Lower Ct Values Research Articles

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 reactioncycle 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 withthe 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.

Omicron-COVID-19 Manifestations in Sickle Cell Disease: A Brief Report

Background: Sickle cell disease (SCD) is an inherited red blood cell (RBC) disorder that is secondary to a single amino acid change in the beta-chain of the human hemoglobin protein. Patients with SCD suffer from a chronic hemolytic anemia, which can lead to recurrent vascular occlusion with pain crises, organ disfunction, early mortality, and increased risk of infection due to functional asplenia. The Omicron (B.1.1.529) variant, first described in South Africa in November 2021, was identified as a variant of concern due to more than 30 changes in the spike protein of the virus, as well as a sharp rise in the number of cases seen in South Africa. Previous data suggested that children with SCD were less likely to experience COVID-19 related severe illness and death compared to adults with SCD and adults without SCD. Methods: We present a retrospective cohort analysis of 20 patients aged 3-20 years old with SCD admitted due to SARS-CoV-2 infection in a single center institution in the Bronx, New York between December 19, 2021 and January 10, 2022 aligned with the Omicron spike in New York City. Bivariate analyses were performed using Stata software, version 17, to compare differences between SCD patients diagnosed with acute chest syndrome (ACS) and those without. Results: In SCD patients admitted due to risk of complications, there were no statistically significant differences between HbSS patients diagnosed with ACS and those without. Average CT values did demonstrate a borderline statistically significant difference with those with ACS having a higher burden of disease with a lower CT value (p=0.07) with those without, with HbSC patients having overall higher CT values and lower burden of disease. Rates of COVID-19 vaccination did not statistically significantly differ between groups but only 25% of HbSS patients diagnosed with ACS and 36% of those without ACS were vaccinated. A higher proportion of HbSC patients were vaccinated (67%). COVID-19 vaccination was offered to all patients who were not vaccinated. No patients developed thromboses of any kind, as had been common during previous surges. Conclusions: Our results demonstrate that the Omicron variant affected patients with SCD in different ways than seen previously. More patients required hospitalization for COVID-modifying therapy due to unvaccinated status than seen previously, confirming the need for continued vigilance for vaccination efforts. Table 1. Comparison of baseline characteristics and markers of COVID-19 disease severity in HbSS and HbSC patients with and without ACS in a single center cohort analysis (n=20). Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Characteristics of COVID-19 (Delta Variant)/HIV Co-infection: A Cross-sectional Study in Henan Province, China

BackgroundSince the end of July 2021, SARS-CoV-2 (Delta variant) invaded Henan Province, China, causing a rapid COVID-19 spread in the province. Among them, the clinical features of COVID-19 (Delta Variant)/HIV co-infection have attracted our attention.MethodsWe included 12 COVID-19 patients living with HIV (human immunodeficiency virus) from July 30, 2021 to September 17, 2021 in Henan Province, China. Demographic, clinical, laboratory, and computed tomography (CT) imaging data were dynamically collected from first nucleic acid positive to hospital discharge. Laboratory findings included SARS-CoV-2 viral load, HIV viral load, IgM, IgG, cytokines, lymphocyte subpopulation, ferritin, etc. Statistical analyses were performed using IBM SPSS version 26·0 and GraphPad Prism version 9·0.ResultsIt was founded that the low Ct value persisted for about 21 days, and the viral shedding time (turn negative time) of the patients was 32·36 ± 2·643 days. Furthermore, chest CT imaging revealed that lesions were obviously and rapidly absorbed. It was surprising that IgM levels were statistically higher in patients taking azvudine or convalescent plasma than in patients not taking these drugs (P < 0·001, P = 0·0002, respectively). IgG levels were significantly higher in patients treated with the combined medication of BRII/196 and BRII/198 than in those not treated with these drugs (P = 0·0029). IgM was significantly higher in those with low HIV viral load than those with high HIV viral load (P < 0·001). In addition, as treatment progressed and patients' condition improved, IL-17a showed a decreasing trend.ConclusionsBased on this study, we found that HIV infection might not exacerbate COVID-19 severity.

Omicron Subvariants: Clinical, Laboratory, and Cell Culture Characterization.

The variant of concern Omicron has become the sole circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant for the past several months. Omicron subvariants BA.1, BA.2, BA.3, BA.4, and BA.5 evolved over the time, with BA.1 causing the largest wave of infections globally in December 2021-January 2022. This study compared the clinical outcomes in patients infected with different Omicron subvariants and the relative viral loads and recovery of infectious virus from upper respiratory specimens. SARS-CoV-2-positive remnant clinical specimens, diagnosed at the Johns Hopkins Microbiology Laboratory between December 2021 and July 2022, were used for whole-genome sequencing. The clinical outcomes of infections with Omicron subvariants were compared with infections with BA.1. Cycle threshold (Ct) values and the recovery of infectious virus on the VeroTMPRSS2 cell line from clinical specimens were compared. BA.1 was associated with the largest increase in SARS-CoV-2 positivity rate and coronavirus disease 2019 (COVID-19)-related hospitalizations at the Johns Hopkins system. After a peak in January, cases decreased in the spring, but the emergence of BA.2.12.1 followed by BA.5 in May 2022 led to an increase in case positivity and admissions. BA.1 infections had a lower mean Ct value when compared with other Omicron subvariants. BA.5 samples had a greater likelihood of having infectious virus at Ct values <20. Omicron subvariants continue to be associated with a relatively high rate of polymerase chain reaction (PCR) positivity and hospital admissions. The BA.5 infections are more while BA.2 infections are less likely to have infectious virus, suggesting potential differences in infectibility during the Omicron waves.

Correlation of SARS-CoV2 Viral Growth on Cultures, Ct Values, SARS-CoV-2 Variant and Vaccination Status in Asymptomatic, Pre-Symptomatic and Post-Infection Asymptomatic COVID Patients

Abstract Introduction/Objective COVID-19 large scale immunizations have helped control the infectious spread, but breakthrough infections are still observed and some of these patients remain asymptomatic. In this study, we compared the viral growth characteristics with vaccination status in asymptomatic patients. Methods/Case Report We searched our institutional laboratory database for asymptomatic patients infected with delta variant (November-December 2021, n=65) and omicron variant (December 2021, n=68), that were further classified as “truly asymptomatic”, “pre-symptomatic” and “post-infection asymptomatic” based on detailed chart reviews. The patients’ left-over nasopharyngeal swab samples’ cycle threshold values and the recovery of infectious virus in cell culture were compared. Results (if a Case Study enter NA) In the delta cohort, out of 65 asymptomatic patients, 36 were truly asymptomatic, 26 presymptomatic and 3 post infection asymptomatic patients. In the omicron cohort, out of 68 asymptomatic patients, 45 were truly asymptomatic and 23 were presymptomatic patients. The vaccination rate was 59% in truly asymptomatic (delta cohort=56%, omicron cohort=62%), 55% in presymptomatic (delta cohort=50%, omicron cohort=61%) and 67% in post-infection patients (delta cohort only). There was no significant difference in the Ct values of truly asymptomatic (mean Ct=21.08), presymptomatic (mean Ct=20.30) and post-infection asymptomatic patients (mean Ct=20.84) in the combined cohort (p=0.78) and in the delta (p=0.95) or omicron (p=0.45) subcohorts. The Ct values were not correlated with the vaccination status of the patients (vaccinated patients mean Ct=20.56, non-vaccinated patients mean Ct=20.16, p=0.68). Samples with positive viral growth on cultures had significantly lower Ct values (mean Ct= 17.16), compared to samples with negative viral culture results (mean Ct= 24.61) (p&amp;lt;0.0001). The viral growth on culture was not associated with the symptom status, SARS-CoV-2 variant type (delta vs omicron) and vaccination status of the patients in the delta and omicron subcohorts. Conclusion Our findings show that there is no significant correlation between vaccination status and viral loads and culture results in asymptomatic patients.

Wildlife Hosts of Leishmania infantum in a Re-Emerging Focus of Human Leishmaniasis, in Emilia-Romagna, Northeast Italy.

In the last decade, an upsurge of human leishmaniasis has been reported in the Emilia-Romagna region, Northeast Italy. Epidemiologic data have raised doubts about the role of dogs as the main reservoirs for Leishmania infantum. In the present study, a total of 1,077 wild animals were screened for L. infantum DNA in earlobe and spleen samples from 2019 to 2022. The lymph nodes were tested only in 23 animals already positive in the earlobe and/or spleen. A total of 71 (6.6%) animals resulted positive in at least one of the sampled tissues, including 3/18 (16.7%) wolves, 6/39 (15.4%) European hares, 38/309 (12.3%) roe deer, 1/11 (9.1%) red deer, 8/146 (4.9%) wild boars, 13/319 (4.1%) red foxes, 1/54 (1.9%) porcupine, and 1/59 (1.7%) European badger. Most of the infected animals (62/71) tested positive only in the earlobe tissue, only four animals (two roe deer and two wild boars) tested positive only in the spleen, and five animals (three roe deer and two red foxes) resulted positive for both tissues. L. infantum DNA was detected in the lymph nodes of 6/23 animals. L. infantum detection occurred in all seasons associated with low real-time PCR Ct values. Further research is needed in order to clarify the role of wildlife in the re-emerging focus of leishmaniasis in Northeast Italy.

Prolonged replication of BA.1 and BA.2 Omicron lineages compared to Delta variant in nasopharyngeal samples from COVID-19 patients

ObjectivesWe aimed to characterize and compare the viral loads (VL) of the Omicron BA.1 and BA.2 lineages and the Delta variant in nasopharyngeal samples from newly diagnosed COVID-19 patients and their kinetics over time. Patients and methodsThe kinetics of the VL were measured on the CT data from 215 SARS-CoV-2 positive patients who presented at least two positive PCRs a day apart and were screened for SARS-CoV-2 viral lineages. ResultsWe observed no significant difference in median CT value during the first diagnostic test between the Delta variant and the two Omicron lineages. However, the kinetics of CT decreases for the BA.1 and BA.2 lineage were significantly lengthier in time than the kinetics for the Delta variant. The BA.2 lineage presented lower median CT value (-2 CT) (inversely proportional to the VL) than the BA.1 lineage. ConclusionsBA.2 Omicron lineage presented higher VL than BA.1 Omicron lineage at diagnostic. Omicron BA.1 and BA.2 lineages have more prolonged replication than the Delta variant.

Comparing Two Methods for the Isolation of Exosomes.

Exosomes are membrane-bound nanovesicles released by cells into their extracellular environment. They carry different types of RNA including mRNA which may be useful in the diagnosis of various diseases. Exosome isolation has been a challenge because of their small size; therefore, two exosome isolation methods were compared in this study. The Exoquick-TC PLUS™ exosome isolation kit (kit) was compared with the classic ultracentrifugation (UC) method for exosome isolation. In samples obtained using both methods, cryo-electron microscopy showed round or slightly elongated vesicles with diameters ranging from 50 to 150 nm and delimited by a bilayered membrane. Dynamic light scattering resulted in multiple peaks for kit exosomes, whereas a single peak was observed for UC exosomes. Significantly, more total RNA was present in UC exosomes in contrast to kit exosomes (P < 0.0001). This was reflected in subsequent mRNA analysis using qPCR, where UC exosomes had lower Ct values compared to kit exosomes. In conclusion, exosome characterization revealed the presence of exosomes in both UC and the kit samples. The kit samples presented additional peaks from DLS which might be due to impurities. Overall, due to a higher total RNA and mRNA content, UC is a better option for subsequent mRNA analysis; nevertheless, the kit can still be used if an ultracentrifuge is not available as four out of the five genes selected were detected and quantified using the kit.

Diversity of respiratory viruses present in nasal swabs under influenza suspicion in respiratory disease cases of weaned pigs

Respiratory diseases in weaned pigs are a common problem, with a complex etiology involving both viruses and bacteria. In the present study, we investigated the presence of eleven viruses in nasal swabs, collected from nurseries (55 cases) under the suspicion of swine influenza A virus (swIAV) and submitted by swine veterinarians for diagnosis. The other ten viruses included in the study were influenza B (IBV) and D (IDV), Porcine reproductive and respiratory syndrome virus (PRRSV), Porcine respiratory coronavirus (PRCV), Porcine cytomegalovirus (PCMV), Porcine circovirus 2 (PCV2), 3 (PCV3) and 4 (PCV), Porcine parainfluenza 1 (PPIV1) and Swine orthopneumovirus (SOV). Twenty-six swIAV-positive cases and twenty-nine cases of swIAV-negative respiratory disease were primarily established. While IBV, IDV, PCV4 and PPIV1 were not found in any of the cases, PRCV, SOV, and PCMV were more likely to be found in swIAV-positive nurseries with respiratory disease (p < 0.05). Overall, PCV3, PRRSV, and PCMV were the most frequently detected agents at herd level. Taken individually, virus prevalence was: swIAV, 48.6%; PRCV, 48.0%; PRRSV, 31.6%; SOV, 33.8%; PCMV, 48.3%, PCV2, 36.0%; and PCV3, 33.0%. Moreover, low Ct values (<30) were common for all agents, except PCV2 and PCV3. When the correlation between pathogens was individually examined, the presence of PRRSV was negatively correlated with swIAV and PRCV, while was positively associated to PCMV (p < 0.05). Also, PRCV and SOV were positively correlated between them and negatively with PCMV. Besides, the analysis of suckling pig samples, collected in subclinically infected farrowing units under an influenza monitoring program, showed that circulation of PRCV, PCMV, SOV, and PCV3 started during the early weeks of life. Interestingly, in those subclinically infected units, none of the pathogens was found to be correlated to any other. Overall, our data may contribute to a better understanding of the complex etiology and epidemiology of respiratory diseases in weaners. This is the first report of SOV in Spain and shows, for the first time, the dynamics of this pathogen in swine farms.

A 30-day follow-up study on the prevalence of SARS-COV-2 genetic markers in wastewater from the residence of COVID-19 patient and comparison with clinical positivity

Wastewater based epidemiology (WBE) is an important tool to fight against COVID-19 as it provides insights into the health status of the targeted population from a small single house to a large municipality in a cost-effective, rapid, and non-invasive way. The implementation of wastewater based surveillance (WBS) could reduce the burden on the public health system, management of pandemics, help to make informed decisions, and protect public health. In this study, a house with COVID-19 patients was targeted for monitoring the prevalence of SARS-CoV-2 genetic markers in wastewater samples (WS) with clinical specimens (CS) for a period of 30 days. RT-qPCR technique was employed to target nonstructural (ORF1ab) and structural-nucleocapsid (N) protein genes of SARS-CoV-2, according to a validated experimental protocol. Physiological, environmental, and biological parameters were also measured following the American Public Health Association (APHA) standard protocols. SARS-CoV-2 viral shedding in wastewater peaked when the highest number of COVID-19 cases were clinically diagnosed. Throughout the study period, 7450 to 23,000 gene copies/1000 mL were detected, where we identified 47 % (57/120) positive samples from WS and 35 % (128/360) from CS. When the COVID-19 patient number was the lowest (2), the highest CT value (39.4; i.e., lowest copy number) was identified from WS. On the other hand, when the COVID-19 patients were the highest (6), the lowest CT value (25.2 i.e., highest copy numbers) was obtained from WS. An advance signal of increased SARS-CoV-2 viral load from the COVID-19 patient was found in WS earlier than in the CS. Using customized primer sets in a traditional PCR approach, we confirmed that all SARS-CoV-2 variants identified in both CS and WS were Delta variants (B.1.617.2). To our knowledge, this is the first follow-up study to determine a temporal relationship between COVID-19 patients and their discharge of SARS-CoV-2 RNA genetic markers in wastewater from a single house including all family members for clinical sampling from a developing country (Bangladesh), where a proper sewage system is lacking. The salient findings of the study indicate that monitoring the genetic markers of the SARS-CoV-2 virus in wastewater could identify COVID-19 cases, which reduces the burden on the public health system during COVID-19 pandemics.

Detection of Higher Cycle Threshold Values in Culturable SARS-CoV-2 Omicron BA.1 Sublineage Compared with Pre-Omicron Variant Specimens - San Francisco Bay Area, California, July 2021-March 2022.

Before emergence in late 2021 of the highly transmissible B.1.1.529 (Omicron) variant of SARS-CoV-2, the virus that causes COVID-19 (1,2), several studies demonstrated that SARS-CoV-2 was unlikely to be cultured from specimens with high cycle threshold (Ct) values§ from real-time reverse transcription-polymerase chain reaction (RT-PCR) tests (suggesting low viral RNA levels) (3). Although CDC and others do not recommend attempting to correlate Ct values with the amount of infectious virus in the original specimen (4,5), low Ct values are sometimes used as surrogate markers for infectiousness in clinical, public health, or research settings without access to virus culture (5). However, the consistency in reliability of this practice across SARS-CoV-2 variants remains uncertain because Omicron-specific data on infectious virus shedding, including its relationship with RNA levels, are limited. In the current analysis, nasal specimens collected from an ongoing longitudinal cohort¶ (6,7) of nonhospitalized participants with positive SARS-CoV-2 test results living in the San Francisco Bay Area** were used to generate Ct values and assess for the presence of culturable SARS-CoV-2 virus; findings were compared between specimens from participants infected with pre-Omicron variants and those infected with the Omicron BA.1 sublineage. Among specimens with culturable virus detected, Ct values were higher (suggesting lower RNA levels) during Omicron BA.1 infections than during pre-Omicron infections, suggesting variant-specific differences in viral dynamics. Supporting CDC guidance, these data show that Ct values likely do not provide a consistent proxy for infectiousness across SARS-CoV-2 variants.

Correlation of SARS-CoV-2 Nasopharyngeal CT Values With Viremia and Mortality in Adults Hospitalized With COVID-19.

BackgroundBoth severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viremia and nasopharyngeal viral load have been suggested to be predictors of unfavorable outcome in coronavirus disease 2019 (COVID-19). This study aimed to investigate whether nasopharyngeal viral load is correlated with viremia and unfavorable outcome.MethodsThe presence of SARS-CoV-2 RNA was determined in paired nasopharyngeal and serum samples collected at admission from patients hospitalized for COVID-19. Standardized cycle threshold values (CT values) were used as an indicator of viral load. An adjusted logistic regression was used to estimate the risk of viremia at different nasopharyngeal CT values. A Cox regression was used to estimate the risk of 60-day mortality.ResultsA total of 688 patients were included. Viremia at admission was detected in 63% (146/230), 46% (105/226), and 31% (73/232) of patients with low, intermediate, and high nasopharyngeal CT values. The adjusted odds ratios of being viremic were 4.4 (95% CI, 2.9–6.8) and 2.0 (95% CI, 1.4–3.0) for patients with low and intermediate CT values, compared with high CT values. The 60-day mortality rate was 37% (84/230), 15% (36/226), and 10% (23/232) for patients with low, intermediate, and high nasopharyngeal CT values at admission, respectively. Adjusted hazard ratios were 2.6 (95% CI, 1.6–4.2) and 1.4 (95% CI, 0.8–2.4) for patients with low and intermediate CT values compared with high CT values.ConclusionsThere was a dose-dependent correlation between nasopharyngeal CT values and viremia at admission for COVID-19. Moreover, there was an increased risk of 60-day mortality for patients with low, compared with high, nasopharyngeal CT values.

RT-PCR Ct values combined with age predicts invasive mechanical ventilation and mortality in hospitalized COVID-19 patients in a MERS-CoV-endemic country

BackgroundSeveral risk factors have been used to predict severity of coronavirus disease 2019 (COVID-19), real-time reverse transcriptase polymerase chain reaction (RT-PCR) cycle threshold (Ct) values have not been included. MethodsA retrospective analysis of laboratory-confirmed COVID-19 patients who were hospitalized between March 2 and September 1, 2020, in an academic hospital in Riyadh that serves as a Middle East respiratory syndrome coronavirus (MERS-CoV) referral center was conducted. Nasopharyngeal (NP) and endotracheal (ET) samples were tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by RT-PCR, and viral load (VL) was determined based on the Ct values of E genes. The Ct values were distributed into four groups, with group Ct1 (≤19) indicating the highest VL and Ct4 (≥31) indicating the lowest VL. Univariate logistic regression was used to analyze age, gender, and comorbidities in relation to Ct groups for a primary endpoint of either invasive mechanical ventilation (IMV) or mortality. Significant variables were further analyzed by multivariate logistic regression. ResultsThe analysis included 728 patients hospitalized with COVID-19 (38% female; median age = 53 years; 41.3% diabetic; 39.4% hypertensive). Overall, 13.6% of these patients required IMV, and the in-hospital mortality rate was 15.5%. The IMV rate was higher in the Ct1 and Ct2 groups (15.2% and 15.5%, respectively) than in the Ct4 group (6.4%; p = 0.01). The mortality rate was also higher in the Ct1 and Ct2 groups (19.4% and 18.9%, respectively) than in the Ct4 group (8.9%; p = 0.02). The univariate analysis showed that lower Ct values and increasing age were associated with an increased risk of IMV (OR: 1.03; 95% CI: 1.01, 1.04; P < 0.0001) and mortality (OR: 1.04; 95% CI: 1.03, 1.06; P < 0.0001). The multivariate analysis showed that Ct1 was associated with the highest risk of mortality (OR: 2.29; 95% CI: 1.16, 5.52; P = 0.016), while Ct2 was associated with the highest risk of IMV (OR: 3.1; 95% CI: 1.47, 6.53; P = 0.003). ConclusionThe SARS-CoV-2 RT-PCR Ct values of hospitalized COVID-19 patients can be used as predictors of IMV and mortality, and this effect increases when combined with age. Clinicians could use these predictors to triage older patients for risk stratification and allocate IMV.

Genomic surveillance of SARS-COV-2 reveals diverse circulating variant lineages in Nairobi and Kiambu Counties, Kenya

Genomic surveillance and identification of COVID-19 outbreaks are important in understanding the genetic diversity, phylogeny, and lineages of SARS-CoV-2. Genomic surveillance provides insights into circulating infections, and the robustness and design of vaccines and other infection control approaches. We sequenced 57 SARS-CoV-2 isolates from a Kenyan clinical population, of which 55 passed quality checks using the Ultrafast Sample placement on the Existing tRee (UShER) workflow. Phylo-genome-temporal analyses across two regions in Kenya (Nairobi and Kiambu County) revealed that B.1.1.7 (Alpha; n = 32, 56.1%) and B.1 (n = 9, 15.8%) were the predominant lineages, exhibiting low Ct values (5–31) suggesting high infectivity, and variant mutations across the two regions. Lineages B.1.617.2, B.1.1, A.23.1, A.2.5.1, B.1.596, A, and B.1.405 were also detected across sampling sites within target populations. The lineages and genetic isolates were traced back to China (A), Costa Rica (A.2.5.1), Europe (B.1, B.1.1, A.23.1), the USA (B.1.405, B.1.596), South Africa (B.1.617.2), and the United Kingdom (B.1.1.7), indicating multiple introduction events. This study represents one of the genomic SARS-CoV-2 epidemiology studies in the Nairobi metropolitan area, and describes the importance of continued surveillance for pandemic control.

On the relationship between tripartite motif-containing 22 single-nucleotide polymorphisms and COVID-19 infection severity

BackgroundThe tripartite motif containing (TRIM)-22 participates in innate immune responses and exhibits antiviral activities. The present study aimed to assess of the relationship between TRIM22 single-nucleotide polymorphisms and clinical parameters with the coronavirus disease 2019 (COVID-19) infection severity.MethodsTRIM22 polymorphisms (rs7113258, rs7935564, and rs1063303) were genotyped using TaqMan polymerase chain reaction (PCR) assay in 495 dead and 497 improved severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-positive patients.ResultsIn this study, the frequencies of TRIM22 rs1063303 GG, rs7935564 GG, and rs7113258 TT were significantly higher in dead patients than in improved patients, and higher viral load with low PCR Ct value was noticed in dead patients. The multivariate logistic regression analysis revealed that the lower levels of low-density lipoprotein (LDL), cholesterol, PCR Ct value, and lower 25-hydroxyvitamin D, and also higher levels of erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), and TRIM22 rs1063303 GG, rs7113258 TT, and rs3824949 GG genotypes were related to the COVID-19 infection severity.ConclusionOur finding proved the probable relationship between the COVID-19 infection severity with the genotypes of TRIM22 SNPs and clinical parameters. More research is required worldwide to show the association between the COVID-19 infection severity and host genetic factors.

Evaluation of the 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 &lt; 20, between 20-24 and &gt;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 &lt;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. Keywords: Ct value, cycle threshold, COVID-19, clinical course, mortality

Pathogen Profile of Children Hospitalised with Severe Acute Respiratory Infections during COVID-19 Pandemic in the Free State Province, South Africa.

Severe acute respiratory infections (SARI) contribute to mortality in children ≤5 years. Their microbiological aetiologies are often unknown and may be exacerbated in light of coronavirus disease 19 (COVID-19). This study reports on respiratory pathogens in children ≤5 years (n = 84) admitted with SARI during and between the second and third waves of COVID-19 infection in South Africa. Nasopharyngeal/oropharyngeal swabs collected were subjected to viral detection using QIAstat-Dx® Respiratory SARS-CoV-2 Panel. The results revealed viral positivity and negativity detection rates of 88% (74/84) and 12% (10/84), respectively. Of the 21 targeted pathogens, human rhinovirus/enterovirus (30%), respiratory syncytial virus (RSV; 26%), and severe acute respiratory syndrome coronavirus 2 (24%) were mostly detected, with other viruses being 20% and a co-infection rate of 64.2% (54/84). Generally, RSV-positive samples had lower Ct values, and fewer viruses were detected during the third wave. Changes in the circulation patterns of respiratory viruses with total absence of influenza virus could be attributed to measures against COVID-19 transmission, which may result in waned immunity, thereby increasing susceptibility to severe infections in the following season. High viral co-infection rate, as detected, may complicate diagnosis. Nonetheless, accurate identification of the pathogens may guide treatment decisions and infection control.

The Hypercoagulable Profile of Patients with Bone Tumors: A Pilot Observational Study Using Rotational Thromboelastometry.

Introduction: A detailed evaluation of the malignancy-associated coagulopathy (MAC) in surgical patients with bone tumors may allow for more effective thromboprophylactic measures. The purpose of this study was to assess the perioperative hemostatic changes in patients with bone tumors, using rotational thromboelastometry (ROTEM). Methods: An observational study was performed, including 50 patients with bone tumors who underwent oncologic resection and 30 healthy controls, matched for age and gender. The preoperative and postoperative laboratory evaluation of coagulation in both groups included conventional coagulation tests and a ROTEM analysis. The results of the conventional coagulation tests and the ROTEM analysis were compared between the two groups. Results: The results of the conventional coagulation tests were comparable between the tumor patients and the healthy controls. However, compared to the healthy adults, the tumor patients had lower CT (p < 0.001) and CFT (p < 0.001) values suggesting a rapid induction of the coagulation cascade, elevated A10 (p < 0.001) and MCF (p < 0.001) values indicating a higher clot strength and platelet activation, and elevated LI60 (p < 0.001) values indicating hypofibrinolysis in patients with bone tumors. The multiple linear regression analysis (controlling for potential confounding factors) confirmed the independent association of bone tumors with these hemostatic changes. Conclusions: Our results support the advantageous use of a ROTEM in patients with bone tumors over conventional coagulation tests because the qualitative changes in the hemostatic profile of these patients that can be detected by a ROTEM analysis cannot be identified by conventional tests. The ROTEM results indicate that the hypercoagulable state in patients with bone tumors is caused by the malignancy-associated activation of the coagulation cascade, platelet activation, and hypofibrinolysis.

Descriptive analysis of clinical and laboratory findings in relation to changes in SARS-CoV-2 viral dynamics and cyclic threshold: a retrospective, single center observational study in patients treated with Hydroxychloroquine/Azithromycin combination therapy

Background: Cases of undiagnosed pneumonia have emerged, and sequencing of respiratory samples indicated the presence of SARS-CoV-2 causing COVID-19. Patients with higher viral load and lower Ct values tend to have progressive disease and severe lung injury. The objective of this study is to describe the clinical manifestation and disease outcomes of COVID-19 patients in relation to their Ct values. Methods: A retrospective, single center observational study was performed, including patients admitted to King Faisal Specialist Hospital and Research Centre (KFSH&amp;RC) Riyadh between March 1st-29th, 2020 and have a confirmed diagnosis of COVID-19. The Ct value was identified to determine the viral load. All patients were treated according to KFSH&amp;RC guidelines. Patients were divided into HCQ/AZI and non HCQ/AZI treated groups. Results: There were many days where Ct values were not available. An attempt at imputing information for missing Ct values was made using logic. The logic leads to an ordinal Ct score 1, 2, 3, or 4. As a result, complete Ct score profiles were available. There was no evidence of statistically significant difference between the two groups in regard to clinical severity, duration to negative test or changes in Ct values. Conclusion: There is little knowledge known to the time profile of Ct values and their relation to disease course of COVID-19. This study provides insight on how Ct values might be used to determine treatment efficacy. As it might be difficult to obtain Ct values at all times, this study provides an imputation method that may be used with conservative statistical assumptions for analyses of Ct profiles.

COVID-19 in Children: Correlation Between Epidemiologic, Clinical Characteristics, and RT-qPCR Cycle Threshold Values.

Background:Initially, the impact of SARS-CoV-2 infection on children was unknown. Standard COVID-19 diagnosis is confirmed using real-time qPCR. Cycle threshold (Ct) values of RT-qPCR are inversely proportional to viral load and the test indirectly quantifies viral RNA copy numbers. The objective of this study was to determine the correlation between epidemiology, clinical characteristics, severity of confirmed COVID-19 cases, and Ct values.Methods:An observational, analytical, cross-sectional study. All children with COVID-19 under 18 years old admitted to the Ricardo Gutiérrez Children’s Hospital between March 1, 2020, and February 28, 2021, were included. SARS-CoV-2 infection was confirmed using RT-qPCR.Results:Median age of patients was 7 years. Ct values were estimated in 419 cases, median Ct value was 23.5 [interquartile range (IQR): 18.9–30.9]. Levels were significantly lower in symptomatic than asymptomatic patients (Ct: 22.1; IQR: 18.4–22.1), in children <2 years of age (Ct: 20.6; IQR: 17.3–27.3) and when sample collection was <4 days after symptom onset (Ct: 21.1; IQR: 18.1–27.5). In children >2 years of age, Ct values were significantly lower in symptomatic (Ct: 22.6; IQR: 18.7–29.3) than asymptomatic (Ct: 31.2; IQR: 24.5–33.3) patients.Conclusions:Children younger than 2 years with COVID-19 have lower values of Ct—as a proxy for higher viral load—than older children. Symptomatic children over 2 years of age had lower Ct values compared with asymptomatic children.