease 2019 (COVID-19).

MATERIALS AND METHODS

This prospective cohort study was conducted on pregnant women with COVID-19. A real-time polymerase chain reaction (RT-PCR) assay of a nasopharyngeal and oropharyngeal specimen was used for the diagnosis. Initial Ct values for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RT-PCR tests were recorded. 22.9 was the 50th percentile Ct value of the study population. The study population was divided into two groups based on their Ct values: (1) Cases with Higher Ct values (Ct > 22.9)(n = 50) and (2) Cases with lower Ct values (Ct ≤ 22.9)(n = 55). Demographic features, clinical characteristics, disease progression, laboratory test results and pregnancy outcomes were compared between the groups. A receiver operating characteristic (ROC) curve was used to assess the performance of Ct values in predicting obstetric complications.

RESULTS

Obstetric complication rate was significantly higher in cases with lower Ct values (p < .001). A significantly lower lymphocyte count together with higher ESR, procalcitonin and IL-6 values were observed in the cases with lower Ct values (p > .05). Additionally, a significantly higher NICU admission rate and longer hospital stays were present in the cases with lower Ct values (p > .05). The value in ROC curves with the best balance of sensitivity/specificity was 22.5 (85.7% sensitivity, 63.6% specificity).

CONCLUSION

Lower Ct values may be associated with an increased rate of obstetric complications in pregnant women with COVID-19. Physicians should be cautious in the management of cases with Ct levels below 22.5.

Serum Amyloid A in Inflammatory Rheumatic Diseases: A Compendious Review of a Renowned Biomarker

Serum amyloid A (SAA) is an acute phase protein with a significant importance for patients with inflammatory rheumatic diseases (IRD). The central role of SAA in pathogenesis of IRD has been confirmed by recent discoveries, including its involvement in the activation of the inflammasome cascade and recruitment of interleukin 17 producing T helper cells. Clinical utility of SAA in IRD was originally evaluated nearly half a century ago. From the first findings, it was clear that SAA could be used for evaluating disease severity and monitoring disease activity in patients with rheumatoid arthritis and secondary amyloidosis. However, cost-effective and more easily applicable markers, such as C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR), overwhelmed its use in clinical practice. In the light of emerging evidences, SAA has been discerned as a more sensitive biomarker in a wide spectrum of IRD, especially in case of subclinical inflammation. Furthermore, a growing number of studies are confirming the advantages of SAA over many other biomarkers in predicting and monitoring response to biological immunotherapy in IRD patients. Arising scientific discoveries regarding the role of SAA, as well as delineating SAA and its isoforms as the most sensitive biomarkers in various IRD by recently developing proteomic techniques are encouraging the revival of its clinical use. Finally, the most recent findings have shown that SAA is a biomarker of severe Coronavirus disease 2019 (COVID-19). The aim of this review is to discuss the SAA-involving immune system network with emphasis on mechanisms relevant for IRD, as well as usefulness of SAA as a biomarker in various IRD. Therefore, over a hundred original papers were collected through an extensive PubMed and Scopus databases search. These recently arising insights will hopefully lead to a better management of IRD patients and might even inspire the development of new therapeutic strategies with SAA as a target.

The association of viral load and disease severity in children with COVID-19

It is still not fully understood how to predict the future prognosis of patients at the diagnosis coronavirus disease 2019 (COVID‐19) due to the wide clinical range of the disease. We aimed to evaluate whether severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) viral load could predict the clinical course of pediatric patients. This study was conducted retrospectively with medical records of pediatric patients who were tested for SARS‐CoV2 between April 12 and October 25, 2020 in the University of Health Sciences, Ankara Educating and Training Hospital and Hacettepe University Faculty of Medicine. We evaluated 518 pediatric patients diagnosed with COVID‐19 and classified according to severity as asymptomatic (16.2%), mild (59.6%), moderate (20.2%), and critical/severe (3.9%) cases. We analyzed patients in four groups in terms of ages: <4, 5‐9, 10–14, and 15–17 years. There was no statistically significant difference in terms of ∆C_t value among age groups, different gender and the existence of underlying diseases in each disease course. The ∆C_t values were relatively lower in the first 2 days of symptoms than after days in all groups. Our study has indicated that children with COVID‐19 have similar amount of viral load in all disease courses irrespective of the age and underlying disease. It should be taken into account that, regardless of the severity of the disease, pediatric patients may have a role in the transmission chain.

Children with COVID‐19 can carry similar amount of viral load in all disease courses irrespective of the age and underlying disease.

The viral load has no prediction utility in terms of the clinical course of children with COVID‐19.

Regardless of the severity of the disease, pediatric patients may have a role in the transmission chain.

Diagnostic SARS-CoV-2 Cycle Threshold Value Predicts Disease Severity, Survival, and Six-Month Sequelae in COVID-19 Symptomatic Patients

To date, there is no severe acute respiratory syndrome coronavirus 2-(SARS-CoV-2)-specific prognostic biomarker available. We assessed whether SARS-CoV-2 cycle threshold (Ct) value at diagnosis could predict novel CoronaVirus Disease 2019 (COVID-19) severity, clinical manifestations, and six-month sequelae. Hospitalized and outpatient cases were randomly sampled from the diagnoses of March 2020 and data collected at 6 months by interview and from the regional database for COVID-19 emergency. Patients were stratified according to their RNA-dependent-RNA-polymerase Ct in the nasopharyngeal swab at diagnosis as follows: Group A ≤ 20.0, 20.0 < group B ≤ 28.0, and Group C > 28.0. Disease severity was classified according to a composite scale evaluating hospital admission, worst oxygen support required, and survival. Two hundred patients were included, 27.5% in Groups A and B both, 45.0% in Group C; 90% of patients were symptomatic and 63.7% were hospitalized. The median time from COVID-19 onset to swab collection was five days. Lethality, disease severity, type, and number of signs and symptoms, as well as six-month sequelae distributed inversely among the groups with respect to SARS-CoV-2 Ct. After controlling for confounding, SARS-CoV-2 Ct at diagnosis was still associated with COVID-19-related death (p = 0.023), disease severity (p = 0.023), number of signs and symptoms (p < 0.01), and presence of six-month sequelae (p < 0.01). Early quantification of SARS-CoV-2 may be a useful predictive marker to inform differential strategies of clinical management and resource allocation.

Temporal profile of SARS-CoV-2 viral load in posterior nasopharyngeal samples: Analysis of 944 patients in Apulia, Italy

Objectives

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has heavily impacted Italy. The government's restriction measures have attenuated the burden on hospitals. The association of high viral replication with disease severity suggests the potential for lower viral load in milder clinical presentations.

Methods

The reverse-transcription-polymerase-chain-reaction (RT-PCR) profile of 944 consecutive, non-replicate, positive retropharyngeal swabs was collected from 3 March to 8 June 2020 to investigate the temporal profile of SARS-CoV-2 viral load in the region of Capitanata, Apulia. Cycle threshold (Ct) values of 3 targets (N [nucleocapsid protein], E [envelope protein] and RdRP [RNA-dependent RNA-polymerase]) were analysed.

Results

The median Ct values of the 3 targets increased considerably over the study period, showing a progressive and constant weekly change. The negative detection rate of E and RdRP increased over time. These data suggest that SARS-CoV-2 viral load progressively decreased along the outbreak course. During the first epidemic peak (March and April) the viral load among patients >80-years was significantly higher than for younger subjects. However, in May this age-dependent difference disappeared, underlying viral load reduction in the elderly.

Conclusions

An attenuation of viral transmission or pathogenicity during the epidemic course is suggested, likely due to restriction measures, although viral factors might also be considered.

Toilets dominate environmental detection of severe acute respiratory syndrome coronavirus 2 in a hospital

Respiratory and fecal aerosols play confirmed and suspected roles, respectively, in transmitting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). An extensive environmental sampling campaign of both toilet and non-toilet environments was performed in a dedicated hospital building for patients with coronavirus disease 2019 (COVID-19), and the associated environmental factors were analyzed. In total, 107 surface samples, 46 air samples, two exhaled condensate samples, and two expired air samples were collected within and beyond four three-bed isolation rooms. The data of the COVID-19 patients were collected. The building environmental design and the cleaning routines were reviewed. Field measurements of airflow and CO₂ concentrations were conducted. The 107 surface samples comprised 37 from toilets, 34 from other surfaces in isolation rooms, and 36 from other surfaces outside the isolation rooms in the hospital. Four of these samples were positive, namely two ward door handles, one bathroom toilet seat cover, and one bathroom door handle. Three were weakly positive, namely one bathroom toilet seat, one bathroom washbasin tap lever, and one bathroom ceiling exhaust louver. Of the 46 air samples, one collected from a corridor was weakly positive. The two exhaled condensate samples and the two expired air samples were negative. The fecal-derived aerosols in patients' toilets contained most of the detected SARS-CoV-2 in the hospital, highlighting the importance of surface and hand hygiene for intervention.

Toilets dominate environmental detection of severe acute respiratory syndrome coronavirus 2 in a hospital

Respiratory and fecal aerosols play confirmed and suspected roles, respectively, in transmitting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). An extensive environmental sampling campaign of both toilet and non-toilet environments was performed in a dedicated hospital building for patients with coronavirus disease 2019 (COVID-19), and the associated environmental factors were analyzed. In total, 107 surface samples, 46 air samples, two exhaled condensate samples, and two expired air samples were collected within and beyond four three-bed isolation rooms. The data of the COVID-19 patients were collected. The building environmental design and the cleaning routines were reviewed. Field measurements of airflow and CO2 concentrations were conducted. The 107 surface samples comprised 37 from toilets, 34 from other surfaces in isolation rooms, and 36 from other surfaces outside the isolation rooms in the hospital. Four of these samples were positive, namely two ward door handles, one bathroom toilet seat cover, and one bathroom door handle. Three were weakly positive, namely one bathroom toilet seat, one bathroom washbasin tap lever, and one bathroom ceiling exhaust louver. Of the 46 air samples, one collected from a corridor was weakly positive. The two exhaled condensate samples and the two expired air samples were negative. The fecal-derived aerosols in patients' toilets contained most of the detected SARS-CoV-2 in the hospital, highlighting the importance of surface and hand hygiene for intervention.

Saliva viral load is a dynamic unifying correlate of COVID-19 severity and mortality

While several clinical and immunological parameters correlate with disease severity and mortality in SARS-CoV-2 infection, work remains in identifying unifying correlates of coronavirus disease 2019 (COVID-19) that can be used to guide clinical practice. Here, we examine saliva and nasopharyngeal (NP) viral load over time and correlate them with patient demographics, and cellular and immune profiling. We found that saliva viral load was significantly higher in those with COVID-19 risk factors; that it correlated with increasing levels of disease severity and showed a superior ability over nasopharyngeal viral load as a predictor of mortality over time (AUC=0.90). A comprehensive analysis of immune factors and cell subsets revealed strong predictors of high and low saliva viral load, which were associated with increased disease severity or better overall outcomes, respectively. Saliva viral load was positively associated with many known COVID-19 inflammatory markers such as IL-6, IL-18, IL-10, and CXCL10, as well as type 1 immune response cytokines. Higher saliva viral loads strongly correlated with the progressive depletion of platelets, lymphocytes, and effector T cell subsets including circulating follicular CD4 T cells (cTfh). Anti-spike (S) and anti-receptor binding domain (RBD) IgG levels were negatively correlated with saliva viral load showing a strong temporal association that could help distinguish severity and mortality in COVID-19. Finally, patients with fatal COVID-19 exhibited higher viral loads, which correlated with the depletion of cTfh cells, and lower production of anti-RBD and anti-S IgG levels. Together these results demonstrated that viral load - as measured by saliva but not nasopharyngeal - is a dynamic unifying correlate of disease presentation, severity, and mortality over time.