Evaluation of Association Between Ct Value of SARS-COV-2 PCR with Disease Progression and Mortality

Objective: Multiple factors have been studied in association with disease severity in COVID-19. The cycle threshold (Ct) value of polymerase chain reaction (PCR) can reflect viral load in the specimens. In this study, we aimed to evaluate the effect of the Ct value on clinical course and mortality in COVID-19 patients. Methods: Adult patients who tested positive for SARS-CoV-2 with PCR test and who were hospitalized with COVID-19-related symptoms between August 1, 2020, and November 30, 2020, were included in the study. In addition, Ct value, demographic and clinical data (length of hospital stay, need for admission to intensive care unit (ICU), need for mechanical ventilation (MV), and mortality) were reviewed retrospectively. Results: 117 patients were included in the study. The mean Ct value was 22.37 +/- 4.72 (11.07-34.06). There was no significant difference in the mean Ct values between the patients who needed ICU admission and those who did not. When the patients were evaluated by dividing them into three groups according to their Ct values, as < 20, between 20-24 and >24;there was no significant difference between these three groups in terms of severity of pneumonia, laboratory parameters (D-dimer, Neutrophil/Lymphocyte ratio, C-reactive protein, lymphocyte count), length of hospital stay, need for ICU admission, need for MV and mortality. When the patients were divided into two groups with Ct values as <23.3 and >= 23.3, no significant difference was found between the groups regarding ICU need, MV need, and 28-day mortality rates. Conclusion: Most of the studies in the literature about Ct value and its effect on clinical course indicate that lower Ct values are potentially associated with worse outcomes in COVID-19. However, there are also studies reporting that the Ct value does not reflect the severity of the disease. We did not find a correlation between Ct value and laboratory markers, length of hospital stay, the severity of pneumonia, need for ICU admission or MV, and mortality in COVID19 patients in this presented study.

Validating saliva as a biological sample for cost-effective, rapid and routine screening for SARS-CoV-2

Purpose: Compared to nasopharyngeal/oropharyngeal swabs (N/OPS-VTM), non-invasive saliva samples have enormous potential for scalability and routine population screening of SARS-CoV-2. In this study, we investigate the efficacy of saliva samples relative to N/OPS-VTM for use as a direct source for RT-PCR based SARS-CoV-2 detection. Method(s): We collected paired nasopharyngeal/oropharyngeal swabs and saliva samples from suspected positive SARS-CoV-2 patients and tested using RT-PCR. We used generalized linear models to investigate factors that explain result agreement. Further, we used simulations to evaluate the effectiveness of saliva-based screening in restricting the spread of infection in a large campus such as an educational institution. Result(s): We observed a 75.4% agreement between saliva and N/OPS-VTM, that increased drastically to 83% in samples stored for less than three days. Such samples processed within two days of collection showed 74.5% test sensitivity. Our simulations suggest that a test with 75% sensitivity, but high daily capacity can be very effective in limiting the size of infection clusters in a workspace. Guided by these results, we successfully implemented a saliva-based screening in the Bangalore Life Sciences Cluster (BLiSC) campus. Conclusion(s): These results suggest that saliva may be a viable alternate source for SARS-CoV-2 surveillance if samples are processed immediately. Although saliva shows slightly lower sensitivity levels when compared to N/OPS-VTM, saliva collection is logistically advantageous. We strongly recommend the implementation of saliva-based screening strategies for large workplaces and in schools, as well as for population-level screening and routine surveillance as we learn to live with the SARS-CoV-2 virus.Copyright © 2023 Indian Association of Medical Microbiologists

Assessing the comparability of cycle threshold values derived from five external quality assessment rounds for omicron nucleic acid testing.

BACKGROUND: A variety of open-system real-time reverse transcriptase polymerase chain reaction (RT-PCR) assays for several acute respiratory syndrome coronavirus 2 are currently in use. This study aimed to ensure the quality of omicron nucleic acid testing and to assess the comparability of cycle threshold (Ct) values derived from RT-PCR. METHODS: Five external quality assessment (EQA) rounds using the omicron virus-like particles were organized between February 2022 and June 2022. RESULTS: A total of 1401 qualitative EQA reports have been collected. The overall positive percentage agreement was 99.72%, the negative percentage agreement was 99.75%, and the percent agreement was 99.73%. This study observed a significant variance in Ct values derived from different test systems. There was a wide heterogeneity in PCR efficiency among different RT-PCR kits and inter-laboratories. CONCLUSION: There was strong concordance among laboratories performing qualitative omicron nucleic acid testing. Ct values from qualitative RT-PCR tests should not be used for clinical or epidemiological decision-making to avoid the potential for misinterpretation of the results.

Evaluation of Association Between Ct Value of SARS-COV-2 PCR with Disease Progression and Mortality

Objective: Multiple factors have been studied in association with disease severity in COVID-19. The cycle threshold (Ct) value of polymerase chain reaction (PCR) can reflect viral load in the specimens. In this study, we aimed to evaluate the effect of the Ct value on clinical course and mortality in COVID-19 patients. Methods: Adult patients who tested positive for SARS-CoV-2 with PCR test and who were hospitalized with COVID-19-related symptoms between August 1, 2020, and November 30, 2020, were included in the study. In addition, Ct value, demographic and clinical data (length of hospital stay, need for admission to intensive care unit (ICU), need for mechanical ventilation (MV), and mortality) were reviewed retrospectively. Results: 117 patients were included in the study. The mean Ct value was 22.37 +/- 4.72 (11.07-34.06). There was no significant difference in the mean Ct values between the patients who needed ICU admission and those who did not. When the patients were evaluated by dividing them into three groups according to their Ct values, as < 20, between 20-24 and >24;there was no significant difference between these three groups in terms of severity of pneumonia, laboratory parameters (D-dimer, Neutrophil/Lymphocyte ratio, C-reactive protein, lymphocyte count), length of hospital stay, need for ICU admission, need for MV and mortality. When the patients were divided into two groups with Ct values as <23.3 and >= 23.3, no significant difference was found between the groups regarding ICU need, MV need, and 28-day mortality rates. Conclusion: Most of the studies in the literature about Ct value and its effect on clinical course indicate that lower Ct values are potentially associated with worse outcomes in COVID-19. However, there are also studies reporting that the Ct value does not reflect the severity of the disease. We did not find a correlation between Ct value and laboratory markers, length of hospital stay, the severity of pneumonia, need for ICU admission or MV, and mortality in COVID-19 patients in this presented study.

Importance of cycle threshold values in detection of severity and outcome in patients with severe acute respiratory syndrome coronavirus 2

Background and Objectives: Severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) is a highly transmissible and pathogenic coronavirus that emerged in late 2019. Cycle threshold (Ct) value of real-time reverse transcription polymerase chain reaction (RT-PCR) assay inversely correlated with viral load and can provide an indirect method of quantifying the number of copies of viral RNA in the sample is not reported clinically. Hence, this study was undertaken to compare the Ct values of patients tested positive for SARS CoV-2 by RT-PCR with severity of illness, duration of hospital stay, and mortality. Materials and Methods: A retrospective study was conducted over a period of 6 months in a tertiary care hospital in Bangalore. All patients tested positive for SARS CoV-2 by RT-PCR and admitted in our hospital were included in the study. Details of the patients on the duration of hospital stay, age, presence of comorbidities, intubation, and mortality were collected. Results: The study comprised of 80 patients, 48 (60%) males and 32 (40%) females. The mean age of the study population was 38.38 years. Majority of patients 41.25% had Ct value between 25 and 30. Patients with lower Ct values were significant associated with increased duration of hospital stay and infected more than one person in family indicating higher probability of transmission of infection. Mortality showed significant association with patients of more than 60 years' age. Interpretation and Conclusions: The study shows possible association between Ct values of SARS-CoV-2 RT-PCR assay with the duration of hospitalization, infectivity, and mortality. Mention of Ct value along with the positive report could potentially be used to guide patient care management, infection control, and occupational health decisions.

SARS-CoV-2 Alpha Variant Infection of a Patient Immunized by Inactive Sinovac (CoronaVac) Vaccine

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected in December 2019, and shortly after pandemic has been declared by the World Health Organization (WHO) due to its unstoppable global spread. Considerable amount of effort has beenput around the World in order to develop a safe and effective vaccine against SARS-CoV-2. Inactivated and RNA vaccines have already passed phase three studies showing sufficient efficacy and safety, respectively. Nowadays, there is a noticeable dominance of SARS-CoV-2 variants with various mutations over the wild type SARS-CoV-2. However, there is no report showing the efficacy of these vaccines on these variants. This case study describes a thirty-eight-year-old male reported to be infected with SARS-CoV-2 alpha variant following two doses of inactive CoronaVac administration with a protective level of SARS-CoV-2 specific antibodies. The variant analysis of the virus reported to be positive for N501Y mutation.This is the first case in the literature demonstrating that inactive SARS-CoV-2 vaccine might have a lower efficacy on alpha variant.Copyright © 2022 Cenk Serhan Ozverel et al., published by Sciendo.

Cycle threshold predicted mortality in a cohort of patients with hematologic malignancies infected with SARS-CoV-2.

When a SARS-CoV-2 RT-qPCR test is performed, it may determine an indirect measure of viral load called cycle threshold (Ct). Respiratory samples with Ct <25.0 cycles are considered to contain a high viral load. We aimed to determine whether SARS-CoV-2 Ct at diagnosis could predict mortality in patients with hematologic malignancies (lymphomas, leukemias, multiple myeloma) who contracted COVID-19. We included 35 adults with COVID-19 confirmed by RT-qPCR performed at diagnosis. We evaluated mortality due to COVID-19 rather than mortality due to the hematologic neoplasm or all-cause mortality. Twenty-seven (27) patients survived and 8 died. The global mean Ct was 22.8 cycles with a median of 21.7. Among the survivors, the mean Ct was 24.2, and the median Ct value was 22.9 cycles. In the deceased patients, the mean Ct was 18.0 and the median Ct value was 17.0 cycles. Using the Wilcoxon Rank Sum test, we found a significant difference (p=0.035). SARS-CoV-2 Ct measured in nasal swabs obtained at diagnosis from patients with hematologic malignancies may be used to predict mortality.

Judicious ending of isolation based on reverse transcription-polymerase chain reaction (RT-PCR) cycle threshold only for patients with coronavirus disease 2019 (COVID-19) requiring in-hospital therapy for longer than 20 days after symptom onset.

BACKGROUND: For patients with coronavirus disease 2019 (COVID-19) requiring hospitalization, extending isolation is warranted. As a cautious protocol, ending isolation based on polymerase chain reaction cycle threshold (Ct) value was introduced for patients requiring therapy for >20 days after symptom onset. METHOD: We compared a Ct-based strategy using Smart Gene® between March 2022 and January 2023 with a preceding control period (March 2021 to February 2022) when two consecutive negative reverse transcription-polymerase chain reaction tests using FilmArray® were required for ending isolation. Ct was evaluated on day 21, and ending isolation was permitted in patients with Ct ≥ 38. Although patients with Ct 35-37 were transferred to a non-COVID-19 ward, isolation was continued. RESULTS: The duration of stay on a COVID-19 ward in the Ct group was 9.7 days shorter than that in controls. The cumulative number of tests was 3.7 in controls and 1.2 in the Ct group. There was no nosocomial transmission after ending isolation in either group. The number of days from symptom onset to testing was 20.7 ± 2.1 in Ct group, and five patients had Ct < 35, nine Ct 35-37, and 71 Ct ≥ 38. No patients were moderately or severely immunocompromised. Steroid use was an independent risk factor for prolonged low Ct (odds ratio 9.40, 95% confidence interval 2.31-38.15, p = 0.002) CONCLUSIONS: The efficacy of ending isolation based on Ct values could improve bed utilization without the risk of transmission among patients with COVID-19 requiring therapy for >20 days after symptom onset.

Convalescent Plasma Treatment of Severe Covid-19 Cases in the Bronx, Ny

Junior Physician Investigator Award Recipient Purpose of study Severe acute respiratory syndrome coronavirus- 2 (SARS-CoV-2) is the causative agent of the Coronavirus disease 2019 (COVID-19) pandemic. Convalescent plasma obtained from recovered persons was used for previous respiratory pandemics. Convalescent plasma with severe acute respiratory disease coronavirus 2 (SARS-CoV-2) antibodies (CCP) was proposed as an option that may hold promise as treatment for COVID-19. Our aim was to retrospectively evaluate the efficacy of CCP treatment of patients with severe to life-threatening COVID-19 hospitalized at Montefiore Medical Center (MMC) in the Bronx, NY between April 13 to May 4, 2020. Methods used We administered CCP as part of the Mayo Clinic expanded access investigational new drug (IND) program for hospitalized patients. We compared the mortality and clinical outcome of 73 patients with COVID-19 who received 200 mL of CCP with a Spike protein IgG titer >=1:2,430 (median 1:47,385) within 72 hours of admission to 1:1 propensity score-matched controls. Matching criteria for controls were age, sex, body mass index, race, ethnicity, comorbidities, week of admission, oxygen requirement, D-dimer, lymphocyte counts, corticosteroids, and anticoagulation use (figure 1). We additionally measured Spike protein IgG and neutralizing antibody titer in CCP and pre- and post-transfusion Spike protein IgG, IgM and IgA titer in CCP recipients. The primary outcome was all-cause mortality at day 28 post-CCP. The secondary outcomes were improvement in oxygenation status or mortality at day 28 post-CCP. Exploratory outcomes were associations between pre-CCP SARS-CoV-2 antibody titers and mortality at day 28. Summary of results There was no difference in mortality or oxygenation between CCP recipients and controls at day 28. When stratified by age, compared to matched controls, CCP recipients < 65 years had 4-fold lower mortality and 4-fold lower deterioration in oxygenation or mortality at day 28 (figure 2, 3). There was no association between CCP IgG or neutralizing antibody titer and clinical outcome. For CCP recipients, pre-transfusion Spike protein IgG, IgM and IgA titers were associated with mortality at day 28 in univariate analyses but not in multivariable analyses. Pre-transfusion Spike protein IgG titer was significantly correlated with Ddimer and detected viral load measured by cycle threshold (Ct) value of nasopharyngeal SARS-CoV-2 reverse-transcriptase- polymerase-chain-reaction (figure 4). No adverse effects of CCP were observed. Conclusions We report that CCP administration within 72 hours of hospitalization demonstrated a possible signal of reduced mortality in patients < 65 years. Pre-transfusion IgG titer may be a proxy for disease severity that may be useful in identifying those who are more likely to respond to CCP. Data from controlled trials is needed to validate this finding and establish the effect of ageing on CCP efficacy. (Figure Presented).

The relationship between serum biomarkers and viral load of COVID-19 with severity of lung involvement on chest computed tomography - A single centre study

Introduction: The objective of this study is to investigate the relationship between Cycle Threshold (Ct) values and serum biomarkers in COVID-19 patients with Total Severity Score (TSS) on chest computed tomography (CT). Apart from this, this study also aims to explore the role of TSS, serum biomarkers and viral load in predicting the disease severity and clinical outcome of patients with COVID-19. Method(s): In this retrospective cross-sectional study, we included 213 confirmed COVID-19 patients from Hospital Sungai Buloh who conform to the inclusion criteria. A search was performed on the picture achieving and communication system (PACS) and Centricity UV to collect data on the clinical features, laboratory findings (the first one upon admission), epidemiological characteristics as well as the chest CT scans of the targeted group. To quantify the extent of COVID- 19 lung involvement in CT scan, TSS was applied. Data was collected and analysed using SPSS. Result(s): There were significant correlations between TSS of chest CT with four out of the six serum biomarkers studied, namely C-Reactive Protein (CRP), Neutrophil-Lymphocyte Ratio (NLR), creatinine and Lactate Dehydrogenase (LDH). There was an inverse relationship between TSS and Ct values. TSS, serum biomarkers (NLR, CRP, LDH and creatinine) as well as Ct value are good predictors of disease severity. Conclusion(s): TSS is a reliable scoring method to determine the severity of COVID-19 patients. Serum biomarkers which include NLR, CRP, LDH and creatinine are good predictors of disease severity and can be used for stratification of patients according to severity. Ct value is a valuable early indicator of disease severity.

SARS-CoV-2 INFECTION AMONG PERSONS WHO INJECT DRUGS AND THEIR PARTNERS IN KENYA

Background: Despite increased social vulnerability and barriers to care, there has been a paucity of data on SARS-CoV-2 incidence among key populations in sub-Saharan Africa. We seek to characterize active infections and define transmission dynamics of SARS-CoV-2 among people who inject drugs (PWID) and their sexual and injecting partners from Nairobi and the coastal region in Kenya. Method(s): This was a nested cross-sectional study of SARS-CoV-2 infection from April to July 2021 within a cohort study of assisted partner services for PWID in Kenya. A total of 1000 PWID and their partners (500 living with and 500 living without HIV) were recruited for SARS-CoV-2 antibody testing, of whom 440 were randomly selected to provide self-collected nasal swabs for real-time PCR testing. Whole genome sequencing (WGS) was completed on a limited subset of samples (N=23) with cycle threshold values 32.0. Phylogenetic tree construction and analysis was performed using the Nextstrain pipeline and compared with publicly available SARS-CoV-2 sequences from GenBank. Result(s): A total of 438 (99.5%) participants provided samples for SARS-CoV-2 PCR testing. Median age was 37 (IQR 32-42);128 (29.2%) were female;and 222 (50.7%) were living with HIV. The overall prevalence of SARS-CoV-2 infection identified by RT-PCR was 86 (19.6%). In univariate analyses, there was no increased relative risk of SARSCoV- 2 infection related to positive HIV status, frequenting an injection den, methadone treatment, unstable housing, report of any high-risk exposure, or having a sexual or injecting partner diagnosed with COVID-19 or who died from COVID-19 or flu-like illness. Eight samples were successfully sequenced via WGS and classified as WHO variants of concern: 3 Delta, 3 Alpha, and 2 Beta. Seven were classified into clades predominantly circulating in Kenya during 2021. Notably, two sequences were identical and matched identically to another Kenyan sequence, which is consistent with, though not indictive of, a transmission linkage. Conclusion(s): Overall, the risk of SARS-CoV-2 infection in this population of PWID and their partners was not significantly associated with risk factors related to injection drug use. At a genomic level, the SARS-CoV-2 strains in this study were consistent with contemporary Kenyan lineages circulating during the time and not unique to PWID. Prevention efforts, therefore, must also focus on marginalized groups for control given the substantial amount of mixing that likely occurs between populations.

Automatic detection of novel corona virus (SARS-CoV-2) infection in computed tomography scan based on local adaptive thresholding and kernel-support vectors

The recent studies have indicated the requisite of computed tomography scan analysis by radiologists extensively to find out the suspected patients of SARS-CoV-2 (COVID-19). The existing deep learning methods distribute one or more of the subsequent bottlenecks. Therefore, a straight forward method for detecting COVID-19 infection using real-world computed tomography scans is presented. The detection process consists of image processing techniques such as segmentation of lung parenchyma and extraction of effective texture features. The kernel-based support vector machine is employed over feature vectors for classification. The performance parameters of the proposed method are calculated and compared with the existing methodology on the same dataset. The classification results are found outperforming and the method is less probabilistic which can be further exploited for developing more realistic detection system.Copyright © 2023 Inderscience Enterprises Ltd.

SARS-CoV-2 WASTEWATER SURVEILLANCE IN A US JAIL: CORRELATION, FEASIBILITY, NEXT STEPS

Background: Jails house vulnerable persons. Crowded conditions, restricted access to medical care, and limited resources facilitate infectious disease outbreaks, particularly for airborne, highly transmissible diseases like COVID-19 (C19). Wastewater-Based Surveillance (WBS) is a low-cost, highly sensitive, non-invasive method that can provide an early warning of C19 surges in communities. We examined the value of SARS-CoV-2 WBS for a mega-jail. Method(s): 28-week study period: 10/20/21- 5/5/22. Wastewater samples were collected x 25 weeks;SARS-CoV-2 RNA was measured using RT-qPCR. We sampled one manhole serving multiple housing units. C19 rapid test data on jail entrants were summarized daily by the jail;16 mass PCR screenings using selfcollected nasal swabs were conducted by the study team. Individual diagnostic tests were collated and analyzed on a weekly basis. Data were summarized by % of the tested jailed individuals found infected. The Spearman correlation coefficient between weekly SARS-CoV-2 RNA in wastewater and % of positive (pos) C19 diagnostic tests were calculated;we also used linear regression to assess the predictability between paired Ct values and weekly % of pos diagnostic tests. Result(s): Weekly WBS coupled with periodic mass testing of jailed individuals was feasible. The efficiency of gathering individual nasal swabs increased to 3 tests collected per minute through a CQI process. PCR signal strength for SARSCoV- 2 RNA in jail wastewater correlated with the % of jail residents tested who had C19. The mean RT-qPCR Cycle threshold (Ct) value was 35.2. Overall, 3.4% of nasal swabs were pos. A strong inverse correlation was observed between % nasal swab pos and WBS Ct value (Figure.) The Spearman correlation coefficient was r= 0.628;linear regression likewise showed a similar correlation. Conclusion(s): Weekly WBS results for C19 correlated with the proportion of C19 individual test results. WBS proved to be a practical strategy to surveil for C19 in this jail setting. We are developing means to identify exact source, by housing unit, of wastewater with positive signal. Future studies will explore WBS for Mpox and HIV in correctional facilities. HIV RNA can be found in wastewater specimens;whether WBS for HIV in congregate facilities is feasible remains an open question.

SARS-CoV-2 VIRAL LOAD CHANGE IN A RANDOMIZED TRIAL ON THREE DIFFERENT EARLY THERAPIES

Background: SARS-CoV-2 Omicron sublineages exhibit evolving escape to in vitro neutralization by monoclonal antibodies (mAbs), with an unclear impact on in vivo treatment response. Our aim is to assess the impact of SARS-Cov-2 variants on the decline of viral load (VL) after treatment with 3 different drugs approved in EU for the early treatment of patients with mild-moderate COVID-19. Method(s): Post-hoc analysis from MONET (EudraCT: 2021-004188-28), phase 4 open-label RCT to assess efficacy of 500 mg intravenous sotrovimab (SOT), 600 mg intramuscular tixagevimab/cilgavimab (TIX/CIL) and oral 5-days course of NMV/r 300/100 mg BID, in non-hospitalized high-risk patients (pts) with early COVID-19. Pts' features were analyzed as binary variables by Chi-squared test. SARS-Cov-2 VL in nasopharyngeal swabs was carried out at randomization (1d) and at day 7 (7d) by cycle threshold value (Ct). Variant sequencing was performed at 1d. Ct variation was assessed by mixed effect log-linear model including random intercept at pts' level, log of Ct as independent variable, time, arm, viral variant as dependent variables, and interaction between time and arm. Multiple comparisons were adjusted by Bonferroni. Result(s): Among the 320 pts included between 4 Mar and 16 Nov, 2022, 108 (33.75%) received NMV/r, 103 (32.19%) TIX/CIL, and 109 (34.06%) SOT. Main characteristics were balanced across arms. Most of the pts were infected either with BA.2 (N=194;60.63%) or BA.4/BA.5 (N=100;31.25%) (Fig1A). VL at 1d was similar across the arms. In contrast, mean 7d VL was significantly lower in pts receiving NMV/r than in those receiving TIX/ CIL or SOT (P< 0.001) No significant VL variation was observed between the mAb arms (Fig1B). The analysis of the impact of viral variants suggests that while VL was significantly affected by variants (P=0.034), the superior effect of NMV/r over mAbs was homogeneous across all variant groups (P=0.290 for interaction) (Fig1C). Conclusion(s): Our study provides for the first time strong in vivo evidence that, when used against Omicron lineages, NMV/r exerts a stronger antiviral effect than mAbs. These results confirm previous in vitro evidence suggesting that mAbs may not retain neutralizing activity against all Omicron sublineages and provide preliminary information on how to use VL variation as a surrogate marker of efficacy. Further studies are needed to investigate whether the superior virologic activity of NMV/r over mAbs is confirmed for newly emerging variants, including BQ.1.1 or XBB.

SARS-CoV-2 OMICRON VIRAL LOAD DECREASE AFTER MONOCLONAL ANTIBODIES OR ANTIVIRALS

Background: Omicron subvariants questioned the efficacy of the approved therapies for the early COVID-19. In vitro data show that remdesivir (RDV), molnupiravir (MLN), and nirmatrelvir/ritonavir (NMV/r) all retained activity against all sub-lineages, while poor neutralizing activity was observed for Sotrovimab (SOT) and Tixagevimab/cilgavimab (TIX/CIL). No data about the risk of clinical failure or even in vivo antiviral activity are available. Method(s): Single-center observational comparison study enrolling all consecutive patients (pts) seen for care with a confirmed SARS-CoV-2 Omicron diagnosis and who met the AIFA criteria for eligibility for treatment with RDV, MLN, NMV/r, TIX/CIL, or SOT. Treatment allocation was subject to drug availability, time from symptoms onset, and comorbidities. Nasopharyngeal swab (NPS) VL was measured on day 1 (D1) and D7 and was expressed by log2 cycle threshold (CT) scale. Comparisons between treatment groups were made by Chi-square, and Wilcoxon paired tests. Primary endpoint was D1-D7 VL variation. Potential decrease in VL and average treatment effect (ATE) were calculated from fitting marginal linear regression models weighted for calendar month of drug initiation, duration of symptoms, and immunodeficiency using NMV/r as the comparator trial arm. Result(s): A total of 971 pts received treatments (SOT 321, MLN 231, NMV/r 211, TIX/CIL 70, and RDV 138): female 457 (47%), median age 67 yrs (IQR 56-78), 93% vaccinated;12% with negative baseline serology. At D1, median time from symptoms onset was 3 days (IQR 2,4). 379 (39%) pts were infected with BA.1, 215 (22%) with BA.2, 372 with BA.4/5 (38%), and 5 with BQ.1 (0,5%). D1 mean viral load was 4.02 log2. Adjusted analysis (ATE) showed that NMV/r significantly reduced VL compared to all the other drugs in pts infected with all sublineages, (Fig.1A-B) while less evidence for a difference vs. TIX/CIL was seen in those infected with BA.2 (p=0.05) (Fig.1 C-D). Conclusion(s): In this analysis of in vivo early VL reductions, NMV/r appears to be the drug showing the greatest antiviral activity, regardless of the underlying subvariant, perhaps with the exception of TIX/CIL in people infected with BA.2 for which there was less evidence for a difference. In the Omicron era, due to the high prevalence of vaccinated people and in absence of clinical events, VL is one of the possible alternative endpoints which guarantees adequate statistical power. Fig 1 SARS-CoV-2 RNA levels at D1 and D7 in patients treated with Nirmatrelvir/ ritonavir, Sotrovimab, Molnupiravir, Remdesivir, and Tixagevimab/cilgavimab. Dot-plots showing the comparison of viral loads detected at D1 and D7 and the variation of RNA levels observed between the two time-points by intervention in (A) all patients treated with Nirmatrelvir/ritonavir (n=211), Sotrovimab (n=321), or Molnupiravir (n=231), or Remdesivir (n=138), or Tixagevimab/ cilgavimab (n=136);(C) patients with Omicron BA.2 infection treated with Nirmatrelvir/ritonavir (n=58), Sotrovimab (n=81), or Molnupiravir (n=21), or Remdesivir (n=37), or Tixagevimab/cilgavimab (n=18);(D) patients with Omicron BA.4/5 infection treated with Nirmatrelvir/ritonavir (n=102), Sotrovimab (n=92), or Molnupiravir (n=110), or Remdesivir (n=16), or Tixagevimab/cilgavimab (n=52). Viral RNA levels are expressed as log2 CT values. The horizontal dashed line represents the limit of detection (CT: 40.0), values >=40 are considered negative. Mean of log2 CT values, and SD are shown in the graph. Statistical analysis of the differences in viral loads by intervention as compared to Nirmatrelvir/ritonavir was performed by Mann-Whitney test. Potential decrease in VL and average treatment effect (ATE) were calculated from fitting marginal linear regression models weighted for calendar month of drug initiation, duration of symptoms, and immunodeficiency using NMV/r as the comparator trial arm. Results are shown (B) for patients infected with all Omicron sublineages and (D) for those infected with Omicron BA.2 sublineage.

Impact of inflammatory markers, dread diseases and cycle threshold (Ct) Values in COVID-19 progression

The link between the inflammatory marker and SARS-CoV-2 cycle threshold (Ct) with disease progression remains undefined, mainly in coronavirus disease-2019 (COVID-19). Therefore, this study aimed to identify several inflammatory markers (Ferritin, LDH, and D-dimer), and Ct values to predict outcomes in hospitalized COVID-19 Iraqi patients. A case study was performed on 426 patients to guess cutoff values of inflammatory markers that were detected by a real-time polymerase chain reaction (RT-PCR) and specific auto-analyzer instrument. Significantly increased levels of inflammatory markers in critical and severe patients compared with mild-moderate (p < 0.001). Compared with aging and disease severity, inflammatory markers and Ct values are significantly related to the aging and severity in critical and severe COVID-19 patients (p < 0.001). Finding the Ct value was negatively associated with Ferritin, LDH, and D-dimer (p < 0.001);moreover, inflammatory markers concentrations and Ct values were significantly higher during the first ten days. The Ct values correlate with some relevant clinical parameters of inflammation. Higher levels of D dimer, S. Ferritin and LDH were associated with older age and the severity of COVID-19. The area under the ROC curve indicates that serum ferritin was the highest and excellent predictor for disease severity. © 2022 by the authors.

Verification of the Performance of the Panbio COVID-19 Ag Rapid Test Device for Implementation in the Clinical Laboratory

Objectives: The Panbio COVID-19 Ag Rapid Test Device (Panbio COVID-19 Ag, Abbott Rapid Diagnostics) is a lateral flow immunochromatographic assay targeting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleoprotein in nasopharyngeal specimens for the diagnosis of coronavirus disease 2019 (COVID-19). This study aimed to verify the performance of the Panbio COVID-19 Ag for implementation in clinical laboratories. Method(s): Sixty nasopharyngeal swab specimens (30 positive and 30 negative) dipped in transport medium, and COVID-19 was confirmed using real-time RT-PCR using Allplex SARS-CoV-2 assay (Seegene), were tested using the Panbio COVID-19 Ag. Reproducibility was evaluated using positive and negative control materials. Sensitivity and specificity were calculated based on the results of realtime RT-PCR as the standard test method. Result(s): Reproducibility was confirmed by the consistent results of repeated tests of the quality control materials. The overall sensitivity and specificity of Panbio COVID-19 Ag were 50.0% and 100.0%, respectively. Panbio COVID-19 Ag demonstrated high sensitivity (88.2%) in analyzing the detection limit cycle threshold (Ct) value of 26.67 provided by the manufacturer as a positive criterion, and the sensitivity was 100.0% for the positive criterion of Ct values <25, although it was less sensitive for Ct > 25. Conclusion(s): Considering the high sensitivity for positive samples with Ct values <25 and the rapid turnaround of results, Panbio COVID-19 Ag can be used in clinical laboratories to diagnose COVID-19 in limited settings. Copyright © 2023 Ewha Womans University College of Medicine and Ewha Medical Research Institute.

Virus variant-specific clinical performance of a SARS-CoV-2 rapid antigen test with focus on Omicron variants of concern.

OBJECTIVES: Antigen rapid diagnostic tests (Ag-RDTs) play an important role in the diagnosis of SARS-CoV-2. They are easier, quicker, and less expensive than the 'reference standard' RT-PCR and therefore widely in use. Reliable clinical data with respect to Ag-RDT performance in SARS-CoV-2 Omicron variants of concern (VOCs) are limited. Consequently, the objective of this study was to determine the impact different VOCs-especially Omicron-have on the clinical performance of an Ag-RDT. METHODS: We compared the clinical performance of the Sofia SARS-CoV-2 Ag-RDT to RT-PCR in a real-world, single-centre study in a clinical point-of-care setting in patients admitted to a large hospital via the emergency department from 2 November 2020 to 4 September 2022. RESULTS: Among 38 434 Ag-RDT/RT-PCR tandems taken, 1528 yielded a SARS-CoV-2 positive RT-PCR test result, with a prevalence of 4.0% (95% CI, 3.8-4.2). Overall sensitivity of the Ag-RDT was 63.7% (95% CI, 61.3-66.1) and overall specificity was 99.6% (95% CI, 99.5-99.6). Ag-RDT sensitivity was dependent on viral load (VL), because the sensitivity increased to 93.2% (95% CI, 91.5-94.6) in samples with a VL > 106 SARS-CoV-2 copies/mL. Furthermore, the Ag-RDT was more sensitive in men, and older patients. Variant-dependent sensitivity assessment showed that the sensitivity was significantly lower in Omicron-VOC (64.1%; 95% CI, 60.5-67.6) compared with SARS-CoV-2 wild-type samples (70.0%; 95% CI, 59,8-78,6) (binomial test; p value < 0.001). Analysing the limits of detection showed a 27 times higher 95% limit of detection for the Omicron-VOC BA.5 compared with the SARS-CoV-2 wild-type. DISCUSSION: Ag-RDT sensitivity for detection of patients with lower VLs and with Omicron-VOC is reduced, limiting the effectiveness of Ag-RDTs. However, Ag-RDTs are still an unreplaceable tool for widely available, quick, and inexpensive point-of-care SARS-CoV-2 diagnostics.

Objective Evaluation of Olfactory and Taste Dysfunction Among COVID-19 Patients: A Cross Sectional Study from Tribal India.

There is a varying prevalence of olfactory and taste dysfunction (OTD) in COVID-19 patients, with a higher prevalence reported in the European population as compared to the Asian population. Psychophysical tests are crucial to determine the exact frequency, extent and clinical characteristics of these OTDs. The present study objectively evaluated the OTD for patients treated in the Dedicated COVID-19 Hospital (DCH) in Shahdol. This prospective cross-sectional study was conducted after IEC approval in DCH Shahdol for a period of four months among RT-PCR positive patients, and they were evaluated using validated chemosensitive psychophysical test during ENT consultation to identify OTD. The sample size was calculated as 92 considering prevalence (p) of OTD as 41.3% by applying formula: n = (Z1-a/2)2 × p (1-p) / d 2. The information pertaining to the subjects was kept anonymous and confidential. During data analysis, an association was significant for p value < 0.05. It was observed that 45.5% of subjects reported either loss of taste or smell. During objective evaluation, olfactory and taste dysfunction was observed among 42.4% of subjects (95/224). The Chi-square analysis reflected statistically significant difference (p < 0.05) between subjects with OTD and without OTD for the variables such as days from onset of symptoms to admission, and symptoms (fever, sore throat and shortness of breath). Taste and smell are among the important senses and in India they are mostly subjectively evaluated for COVID-19 induced OTD which results in underreporting of these symptoms. So, a gold standard objective evaluation should be taken into consideration to evaluate OTD.

Evaluation of the Relationship Between Disease Severity and Viral Cycle Threshold Value in COVID-19 Patients

Objective: There is a positive and significant relationship between severity and viral load in some viral diseases. Studies on the relationship between SARS-CoV-2 viral load at diagnosis and severity of coronavirus disease-2019 (COVID-19) have yielded conflicting results. Therefore, we aimed to evaluate the relationship between viral load and the clinical status of patients with COVID-19.Methods: Data of the patients diagnosed with COVID-19 and admitted to our center between May 01 and June 31, 2020, were retrospectively reviewed. The patients were divided into two groups according to their clinical character-istics as mild-moderate and severe. The demographic, laboratory, clinical, and radiological data were retrieved from electronic folders.Results: The entire cohort included 285 patients;254 had a mild-moderate clinical course, and 31 had a severe course. Statistical analyses revealed that SARS-CoV-2 viral load was not associated with symptom duration and clinical status (p>0.05). According to multivariate logistic regression analysis, only ferritin, C-reactive protein, and lactate dehydro-genase elevations were positively correlated with severe clinical course. (p<0.05).Conclusion: We do not recommend using viral load to predict disease severity in COVID-19. We also found that only ferritin, C-reactive protein, and lactate dehydrogenase accompanied severe clinical course. Keywords: cycle threshold, COVID-19, clinical severity