The association between SARS-CoV-2 RT-PCR cycle threshold and mortality in a community cohort

The Performance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Virus Using the Colorimetric Reverse-Transcription Loop Mediated Isothermal Amplification (RT-LAMP) Method in Saliva Specimens of Suspected COVID-19 Patients

Introduction

Corona Virus Disease-19 (COVID-19) is a disease caused by Severe-Acute-Respiratory-Syndrome-Coronavirus-2 (SARS-CoV-2). The most reliable and widely accepted method for diagnosing this infection, despite facing various challenges, is the Reverse Transcription Polymerase Chain Reaction (RT-PCR) method, which utilizes nasopharyngeal swab sample. Reverse-transcription loop mediated isothermal amplification (RT-LAMP) is a simpler nucleic acid amplification method compared to the RT-PCR method. This method has several advantages, including: of amplification at constant temperature, faster results, and potentially greater examination capacity.

Purpose

This study aimed to compare the validity of the RT-LAMP method using saliva specimens with that of the RT-PCR method using nasopharyngeal smears.

Methods

This was an analytical observational study with a cross-sectional design. The participants were inpatients in the COVID-19 special isolation building of Hasan Sadikin General Hospital, Indonesia with a probable (clinical symptoms of covid, but not confirm NAAT examination) or confirmed diagnosis of COVID-19 from September 2021 to February 2022. The inclusion criteria are COVID-19 patients with symptoms, adult subjects, and composite mentions. Patients who were unable to secrete saliva were also excluded.

Results

In total, 118 specimens were collected. The validity test results of the saliva specimens using the RT-LAMP method showed sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV), of 65.5%, 100%, 100%, and 75%, respectively. The results increased in subjects treated between 3 and 7 days after symptom onset ie 73.2%, 100%, 100%, and 82.3%, respectively.

Conclusion

The very strong specificity accompanied by good sensitivity and NPV in the group of subjects treated 3-7 days after the onset of symptoms indicates that the RT-LAMP method using saliva specimens can be an efficient and reliable alternative tool in detecting the SARS-CoV-2 virus.

The Impact of Viral Load on the Severity and Outcome Among Patients With COVID-19: A Cross-Sectional Study

Objectives This study aimed to assess the relationship between illness severity and mortality among COVID-19 patients along with the cycle threshold (Ct) value measured by viral load. Methods A cross-sectional study was conducted based on records of the emergency room at Rashid Hospital located in Dubai, United Arab Emirates. This research was carried out on all of the appropriate records of patients who were hospitalized at Rashid Hospital in Dubai between May 2020 and January 2021. Clinical and laboratory data were used as severity indicators, and in-hospital death was designated as the outcome. Results A total of 1,633 cases were included in the analysis. The percentage of deceased patients was higher in patients with a low Ct value (11.6%) than in patients with a high Ct value (6.9%) (p-value = 0.003). Logistic analysis revealed a statistically significant correlation (OR=2.046; p-value=0.002) between mortality and viral load, as measured by the Ct value. Patients with low Ct values and aberrant laboratory findings had a higher frequency of respiratory problems and required oxygen therapy, according to clinical and laboratory markers. Conclusions A correlation was found between viral load and mortality. Advanced age, history of chronic disease, and abnormal clinical and laboratory findings were all independently linked to a greater mortality rate in COVID-19 patients, indicating that they might be utilized as predictive and prognostic factors along with the viral load.

Association between SARS-CoV-2 gene specific Ct values and COVID-19 associated in-hospital mortality

Background

Since there are currently no specific SARS-CoV-2 prognostic viral biomarkers for predicting disease severity, there has been interest in using SARS-CoV-2 polymerase chain reaction (PCR) cycle-threshold (Ct) values to predict disease progression.

Objective

This study assessed the association between in-hospital mortality of hospitalized COVID-19 cases and Ct-values of gene targets specific to SARS-CoV-2.

Methods

Clinical data of hospitalized COVID-19 cases from Gauteng Province from April 2020-July 2022 were obtained from a national surveillance system and linked to laboratory data. The study period was divided into pandemic waves: Asp614Gly/wave1 (7 June-22 Aug 2020); beta/wave2 (15 Nov 2020-6 Feb 2021); delta/wave3 (9 May-18 Sept 2021) and omicron/wave4 (21 Nov 2021-22 Jan 2022). Ct-value data of genes specific to SARS-CoV-2 according to testing platforms (Roche-ORF gene; GeneXpert-N2 gene; Abbott-RdRp gene) were categorized as low (Ct < 20), mid (Ct20-30) or high (Ct > 30).

Results

There were 1205 recorded cases: 836(69.4%; wave1), 122(10.1%;wave2) 21(1.7%; wave3) and 11(0.9%;in wave4). The cases' mean age(±SD) was 49 years(±18), and 662(54.9%) were female. There were 296(24.6%) deaths recorded: 241(81.4%;wave1), 27 (9.1%;wave2), 6 (2%;wave3), and 2 (0.7%;wave4) (p < 0.001). Sample distribution by testing platforms was: Roche 1,033 (85.7%), GeneXpert 169 (14%) and Abbott 3 (0.3%). The median (IQR) Ct-values according to testing platform were: Roche 26 (22-30), GeneXpert 38 (36-40) and Abbott 21 (16-24). After adjusting for sex, age and presence of a comorbidity, the odds of COVID-19 associated death were high amongst patients with Ct values 20-30[adjusted Odds Ratio (aOR) 2.25; 95% CI: 1.60-3.18] and highest amongst cases with Ct-values <20 (aOR 3.18; 95% CI: 1.92-5.27), compared to cases with Ct-values >30.

Conclusion

Although odds of COVID19-related death were high amongst cases with Ct-values <30, Ct values were not comparable across different testing platforms, thus precluding the comparison of SARS-CoV-2 Ct-value results.

Extensive acute and sustained changes to neutrophil proteomes post-SARS-CoV-2 infection

BACKGROUND

Neutrophils are important in the pathophysiology of coronavirus disease 2019 (COVID-19), but the molecular changes contributing to altered neutrophil phenotypes following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are not fully understood. We used quantitative mass spectrometry-based proteomics to explore neutrophil phenotypes immediately following acute SARS-CoV-2 infection and during recovery.

METHODS

Prospective observational study of hospitalised patients with PCR-confirmed SARS-CoV-2 infection (May to December 2020). Patients were enrolled within 96 h of admission, with longitudinal sampling up to 29 days. Control groups comprised non-COVID-19 acute lower respiratory tract infection (LRTI) and age-matched noninfected controls. Neutrophils were isolated from peripheral blood and analysed using mass spectrometry. COVID-19 severity and recovery were defined using the World Health Organization ordinal scale.

RESULTS

Neutrophil proteomes from 84 COVID-19 patients were compared to those from 91 LRTI and 42 control participants. 5800 neutrophil proteins were identified, with >1700 proteins significantly changed in neutrophils from COVID-19 patients compared to noninfected controls. Neutrophils from COVID-19 patients initially all demonstrated a strong interferon signature, but this signature rapidly declined in patients with severe disease. Severe disease was associated with increased abundance of proteins involved in metabolism, immunosuppression and pattern recognition, while delayed recovery from COVID-19 was associated with decreased granule components and reduced abundance of metabolic proteins, chemokine and leukotriene receptors, integrins and inhibitory receptors.

CONCLUSIONS

SARS-CoV-2 infection results in the sustained presence of circulating neutrophils with distinct proteomes suggesting altered metabolic and immunosuppressive profiles and altered capacities to respond to migratory signals and cues from other immune cells, pathogens or cytokines.

Approach to hematopoietic cell transplant candidates with respiratory viral detection

The management of respiratory viruses prior to hematopoietic cell transplant (HCT) can be controversial and requires special consideration of host factors, transplant parameters, and the specific respiratory virus (RV). In the setting of adenovirus (ADV), human metapneumovirus (HMPV), influenza, parainfluenza virus (PIV), and respiratory syncytial virus (RSV) detection prior to hematopoietic cell transplant (HCT), clinical practice guidelines recommend transplant delay when possible; however, there is much more ambiguity when other respiratory viruses, such as seasonal coronaviruses (CoVs), human rhinovirus (HRV), and SARS-CoV-2, are detected. Our aims for this review include detailing clinical practical guidelines and reviewing current literature on pre-transplant respiratory viral infections (RVIs), including antiviral therapies and prevention strategies, when available. We will center our discussion on three representative clinical scenarios, with the goal of providing practical guidance to clinicians.

Global Emergence of SARS-CoV2 Infection and Scientific Interventions to Contain its Spread

The global pandemic caused by COVID-19 posed a significant challenge to public health, necessitating rapid scientific interventions to tackle the spread of infection. The review discusses the key areas of research on COVID-19 including viral genomics, epidemiology, pathogenesis, diagnostics, and therapeutics. The genome sequencing of the virus facilitated the tracking of its evolution, transmission dynamics, and identification of variants. Epidemiological studies have provided insights into disease spread, risk factors, and the impact of public health infrastructure and social distancing measures. Investigations of the viral pathogenesis have elucidated the mechanisms underlying immune responses and severe manifestations including the long-term effects of COVID-19. Overall, the article provides an updated overview of the diagnostic methods developed for SARS-CoV-2 and discusses their strengths, limitations, and appropriate utilization in different clinical and public health settings. Furthermore, therapeutic approaches including antiviral drugs, immunomodulatory therapies, and repurposed medications have been investigated to alleviate disease severity and improve patient outcomes. Through a comprehensive analysis of these scientific efforts, the review provides an overview of the advancements made in understanding and tackling SARS-CoV-2, while underscoring the need for continued research to address the evolving challenges posed by this global health crisis.

Risk of acute liver injury following the nirmatrelvir/ritonavir use

BACKGROUND

Elevations in alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were reported as adverse events of nirmatrelvir/ritonavir users in the EPIC-HR trial.

AIM

To quantify the risk and severity of acute liver injury (ALI) associated with nirmatrelvir/ritonavir use.

METHODS

This self-controlled case-series study was conducted using electronic medical records of patients with confirmed diagnosis of SARS-CoV-2 infection between 26th February 2022 and 12th February 2023 in Hong Kong.

RESULTS

Among 2 409 848 patients with SARS-CoV-2 infection during the study period, 153 853 were prescribed with nirmatrelvir/ritonavir, of whom 834 (.5%) had incident ALI (moderate: 30.5%; moderate to severe: 18.9%; severe or fatal: 5.8%). Compared with the non-exposure period, risk of ALI increased significantly during the pre-exposure period (IRR = 38.13, 95% CI = 29.29-49.62) and remained elevated during the five-day nirmatrelvir/ritonavir treatment (IRR = 20.75, 95% CI = 17.06-25.25) and during wash-out period (IRR = 16.27, 95% CI = 13.23-20.01). Compared to the pre-exposure period, risk of ALI was not increased during the five-day nirmatrelvir/ritonavir treatment period (IRR = .54, 95% CI = .43-.70). Compared to 5469 non-nirmatrelvir/ritonavir users with incident ALI, nirmatrelvir/ritonavir users had less severe ALI by the severity index (p < .001) and peak INR (1.7 vs. 2.3; p < .001). ALI cases with nirmatrelvir/ritonavir use had lower risk of all-cause death (29.1% vs. 39.1%; OR = .64; p < .001) and no increase in risk of liver decompensation (1.0% vs. 1.3%; OR = .62; p = .230) compared to non-users.

CONCLUSION

The risk of ALI associated with nirmatrelvir/ritonavir treatment for COVID-19 was elevated in the pre-exposure period, but not following nirmatrelvir/ritonavir initiation. ALI following nirmatrelvir/ritonavir treatment were mostly mild and less severe than ALI events in non-nirmatrelvir/ritonavir users.

No Association Between Ct Value and COVID-19 Severity and Mortality in Qatar

Background

The association between the cycle threshold (Ct) which reflects the SARS-CoV-2 viral load and the severity of COVID-19 is still not clear. We investigated the association between Ct values, symptoms and the risk of ICU admission and mortality from COVID-19 in Qatar.

Methods

This case-control study used data of hospitalized individuals with confirmed COVID-19 during the period March to September 2020. Cases were defined as individuals with confirmed COVID-19 who were admitted to the intensive care unit (ICU) or died and controls as those who were not admitted to the ICU. The association between Ct value, symptoms, ICU admission and mortality was investigated using Ct value as a categorical variable (below and above 25) in multivariable regression models and adjusted for relevant confounders.

Results

A total of 622 participants with median age 53 (IQR: 53-63), of which 69% were males, were included. There were 236 ICU admissions and 111 deaths. When categorized, Ct value (<25 vs ≥25) had no association with the odds of ICU admission (OR 0.85, 95% CI 0.56 to 1.29) or odds of mortality (OR 1.21, 95% CI 0.71 to 2.08). Respiratory (OR 2.95, 95% CI 1.57 to 5.56) and gastrointestinal symptoms (OR 1.99, 95% CI 1.18 to 3.35) were associated with higher odds of ICU admission. Similarly, respiratory (OR 4.96, 95% CI 1.10 to 22.43) and gastrointestinal symptoms (OR 3.17, 95% CI 1.29 to 7.84) were associated with higher odds of mortality.

Conclusion

Although RT-PCR Ct has good diagnostic value, its prognostic value appears to be unreliable. Respiratory and gastrointestinal symptoms are associated with COVID-19 criticality and mortality in this setting.

Comparative Study on Two COVID-19 Outbreaks at a Long-Term Mental Health Facility in Korea in 2020 and 2022

(1) Background and Objectives: There were two distinct coronavirus disease 2019 (COVID-19) outbreaks in 2020 and 2022 at a long-term mental health facility (LTMHF) in Gyeonggi Province, Korea. We aimed to compare the two outbreaks and identify differences in epidemiological and clinical outcomes due to changes in epidemic timing and management methods. (2) Materials and Methods: The structural, operational, and case-specific LTMHF data of COVID-19-confirmed patients during these outbreaks in 2020 and 2022 were retrospectively analyzed. (3) Results: Forty individuals (37 residents) in 2020 and thirty-nine (32 residents) in 2022 were confirmed to have COVID-19, and ten were infected twice. Facility isolation was implemented as an infection control measure, and one COVID-19-related death occurred in 2020. All residents and staff were vaccinated at least twice in 2022; moreover, in 2022, 38 patients (97.4%) received a third vaccination less than months before infection. The average Ct value of the cases in 2022 was significantly higher than that in 2020; however, vaccine-breakthrough (V-BT) and reinfection after vaccination rates were similar. (4) Conclusions: COVID-19 vaccination could help lower the viral load of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which was inversely correlated with Ct values, and ventilation system improvements in health facilities might reduce transmissibility.

IL-10/IL-6 ratio from nasal & oral swab samples, acts as an inflammatory indicator for COVID-19 patients infected with the delta variant

Background

Hyper-inflammatory immune response of SARS-CoV-2 is often characterized by the release of multiple pro-inflammatory cytokines with an impact on the expression of numerous other interleukins (ILs). However, from oral and nasal swab samples the specific quantitative association of the different IL-markers with the disease progression and its relationship with the status of vaccination remains unclear.

Materials and methods

Patients' combined oral and nasal swab samples were collected from both non-vaccinated and double-vaccinated individuals with high (Ct value < 25) and low (Ct value > 30) viral loads, along with uninfected donors. None of the patients were critically ill, or needed ICU support. The expression of different cytokines (IL6, IL10, IL1B, IFNG) and mucin (MUC5AC, MUC1) markers were assessed between different groups by qRT-PCR. The important cytokine markers differentiating between vaccinated and non-vaccinated patients were identified by PCA.

Conclusion

IL6 expression was higher in non-vaccinated COVID-19 patients infected with delta-variant irrespective of their viral-load compared to uninfected individuals. However, in double-vaccinated patients, only in high viral-load patients (Ct value < 25), IL6 expression increased. In high viral-load patients, irrespective to their vaccination status, IL10 expression was lower compared to the uninfected control group. Surprisingly, IL10 expression was lower in double-vaccinated patients with Ct value > 30. IL1B, and IFNG expression remained unaltered in uninfected and infected individuals. However, MUC5AC expression was lower in non-vaccinated patients with Ct value < 25 compared to control group. Our study unveiled that IL10/IL6 ratio can be used as a biomarker for COVID-19 patients upon proper establishment of it in a clinical setting.

COVID-19 psychosis versus psychosis due to cytotoxic lesion of the corpus callosum (CLOCC): A case report and review

Background

Cytotoxic lesions of the corpus callosum syndrome (CLOCC) is an inflammatory disorder caused by various etiologies such as medications, malignancies, seizure, metabolic abnormalities, and infections, especially COVID-19. It presents on MRI as an area of restricted diffusion in the corpus callosum. We present a case of psychosis and CLOCC in a patient with mild active COVID-19 infection.

Case

A 25-year-old male with a history of asthma and unclear past psychiatric history presented to the emergency room with shortness of breath, chest pain, and disorganized behavior. His-COVID-19 PCR was negative, and he was voluntarily admitted to psychiatry for management of unspecified psychosis. Overnight, he spiked a fever and was diaphoretic with headache and altered mental status. Repeat COVID-19 PCR at this time was positive and cycle threshold indicated infectivity. A brain MRI showed a new restricted diffusion within the midline of the splenium of the corpus callosum. Lumbar puncture was unremarkable. He continued to have flat affect and exhibit disorganized behavior with unspecified grandiosity, unclear auditory hallucinations, echopraxia, and poor attention and working memory. He was started on risperidone, with an MRI after 8 days showing complete resolution of the lesion in the corpus callosum and symptoms.

Conclusion

This case discusses diagnostic difficulties and treatment options for a patient presenting with psychotic symptoms and disorganized behavior in the context of active COVID-19 infection and CLOCC and highlights differences between delirium, COVID-19 psychosis and neuropsychiatric symptoms of CLOCC. Future research directions are also discussed.

Expression of TRIM56 gene in SARS-CoV-2 variants and its relationship with progression of COVID-19

Aim

The present study aimed to determine a correlation between differential TRIM56 expression levels and severe infections of COVID-19 between the Alpha, Delta and Omicron BA.5 variants.

Materials & methods

This study was performed on 330 COVID-19 patients, including 142 with severe and 188 with mild infections, as well as 160 healthy controls. The levels of TRIM56 gene expression were determined using a qPCR.

Results

TRIM56 gene showed significantly lower mRNA expression in the severe and mild groups compared with healthy individuals. Our finding indicated the high and low reduction of TRIM56 mRNA expression in Delta and Omicron BA.5 variant, respectively.

Conclusion

Further research is needed to characterize the impact of TRIM proteins on the severity of COVID-19.

An Oral Galectin Inhibitor in COVID-19—A Phase II Randomized Controlled Trial

Background: SARS-CoV-2 vaccines play an important role in reducing disease severity, hospitalization, and death, although they failed to prevent the transmission of SARS-CoV-2 variants. Therefore, an effective inhibitor of galectin-3 (Gal-3) could be used to treat and prevent the transmission of COVID-19. ProLectin-M (PL-M), a Gal-3 antagonist, was shown to interact with Gal-3 and thereby prevent cellular entry of SARS-CoV-2 in previous studies. Aim: The present study aimed to further evaluate the therapeutic effect of PL-M tablets in 34 subjects with COVID-19. Methods: The efficacy of PL-M was evaluated in a randomized, double-blind, placebo-controlled clinical study in patients with mild to moderately severe COVID-19. Primary endpoints included changes in the absolute RT-PCR Ct values of the nucleocapsid and open reading frame (ORF) genes from baseline to days 3 and 7. The incidence of adverse events, changes in blood biochemistry, inflammatory biomarkers, and levels of antibodies against COVID-19 were also evaluated as part of the safety evaluation. Results: PL-M treatment significantly (p = 0.001) increased RT-PCR cycle counts for N and ORF genes on days 3 (Ct values 32.09 ± 2.39 and 30.69 ± 3.38, respectively) and 7 (Ct values 34.91 ± 0.39 and 34.85 ± 0.61, respectively) compared to a placebo treatment. On day 3, 14 subjects in the PL-M group had cycle counts for the N gene above the cut-off value of 29 (target cycle count 29), whereas on day 7, all subjects had cycle counts above the cut-off value. Ct values in placebo subjects were consistently less than 29, and no placebo subjects were RT-PCR-negative until day 7. Most of the symptoms disappeared completely after receiving PL-M treatment for 7 days in more patients compared to the placebo group. Conclusion: PL-M is safe and effective for clinical use in reducing viral loads and promoting rapid viral clearance in COVID-19 patients by inhibiting SARS-CoV-2 entry into cells through the inhibition of Gal-3.

Real-time transcription polymerase chain reaction cycle threshold values as criteria for utilization of incidental COVID-19 positive lung donors

Shortage of organ donors is an ongoing limiting factor in lung transplantation (LT). Despite increasing prevalence of asymptomatic COVID-19 infection, positive COVID-19 testing from a potential donor remains a contraindication at many LT centers. In this report, we present the outcomes of LT utilizing an algorithm based on donor clinical presentation, and COVID-19 real-time reverse transcription polymerase chain reaction (RT-PCR) with cycle threshold (Ct) values evaluation. The Ct value threshold for organ acceptance was >35. A total of 8 COVID-positive donors were included. No donor-to-recipient transmissions of COVID-19 were observed. Short-term outcomes were comparable to those reported in pre-COVID literature. Survival-to-date is 100% with median POD of 161 days. Our findings support the safety and efficacy of utilizing our algorithm including Ct value threshold for selection of donors with incidental COVID-19 positive testing.

COVID-19 patients' clinical profile and outcome with respect to their vaccination status: A prospective observational multicentre cohort study during third wave in Western India

PURPOSE

To understand the benefits of COVID-19 vaccination (Covishield, Covaxin) on clinical features and outcome of COVID-19 during the third wave in India.

MATERIALS AND METHODS

The primary study aim was to describe the clinical profile and outcome of COVID-19 regarding their vaccination and to identify risk factors for disease progression in vaccinated patients. This was a prospective observational multicentric study of COVID-19 attended by Infectious Disease physicians during January 15, 2022 to February 15, 2022. Adult patients with positive RT-PCR or rapid antigen test for COVID-19 were enrolled. Patient received treatment as per local institutional protocol. Chi square test for categorical and Mann Whitney test for continuous variables were applied for the analysis. Logistic regression was used to calculate adjusted odds ratios.

RESULTS

A total of 788 patients were included in analysis out of 883 enrolled patients from 13 centers across Gujarat. By the end of two weeks' follow up, 22 patients (2.8%) had expired. The Median age of subjects was 54 years, with a (55.8%) male. 90% of the subjects were vaccinated, majority (77%) of them had received 2 doses of vaccine with Covishield (659, 93%). Mortality among the non-vaccinated was significantly (11.4%) higher than vaccinated (1.8%). Logistic regression analysis showed numbers of comorbidities (p ​= ​0.027), baseline higher WBC count (p ​= ​0.02), higher NLR (p ​= ​0.016), and Ct value (p ​= ​0.046) were associated with mortality while vaccination was associated with survival (p ​= ​0.001). The factors associated with mortality among vaccinated were age, comorbidities, baseline higher WBC, NLR, and CRP.

CONCLUSIONS

Omicron variant was associated with mild symptoms. Clinical and laboratory risk factors for getting severe disease with Omicron variant were the same with previous SARS CoV-2 strain. Two doses of vaccine protect people against severe disease and death. Age, comorbidities, baseline leucocytosis, high NLR, elevated CRP are the risk factors for poor outcome in vaccinated patients.

The "vaccine" hubbub: Viral load comparisons of SARS-CoV-2 Delta and Omicron variants against different vaccine-booster vaccine combinations

There is a significant body of evidence showing that efficient vaccination schemes against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is helping control the coronavirus disease 2019 (COVID-19) pandemic. However, this goal cannot be achieved without real world data highlighting the impact of vaccines against viral spread. In this study, we have aimed at differentially investigating the impact of COVID-19 vaccines (CoronaVac, Pfizer/BioNTech, Astra/Zeneca Oxford, Janssen) used in North Cyprus in limiting the viral load of Delta and Omicron variants of SARS-COV-2. We have utilized real-time quantitative polymerase chain reaction cycle threshold values (Ct values) as a proxy of viral load of the two SARS-CoV-2 variants. Our results indicate that the administration of at least two doses of the messenger RNA-based Pfizer/BioNTech vaccine leads to the lowest viral load (highest Ct values) obtained for both Omicron and Delta variants. Interestingly, regardless of the vaccine type used, our study revealed that Delta variant produced significantly higher viral loads (lower Ct values) compared with the Omicron variant, where the latter was more commonly associated with younger patients. Viral spread is a crucial factor that can help determine the future of the pandemic. Thus, prioritizing vaccines that will play a role in not only preventing severe disease but also in limiting viral load and spread may contribute to infection control strategies.

Choice of SARS-CoV-2 diagnostic test: challenges and key considerations for the future

A plethora of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic tests are available, each with different performance specifications, detection methods, and targets. This narrative review aims to summarize the diagnostic technologies available and how they are best selected to tackle SARS-CoV-2 infection as the pandemic evolves. Seven key settings have been identified where diagnostic tests are being deployed: symptomatic individuals presenting for diagnostic testing and/or treatment of COVID-19 symptoms; asymptomatic individuals accessing healthcare for planned non-COVID-19-related reasons; patients needing to access emergency care (symptom status unknown); patients being discharged from healthcare following hospitalization for COVID-19; healthy individuals in both single event settings (e.g. airports, restaurants, hotels, concerts, and sporting events) and repeat access settings (e.g. workplaces, schools, and universities); and vaccinated individuals. While molecular diagnostics remain central to SARS-CoV-2 testing strategies, we have offered some discussion on the considerations for when other tools and technologies may be useful, when centralized/point-of-care testing is appropriate, and how the various additional diagnostics can be deployed in differently resourced settings. As the pandemic evolves, molecular testing remains important for definitive diagnosis, but increasingly widespread point-of-care testing is essential to the re-opening of society.

Ultrastructural Changes in Autopsy Tissues of COVID-19 Patients

INTRODUCTION

The COVID-19 pandemic resulted in substantial morbidity and mortality across the world. The prognosis was found to be poor in patients with co-morbidities such as diabetes, hypertension, interstitial lung disease, etc. Although biochemical studies were done in patient samples, no study has been reported from the Indian subcontinent about ultrastructural changes in the vital organs of COVID-19 patients. The present study was, therefore, conducted to understand the ultrastructural changes in the lung, liver, and brain of the deceased patients.

METHODS

The present study was conducted on samples obtained from reverse transcription-polymerase chain reaction (RT-PCR)-positive patients who were admitted to a tertiary care hospital in Western India. Core needle biopsies were done in eight fatal cases of COVID-19. The samples were taken from the lungs, liver, and brain and subjected to light microscopy, immunohistochemistry (IHC), and transmission electron microscopy (TEM). Clinical details and biochemical findings were also collected.  Results: The study participants included seven males and one female. The presenting complaints included fever, breathlessness, and cough. Light microscopy revealed diffuse alveolar damage in the lungs. Further, a positive expression of SARS-CoV-2 nucleocapsid protein was observed in the pulmonary parenchyma of five patients. Also, the TEM microphotograph showed viral particles of size up to 80nm localized in alveolar epithelial cells. However, no viral particles were found in liver or brain samples. In the liver, macrovesicular steatosis and centrizonal congestion with loss of hepatocytes were observed in light microscopy.

CONCLUSION

 This is the first study in the Indian population showing the in-situ presence of viral particles in core biopsies from fatal cases of COVID-19. As evident from the results, histology and ultrastructural changes in the lung correlated with the presence of viral particles. The study revealed a positive correlation between the damage in the lungs and the presence of viral particles.

Retrospective Analysis of the SARS-CoV-2 Infection Profile in COVID-19 Positive Patients in Vitoria da Conquista, Northeast Brazil

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is responsible for causing Coronavirus Disease-2019 (COVID-19), a heterogeneous clinical condition that manifests varying symptom severity according to the demographic profile of the studied population. While many studies have focused on the spread of COVID-19 in large urban centers in Brazil, few have evaluated medium or small cities in the Northeast region. The aims of this study were: (i) to identify risk factors for mortality from SARS-CoV-2 infection, (ii) to evaluate the gene expression patterns of key immune response pathways using nasopharyngeal swabs of COVID-19 patients, and (iii) to identify the circulating SARS-CoV-2 variants in the residents of a medium-sized city in Northeast Brazil. A total of 783 patients infected with SARS-CoV-2 between May 2020 and August 2021 were included in this study. Clinical-epidemiological data from patients who died and those who survived were compared. Patients were also retrospectively divided into three groups based on disease severity: asymptomatic, mild, and moderate/severe. Samples were added to a qPCR array for analyses of 84 genes involved with immune response pathways and sequenced using the Oxford Nanopore MinION technology. Having pre-existing comorbidity; being male; having cardiovascular disease, diabetes, and/or chronic obstructive pulmonary disease; and PCR cycle threshold (Ct) values under 22 were identified as risk factors for mortality. Analysis of the expression profiles of inflammatory pathway genes showed that the greater the infection severity, the greater the activation of inflammatory pathways, triggering the cytokine storm and downregulating anti-inflammatory pathways. Viral genome analysis revealed the circulation of multiple lineages, such as B.1, B.1.1.28, Alpha, and Gamma, suggesting that multiple introduction events had occurred over time. This study's findings help identify the specific strains and increase our understanding of the true state of local health. In addition, our data demonstrate that epidemiological and genomic surveillance together can help formulate public health strategies to guide governmental actions.

Clinical and computed tomography features of patients suspected of COVID-19 in the university hospital of Oran, Algeria

BACKGROUND

The analysis of the clinical and radiological characteristics of COVID-19 patients around the world observed a rich semiology, different from one country to another, and within the same country.

AIM

To analyze the clinical, computed tomography (CT) features, and the outcome of patients suspected of COVID-19 hospitalized in a COVID-19 unit of Oran university hospital (Algeria).

METHODS

We collected retrospectively the files of patients suspected of COVID-19 admitted in a COVID-19 unit during July 2020. Data were collected on standardized questionnaire with prior coding of parameters. Patients were admitted according to a triage based on their clinical situation and the chest CT aspects suggestive of COVID-19. Two physicians reviewed the high-resolution CT (HR-CT) images independently, and discrepancies were resolved by consensus with the input of two others experimented physicians.

RESULTS

112 patients (64% males, median age: 68 (18-88) years) were included. The main symptoms were dyspnea (51.7%), cough (34%), fatigue (14%). Almost the half (49.1%) of patients had hypoxemia. The HR-CT findings were typical of COVID-19 in 96% of patients. Although 61% of patients had favorable prognosis, mortality rate was 30%. Mutlivariate analysis of risk factors for death showed that patients aged > 60 years had a 4-fold risk of death (95% confidence interval: [1.27-12.58], p=0.018).

CONCLUSION

Dyspnea, cough and fatigue were predominant symptoms, moderate and severe COVID-19 characterized our patients. Age > 60 years was a major risk factor for the deaths of our patients.

Factors associated with weak positive SARS-CoV-2 diagnosis by reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR)

During the COVID-19 pandemic, the reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) assay has been the primary method of diagnosis of SARS-CoV-2 infection. However, RT-qPCR assay interpretation can be ambiguous with no universal absolute cut-off value to determine sample positivity, which particularly complicates the analysis of samples with high Ct values, or weak positives. Therefore, we sought to analyse factors associated with weak positive SARS-CoV-2 diagnosis.

We analysed sample data associated with all positive SARS-CoV-2 RT-qPCR diagnostic tests performed by the Victorian Infectious Diseases Reference Laboratory (VIDRL) in Melbourne, Australia, during the Victorian first wave (22 January 2020–30 May 2020). A subset of samples was screened for the presence of host DNA and RNA using qPCR assays for CCR5 and 18S, respectively.

Assays targeting the viral RNA-dependent RNA polymerase (RdRp) had higher Ct values than assays targeting the viral N and E genes. Weak positives were not associated with the age or sex of individuals’ samples nor with reduced levels of host DNA and RNA. We observed a relationship between Ct value and time post-SARS-CoV-2 diagnosis.

High Ct value or weak positive SARS-CoV-2 was not associated with any particular bias including poor biological sampling.

Biological Properties of SARS-CoV-2 Variants: Epidemiological Impact and Clinical Consequences

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a virus that belongs to the coronavirus family and is the cause of coronavirus disease 2019 (COVID-19). As of May 2022, it had caused more than 500 million infections and more than 6 million deaths worldwide. Several vaccines have been produced and tested over the last two years. The SARS-CoV-2 virus, on the other hand, has mutated over time, resulting in genetic variation in the population of circulating variants during the COVID-19 pandemic. It has also shown immune-evading characteristics, suggesting that vaccinations against these variants could be potentially ineffective. The purpose of this review article is to investigate the key variants of concern (VOCs) and mutations of the virus driving the current pandemic, as well as to explore the transmission rates of SARS-CoV-2 VOCs in relation to epidemiological factors and to compare the virus's transmission rate to that of prior coronaviruses. We examined and provided key information on SARS-CoV-2 VOCs in this study, including their transmissibility, infectivity rate, disease severity, affinity for angiotensin-converting enzyme 2 (ACE2) receptors, viral load, reproduction number, vaccination effectiveness, and vaccine breakthrough.

Initial SARS-CoV-2 viral load is associated with disease severity: a retrospective cohort study

Background

We assessed the association between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load and hospital admission, intensive care unit (ICU) admission, and in-hospital mortality.

Methods

All SARS-CoV-2–positive persons with a combined nasopharyngeal and oropharyngeal swab that was collected between 17 March 2020 and 31 March 2021 in public health testing facilities were included.

Results

From 20 207 SARS-CoV-2–positive persons, 310 (1.5%) were hospitalized within 30 days. High viral loads (crossing point [Cp] <25) were associated with an increased risk of hospitalization as compared to low viral loads (Cp >30), adjusted for age and sex (adjusted odds ratio [aOR], 1.57 [95% confidence interval {CI}, 1.11–2.26]). The same association was seen for ICU admission (aOR, 7.06 [95% CI, 2.15–43.57]). The median [interquartile range] Cp value of the 17 patients who died in hospital was significantly lower compared to the 226 survivors (22.7 [3.4] vs 25.0 [5.2]).

Conclusions

Higher initial SARS-CoV-2 viral load is associated with an increased risk of hospital admission, ICU admission, and in-hospital mortality. Our findings emphasize the added value of reporting SARS-CoV-2 viral load or cycle threshold/Cp values to identify persons who are at the highest risk of adverse outcomes such as hospital or ICU admission and who therefore may benefit from more intensive monitoring or early initiation of antiviral therapy.

Portable air cleaners and residential exposure to SARS-CoV-2 aerosols: A real-world study

Individuals with COVID-19 who do not require hospitalization are instructed to self-isolate in their residences. Due to high secondary infection rates in household members, there is a need to understand airborne transmission of SARS-CoV-2 within residences. We report the first naturalistic intervention study suggesting a reduction of such transmission risk using portable air cleaners (PACs) with HEPA filters. Seventeen individuals with newly diagnosed COVID-19 infection completed this single-blind, crossover, randomized study. Total and size-fractionated aerosol samples were collected simultaneously in the self-isolation room with the PAC (primary) and another room (secondary) for two consecutive 24-h periods, one period with HEPA filtration and the other with the filter removed (sham). Seven out of sixteen (44%) air samples in primary rooms were positive for SARS-CoV-2 RNA during the sham period. With the PAC operated at its lowest setting (clean air delivery rate [CADR] = 263 cfm) to minimize noise, positive aerosol samples decreased to four out of sixteen residences (25%; p = 0.229). A slight decrease in positive aerosol samples was also observed in the secondary room. As the world confronts both new variants and limited vaccination rates, our study supports this practical intervention to reduce the presence of viral aerosols in a real-world setting.

Severity of coronavirus disease 19: Profile of inflammatory markers and ACE (rs4646994) and ACE2 (rs2285666) gene polymorphisms in Iraqi patients

Susceptibility to coronavirus disease 2019 (COVID-19) and disease severity has recently been associated with inflammatory markers and genetic polymorphisms of ACE (angiotensin-converting enzyme) and ACE2 genes, but the evidence has been inconclusive. This case-control study (99 COVID-19 patients and 96 controls) sought to assess the significance of age, C-reactive protein (CRP), neutrophil-to-lymphocyte ratio (NLR) and SARS-CoV-2 RT-PCR cycle threshold (Ct) in severity of COVID-19. Besides, two variants of ACE and ACE2 genes (rs4646994 and rs2285666, respectively) were analyzed to determine their role in COVID-19 susceptibility and/or disease severity. Results revealed that age, CRP and NLR were significantly elevated in severe cases compared to moderate cases, while RT-PCR Ct value was significantly decreased. Allele and genotypes of both variants were not associated with COVID-19 risk, with the exception of rs2285666 A allele. It showed a significantly higher frequency in female patients than in female controls (probability = 0.041). In conclusion, the study indicated the role of age, CRP, NLR and SARS-CoV-2 RT-PCR Ct in susceptibility to COVID-19 severity. However, analysis of the ACE and ACE2 gene variants (rs4646994 and rs2285666, respectively) showed that the two variants were not associated with the risk of developing COVID-19.

One-year prevalence and the association between SARS-CoV-2 cycle threshold, comorbidity and outcomes in population of Babol, North of Iran (2020-2021)

BACKGROUND

The present study aimed to investigate the one-year prevalence of SARS-CoV-2, common comorbidities and demographic information among negative- and positive rRT-PCR in health care workers (HCW), hospitalized and outpatients. Also, the association between SARS-CoV-2 cycle threshold (Ct) and the outcomes of patients were analyzed in Babol, northern Iran.

METHODS

This large retrospective cross-sectional study was performed between March 2020 and March 2021. The records of 19232 hospitalized, outpatients and HCW suspected to COVID-19 were collected from teaching hospitals in the North of Iran.

RESULTS

Out of the 19232 suspected to COVID-19 patients, 7251 (37.7%) had a positive rRT-PCR result; 652 (9%), 4599 (63.4%) and 2000 (27.6%) of those were categorized as HCW, hospitalized and outpatients, respectively. Moreover, between the hospitalized and the outpatient group, 10.2 and 0.8% cases died, whereas no death cases were reported in the HCW. Furthermore, it seems that death rate was significantly different between the three groups of Ct value, the highest mortality in those with Ct between 21 and 30 (group B=7.6%) and the lowest in the group with the highest Ct (between 31 and 40 = 5.5%) (p<0.001).

CONCLUSION

In summary, 37.7% of cases were positive for SARS-CoV-2; of which, 63.4, 27.6 and 9% were hospitalized, outpatients and HCW, respectively. With regard to the mortality rate in hospitalized patients and the significant association with Ct under 20 and 30, it seems that the early detection and the initial quantification of SARS-CoV-2 in the first week of the conflict and therapeutic considerations to reduce the relative load can reduce the mortality rate.

Transmission dynamics of the Delta variant of SARS-CoV-2 infections in South Korea

BACKGROUND

The Delta variant of SARS-CoV-2 is now the predominant variant worldwide. However, its transmission dynamics remain unclear.

METHODS

We analyzed 405 local case-patients infected with the Delta variant of SARS-CoV-2 and temporal patterns of viral shedding identified between 22 June and 31 July 2021 in Daejeon, South Korea.

RESULTS

Overall, 20% were presymptomatic at the time of epidemiological investigation. We identified six clustered outbreaks, and all were associated with indoor facilities. In 23 household contacts, the secondary attack rate was 63%. We estimated the mean serial interval as 3.26 days (95% credible interval, 2.92-3.60), and 15% (95% confidence interval, 13-18%) of cases seeded 80% of all local transmission. Analysis of the nasopharyngeal swab samples identified virus shedding from the presymptomatic patients, and the highest viral load was observed two days after symptom onset.

CONCLUSIONS

Our findings suggest that the Delta variant is highly transmissible in indoor settings and households. Rapid contact tracing, isolation of the asymptomatic contacts, strict adherence to public health measures, and increased uptake of COVID-19 vaccination including booster doses are needed to reduce the community transmission of the Delta variant.