PCR Ct Research Articles

Comparison of Nasal Swabs, Nasopharyngeal Swabs, and Saliva Samples for the Detection of SARS-CoV-2 and other Respiratory Virus Infections.

Nasal swabs and saliva samples are being considered alternatives to nasopharyngeal swabs (NPSs) for detecting severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2); however, few studies have compared the usefulness of nasal swabs, NPSs, and saliva samples for detecting SARS-CoV-2 and other respiratory virus infections. We compared the positivity rates and concentrations of viruses detected in nasal swabs, NPSs, and saliva samples using cycle threshold (Ct) values from real-time PCR tests for respiratory viruses. In total, 236 samples (48 five-rub and 10 10-rub nasal swabs, 96 NPSs collected using two different products, 48 saliva swabs, and 34 undiluted saliva samples) from 48 patients (34 patients with SARS-CoV-2 and 14 with other respiratory virus infections) and 40 samples from eight healthy controls were obtained. The PCR positivity and Ct values were compared using Allplex Respiratory Panels 1/2/3 and Allplex SARS-CoV-2 real-time PCR. NPSs showed the lowest Ct values (indicating the highest virus concentrations); however, nasal and saliva samples yielded positive results for SARS-CoV-2 and other respiratory viruses. The median Ct value for SARS-CoV-2 E gene PCR using nasal swab samples collected with 10 rubs was significantly different from that obtained using nasal swabs collected with five rubs (Ct=24.3 vs. 28.9; P=0.002), but not from that obtained using NPSs. Our results confirm that the NPS is the best sample type for detecting respiratory viruses, but nasal swabs and saliva samples can be alternatives to NPSs. Vigorously and sufficiently rubbed nasal swabs can provide SARS-CoV-2 concentrations similar to those obtained with NPSs.

Pathologic Complete Response and Individual Patient Prognosis After Neoadjuvant Chemotherapy Plus Anti–Human Epidermal Growth Factor Receptor 2 Therapy of Human Epidermal Growth Factor Receptor 2–Positive Early Breast Cancer

The achievement of pathologic complete response (pCR) is strongly prognostic for event-free survival (EFS) and overall survival (OS) in patients with early breast cancer (EBC), and adapting postneoadjuvant therapy improves long-term outcomes for patients with HER2-positive disease not achieving pCR. We sought to investigate prognostic factors for EFS and OS among patients with and without pCR after neoadjuvant systemic treatment consisting of chemotherapy plus anti-HER2 therapy. We used individual data from 3,710 patients randomly assigned in 11 neoadjuvant trials for HER2-positive EBC with ≥100 patients enrolled, available data for pCR, EFS, and OS, and follow-up ≥3 years. We assessed baseline clinical tumor size (cT) and clinical nodal status (cN) as prognostic factors using stratified (by trial and treatment) Cox models separately for hormone receptor-positive versus hormone receptor-negative disease, and for patients who had pCR (pCR+; ypT0/is, ypN0) versus patients who did not achieve a pCR (pCR-). The median follow-up overall was 61.2 months. In pCR+ patients, cT and cN were significant independent prognostic factors for EFS, whereas only cT was a significant predictor for OS. In pCR- patients, cT, cN, and hormone receptor status were significant independent predictors for both EFS and OS. Regardless of hormone receptor status, cT, and cN, the 5-year EFS/OS rates were higher in pCR+ patients than in pCR- patients. In most subsets with regards to hormone receptor and pCR status, cT and cN were independent prognostic factors for both EFS and OS, including pCR+ patients. These results confirm that patients achieving pCR have far better survival outcomes than patients who do not. The traditional poor prognostic features, namely tumor size and nodal status, remain important even after a pCR.

Genotyping of Mycobacterium leprae strains in south central coast and central highlands of Vietnam.

Leprosy remains an important health problem worldwide. It is one of the oldest recorded diseases of humankind. In this study, we expanded the analysis of the geographic distribution of Mycobacterium leprae by investigating SNPs and rpoT genotypes in South Central Coast and Central Highlands clinical isolates, providing insights into the distribution and transmission of leprosy in Vietnam and in this geographic region. 27 clinical isolates from the patients, determined the genotypes of M. leprae by SNP and rpoT polymorphism. SNP genotyping was performed by PCR amplification and sequencing, rpoT genotyping by PCR amplification and electrophoresis. All of 27 DNA samples (100%) were positive with RLEP TaqMan PCR (Ct value range is 18-32 on 3 replicates). SNP type 1 was identified in 15 isolates (56%), while SNP type 3 was detected in 12 samples (44%). SNP type 2 and type 4, were not detected. The 6-base repeat region of the rpoT gene was amplified by PCR and analyzed by 4% MetaPhor™ agarose gel electrophoresis. All isolates yielded amplification products of 91-bp, but not 97-bp. This study showed that 56% of isolates belonged to type 1, 44% to type 3. In addition, all samples have the 3-copy hexamer genotype in the rpoT gene.

Feeding Spray-Dried Porcine Plasma to Pigs Reduces African Swine Fever Virus Load in Infected Pigs and Delays Virus Transmission-Study 1.

The objective of this study was to evaluate the potential benefits of feeding spray-dried porcine plasma (SDPP) to pigs infected with African swine fever virus (ASFV). Two groups of twelve weaned pigs each were fed with CONVENTIONAL or 8% SDPP enriched diets. Two pigs (trojans)/group) were injected intramuscularly with the pandemic ASFV (Georgia 2007/01) and comingled with the rest of the pigs (1:5 trojan:naïve ratio) to simulate a natural route of transmission. Trojans developed ASF and died within the first week after inoculation, but contact pigs did not develop ASF, viremia, or seroconversion. Therefore, three more trojans per group were introduced to optimize the ASFV transmission (1:2 trojan:naïve ratio). Blood, nasal, and rectal swabs were weekly harvested, and at end of the study ASFV-target organs collected. After the second exposure, rectal temperature of conventionally fed contact pigs increased >40.5 °C while fever was delayed in the SDPP contact pigs. Additionally, PCR Ct values in blood, secretions, and tissue samples were significantly lower (p < 0.05) for CONVENTIONAL compared to SDPP contact pigs. Under these study conditions, contact exposed pigs fed SDPP had delayed ASFV transmission and reduced virus load, likely by enhanced specific T-cell priming after the first ASFV-exposure.

A comparison of five Illumina, Ion Torrent, and nanopore sequencing technology-based approaches for whole genome sequencing of SARS-CoV-2

Rapid identification of the rise and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern remains critical for monitoring of the efficacy of diagnostics, therapeutics, vaccines, and control strategies. A wide range of SARS-CoV-2 next-generation sequencing (NGS) methods have been developed over the last years, but cross-sequence technology benchmarking studies have been scarce. In the current study, 26 clinical samples were sequenced using five protocols: AmpliSeq SARS-CoV-2 (Illumina), EasySeq RC-PCR SARS-CoV-2 (Illumina/NimaGen), Ion AmpliSeq SARS-CoV-2 (Thermo Fisher), custom primer sets (Oxford Nanopore Technologies (ONT)), and capture probe-based viral metagenomics (Roche/Illumina). Studied parameters included genome coverage, depth of coverage, amplicon distribution, and variant calling. The median SARS-CoV-2 genome coverage of samples with cycle threshold (Ct) values of 30 and lower ranged from 81.6 to 99.8% for, respectively, the ONT protocol and Illumina AmpliSeq protocol. Correlation of coverage with PCR Ct values varied per protocol. Amplicon distribution signatures differed across the methods, with peak differences of up to 4 log10 at disbalanced positions in samples with high viral loads (Ct values ≤ 23). Phylogenetic analyses of consensus sequences showed clustering independent of the workflow used. The proportion of SARS-CoV-2 reads in relation to background sequences, as a (cost-)efficiency metric, was the highest for the EasySeq protocol. The hands-on time was the lowest when using EasySeq and ONT protocols, with the latter additionally having the shortest sequence runtime. In conclusion, the studied protocols differed on a variety of the studied metrics. This study provides data that assist laboratories when selecting protocols for their specific setting.

Diagnosis of Anaplasma marginale in cattle at the Iowa State University veterinary diagnostic laboratory 2003–2021

Anaplasma marginale is a blood-borne rickettsia-like organism that infects cattle erythrocytes and causes anaplasmosis. This study reviews diagnostic data of all A. marginale diagnostics performed from 2003 to August 2021 in the Iowa State Veterinary Diagnostic Laboratory. Typically, the referring veterinarian's initial tentative diagnosis was based on presenting clinical signs or necropsy findings. Confirmatory testing at the ISU-VDL consisted of light microscopy evaluation of stained blood smears or molecular diagnostic procedures. A total of 94 cases were submitted with tissue samples from deceased animals, of which 79 were from Iowa and 15 were from other states. The most typical gross lesions were widespread yellow adipose tissue and splenomegaly. Typical histopathological lesions included marked bile stasis and hemosiderin-laden macrophages in the liver and spleen, respectively. Starting in 2013, when PCR was implemented to confirm cases of anaplasmosis, 315/1125 (28%) were positive to A. marginale, and 810 were negative, using a cut-off of 35.0 Ct. The average (±SD) of the positive PCR Ct was 19.5 (±6.0), and the first and third quartiles were 14.9 and 23.4. Most cases occurred between August and November, peaking in September, whether from necropsies or positive blood samples by PCR. The most common tick observed in Iowa, Dermacentor variabilis, is likely the main vector for transmission. Further surveys should be conducted to estimate seroprevalence by geographical location, the density of cattle populations, distribution of known vectors according to season, and strains of A. marginale.

Simultaneous detection of omicron and other SARS-CoV-2 variants by multiplex PCR MassARRAY technology

The rapid emergence of SARS-CoV-2 variants with high severity and transmutability adds further urgency for rapid and multiplex molecular testing to identify the variants. A nucleotide matrix-assisted laser-desorption-ionization time-of-flight mass spectrophotometry (MALDI-TOF MS)-based assay was developed (called point mutation array, PMA) to identify four major SARS-CoV-2 variants of concern (VOCs) including Alpha, Beta, Delta, and Omicron (namely PMA-ABDO) and differentiate Omicron subvariant (namely PMA-Omicron). PMA-ABDO and PMA-Omicron consist of 24 and 28 mutation sites of the spike gene. Both PMA panels specifically identified VOCs with as low as 10 viral copies/µl. The panel has shown a 100% concordant with the Next Generation Sequencing (NGS) results testing on 256 clinical specimens with real-time PCR cycle threshold (Ct) values less than 26. It showed a higher sensitivity over NGS; 25/28 samples were positive by PMA but not NGS in the clinical samples with PCR Ct higher than 26. Due to the mass of nucleotide used to differentiate between wild-type and mutation strains, the co-infection or recombination of multiple variants can be determined by the PMA method. This method is flexible in adding a new primer set to identify a new emerging mutation site among the current circulating VOCs and the turnaround time is less than 8 h. However, the spike gene sequencing or NGS retains the advantage of detecting newly emerged variants.

Hands off the Mink! Using Environmental Sampling for SARS-CoV-2 Surveillance in American Mink.

Throughout the COVID-19 pandemic, numerous non-human species were shown to be susceptible to natural infection by SARS-CoV-2, including farmed American mink. Once infected, American mink can transfer the virus from mink to human and mink to mink, resulting in a high rate of viral mutation. Therefore, outbreak surveillance on American mink farms is imperative for both mink and human health. Historically, disease surveillance on mink farms has consisted of a combination of mortality and live animal sampling; however, these methodologies have significant limitations. This study compared PCR testing of both deceased and live animal samples to environmental samples on an active outbreak premise, to determine the utility of environmental sampling. Environmental sampling mirrored trends in both deceased and live animal sampling in terms of percent positivity and appeared more sensitive in some low-prevalence instances. PCR CT values of environmental samples were significantly different from live animal samples' CT values and were consistently high (mean CT = 36.2), likely indicating a low amount of viral RNA in the samples. There is compelling evidence in favour of environmental sampling for the purpose of disease surveillance, specifically as an early warning tool for SARS-CoV-2; however, further work is needed to ultimately determine whether environmental samples are viable sources for molecular epidemiology investigations.

Evaluation of Liver Function Tests (LFT) and C-reactive protein in COVID-19 (SARS Cov-2) positive patients diagnosed by Real-time PCR

Background/Aim: Unpredicted social and economic consequences have resulted from the SARS-CoV-2 pandemic worldwide. Limited information is currently available addressing the COVID-19 infection impact on the RT-PCR Cycle threshold value trend, infection risk factors, impact on liver enzymes, etc. Methods: From November 2020 to March 2021, a cross-sectional study was carried out in the Chemical Pathology also Molecular Biology divisions of the Pathology Department of Shalamar Hospital, Lahore. Results: Males had a higher risk of contracting SARS-CoV-2 infection than females about 51%. 36.5 percent of total infected people fell within the 20–40 age range. Significant factors that affect the severity of COVID-19 include age and underlying comorbidities. The majority of the patients (78.3%) reported fever, 50.4% had a cough, and 50.1% had myalgias. Low Ct value of RT-PCR may be asignificant predictor of illness severity and risk of mortality, with p values of 0.001 and 0.003, correspondingly. Disease severity was substantially associated with CRP, AST, ALT, and bilirubin indirect. It was observed that the Deritis ratio and CRP were highly associated with the risk of mortality. These markers can therefore be used to evaluate a patient's status as it progresses toward a severe disease, liver damage from treatment, and death risk. Conclusions: For doctors making patient management decisions, real-time PCR data and Ct values for SARS-CoV-2 may be useful. Age and comorbidities, among other risk variables, have been recognized as being associated with the likelihood of having a fatal illness. ALT, AST, Deritis ratio, and CRP are biochemical laboratory indicators that can be considered prognostic biomarkers for the development of severe disease and risk of mortality. Keywords: SARS-CoV-2, COVID-19, Liver, Cough, Pandemic

307. Diagnostic Test Kinetics, Infectivity, and Immunological Responses Among Unvaccinated Adults During Acute SARS-CoV-2 Infection

Abstract Background Appropriate diagnostic testing can be used to inform infection control measures and reduce SARS-CoV-2 transmission, yet the test kinetics, infectivity, and immunological responses during acute, non-severe SARS-CoV-2 infection need clarity. Methods We conducted a prospective cohort study between Nov 2020-July 2021 in Seattle, Washington of 95 unvaccinated, immunocompetent adults with no prior SARS-CoV-2 infection. Nasal swabs (nasopharyngeal and anterior) and blood serum samples were serially collected at six visits over two months. Viral RNA, N and S antigen concentrations, and viral growth/infectivity were measured from nasal samples. Anti-S total antibody and IgG assays were performed on serum. We fit loess curves to quantitative data corresponding to each testing modality by days since symptom onset (DSSO) and compared qualitative test results across time points to demonstrate time-dependent agreement of PCR, N antigen, and culture results. Generalized estimating equations were used to approximate relative risk of culture positivity (a proxy for infectiousness) for positive vs. negative test results (antigen and PCR), stratified by presence/absence of symptoms and DSSO. Sampling Schema Nasal swabs and venous blood were collected at visits 1-4; venous blood only at visits 5-6. All participants were enrolled within 14 days of symptom onset (median: 6) and 7 days of a positive test (median: 4). Results Infections in this cohort (median age: 29y) were mild (no hospitalization). Median (IQR) time to negative result was 11 (4), 13 (6), and 20 (7) DSSO for culture growth, N antigen, and PCR tests, respectively. Viral RNA quantities declined more slowly than antigen and culturable virus; antibody titers rose rapidly 5-15 DSSO and plateaued 20-30 DSSO. All culture-positive samples collected 0-5 DSSO were positive by PCR, but relative risk of culture positivity (infectiousness) for positive vs. negative PCR results declined 6-10 DSSO. Relative risk of culture positivity for positive vs. negative antigen results was consistently high 0-10 DSSO, with similar results when stratified by presence of symptoms. Diagnostic test kinetics and immunological responses Diagnostic test kinetics and immunological responses measured in adults with non-severe, symptomatic SARS-CoV-2 infection: loess trendlines and 95% confidence intervals are given for SARS-CoV-2 viral load (calculated from PCR Ct value using a calibration curve), TCID50 from viral culture, mean concentrations of nucleocapsid and spike antigen proteins, and anti-S total and IgG antibody concentrations. Conclusion The results reinforce the importance of molecular PCR testing as a highly sensitive diagnostic tool but with limited utility as an indicator of viral culturability and likely infectiousness. N antigen testing may be a preferable diagnostic test within two weeks of symptom onset, especially 6-10 DSSO, because it more closely correlates with culture growth over the course of infection. Disclosures Daphne Hamilton, BA, Roche (spouse is employed by Roche): Employee Alexander L. Greninger, MD, PhD, Abbott: Contract Testing|Cepheid: Contract Testing|Gilead: Grant/Research Support|Gilead: Contract Testing|Hologic: Contract Testing|Merck: Grant/Research Support|Novavax: Contract Testing|Pfizer: Contract Testing Geoffrey S. Gottlieb, MD, PhD, Abbott Molecular Diagnostics: Grant/Research Support|Alere Technologies: Grant/Research Support|BMGF: Grant/Research Support|BMS: Grant/Research Support|Cerus Corp.: Grant/Research Support|Gilead Sciences: Grant/Research Support|Janssen Pharmaceutica: Grant/Research Support|Merck &amp; Co: Grant/Research Support|Roche Molecular Systems: Grant/Research Support|THERA Technologies/TaiMed Biologics: Grant/Research Support|ViiV Healthcare: Grant/Research Support.

310. Longitudinal Assessment of Point-of-Care LumiraDx Antigen and Antibody Test Performance During Acute SARS-CoV-2 Infection and Recovery

Abstract Background Rapid COVID-19 tests can offer significant advantages and reduce health disparities. The LumiraDx SARS-CoV-2 platform can perform microfluidic fluorescence assays for the rapid detection of SARS-CoV-2 antigen (Ag) and antibodies (Ab). We evaluated both tests in a longitudinal cohort to evaluate performance during acute SARS-CoV-2 infection and recovery. Methods We collected nasal samples from 71 unique participants at four clinic visits spanning 0-21 days since symptom onset (DSSO); blood samples were collected from the same participants over six visits spanning 0-87 DSSO. For Ag testing, 232 anterior nasal swabs were assayed by: 1) the LumiraDx Ag test, 2) a laboratory-based electrochemiluminescence immunoassay for N Ag, 3) RT-PCR (Hologic Panther Fusion), and 4) culture (growth in VeroE6AT cells). For Ab testing, 308 serum samples were assayed by: 1) the LumiraDx Ab test and 2) Roche Elecsys Anti-S SARS-CoV-2 total Ab test. Measures of concordance [positive predictive agreement (PPA), negative predictive agreement (NPA), and Cohen’s Kappa (Κ)] were estimated for qualitative results of the LumiraDx tests versus corresponding lab reference tests. Confidence intervals were estimated via bootstrapping. Results LumiraDx Ag results had strong agreement with lab N-Ag results (Κ &amp;gt; 0.80) across all samples. Between 0-5 days, agreement was perfect, except for one sample resulting positive by LumiraDx Ag and negative by lab Ag. Agreement with PCR results was moderate overall (Κ=0.60), though substantial (Κ &amp;gt; 0.6) for both 0-5 DSSO (PPA=0.96/NPA=0.80) and 6-10 DSSO (PPA=0.96/NPA=0.59). Agreement with culture results was moderate overall (Κ=0.46): substantial (Κ=0.6) between 0-5 DSSO (PPA=0.96/NPA=0.60) and fair (Κ=0.29) between 6-10 DSSO (PPA=1.0/NPA=0.32). LumiraDx Ab results showed almost perfect agreement with lab Ab results across all samples (Κ=0.88), with substantial agreement (Κ &amp;gt; 0.7) for samples collected 0-10 DSSO (PPA=0.93/NPA=0.89) and 11-28 DSSO (PPA=0.99/NPA=0.69). Longitudinal agreement of LumiraDx antigen test result and culture positivity, by PCR Ct value. Nasal samples grouped by participant (lines) and agreement of results between LumiraDx antigen test result and culture positivity (proxy for infectiousness). Conclusion LumiraDx rapid tests perform well compared to more costly and time-consuming lab methods of Ag and Ab detection. The rapid Ag test may be helpful in identifying patients infectious between 0-5 DSSO, given the substantial concordance of the rapid Ag test and culture positivity. Disclosures Daphne Hamilton, BA, Roche (spouse is employed by Roche): Employee.

A Brief Report on the Effect of Covid 19 Pandemic on Patients Undergoing Skin Graft Surgery in a Burns Hospital from March 2019 to March 2020

Introduction: The Covid 19 virus has affected the lives of all people on the planet. To deal with it, the virus's behavior at all levels of work must be examined, as, in this article, we have tried to discuss the behavior of this virus with skin graft surgery patients. Methods: In this study, about 5,000 patients from March 2019 to March 2020 referred to Motahhari Burns Hospital were about 155 candidates for skin graft surgery. Skin graft surgery involves removing a layer of a person's skin and placing it on the affected area. The doctor selects a matched tissue close to the affected area, removes the skin, and grafts it where it needs to be repaired. Results: Out of 155 patients included in this study, 101 were men and 54 were women. The patients’ age ranged from 13 to 75 years. All patients had positive PCR tests and CT scans confirming Covid 19. The success rate of surgery was 0.445 in men and 0.388 in women. Discussion: In some cases, reconstructive surgeries such as skin grafting may be required for patients with coronavirus. As Iran has been among countries with the highest number of COVID-19 cases. The success rate of surgery was 0.445 in men and 0.388 in women affected by coronavirus. There is scarcity of data on the association between COVID-19 and skin grafting success. The statistical findings of this study indicated that COVID-19 increased the likelihood of skin graft rejection significantly. Conclusion: The findings of this study showed that COVID-19 increased the likelihood of skin graft rejection significantly.

Infection control behaviours, intra‐household transmission and quarantine duration: a retrospective cohort analysis of COVID‐19 cases

ObjectivesTo study COVID‐19 (Delta Variant) cases and close contacts co‐located within households. Focusing on epidemiology of transmission of COVID‐19, quarantine duration and utilisation of infection control behaviours under a telehealth model of care in an elimination setting. MethodsA retrospective cohort analysis examined household spread of infection, duration of quarantine and change in PCR CT value during illness. A survey explored infection control behaviours used by household members during isolation and quarantine. ResultsThe cohort was 141 individuals in 35 households. Thirty‐seven were index cases, and 48 became positive during quarantine, most within 10 days. Whole‐household infection occurred in 12 households with multiple members. Behaviours focused on fomite transmission reduction rather than preventing aerosol transmission. The median duration of close contact household quarantine was 25 days. The majority of COVID‐19 cases were de‐isolated after 14 days with no evidence of further community transmission. ConclusionIntrahousehold transmission was not universal and, if it occurred, usually occurred quickly. Behaviours utilised focused on fomites, suggesting a need for improved education regarding the potential utilisation of strategies to prevention the transmission of aerosols. Households experienced long durations of home‐based quarantine. Implications for public healthThe impact of long quarantine durations must be considered, particularly where most community benefit from quarantine is achieved within 10 days from exposure in the setting of the Delta Variant. Education of households regarding aerosol risk reduction is a potential strategy in the household setting of individuals at risk of disease progression.

Rs12329760 Polymorphism in Transmembrane Serine Protease 2 Gene and Risk of Coronavirus Disease 2019 Mortality.

The protease produced by the transmembrane serine protease 2 (TMPRSS2) gene enhances viral infections and has been linked to severe acute respiratory syndrome coronavirus 2 pathogenesis. Therefore, this study evaluated the association between TMPRSS2 and coronavirus disease 2019 (COVID-19) mortality. TMPRSS2 rs12329760 polymorphism was genotyped using the tetraprimer amplification refractory mutation system-polymerase chain reaction method in 592 dead and 693 improved patients. In the current study, the frequency of TMPRSS2 rs12329760 CC than TT genotypes was significantly lower in improved patients than in dead patients. According to the findings of the multivariate logistic regression test, higher levels of mean age, creatinine, erythrocyte sedimentation rate, C-reactive protein, aspartate aminotransferase, lower levels of 25-hydroxyvitamin D, uric acid, and real-time PCR Ct values and TMPRSS2 rs12329760 CC genotype were observed to be associated with increased COVID-19 mortality rates. In conclusion, the TMPRSS2 rs12329760 CC genotype was a polymorphism linked to a significantly higher incidence of severe COVID-19. Further studies are required to corroborate the obtained findings.

ABO rs657152 and Blood Groups Are as Predictor Factors of COVID-19 Mortality in the Iranian Population.

Several studies have discovered a relationship between specific blood types, genetic variations of the ABO gene, and coronavirus disease 2019 (COVID-19). Therefore, the aim of this study was to evaluate the association between ABO rs657152 polymorphisms and ABO blood groups with COVID-19 mortality. The tetraprimer amplification refractory mutation system, polymerase chain reaction method, was used for ABO rs657152 polymorphism genotyping in 1,211 dead and 1,442 improved patients. In the current study, the frequency of ABO rs657152 AA than CC genotypes was significantly higher in dead patients than in improved patients. Our findings indicated that blood type A was associated with the highest risk of COVID-19 mortality compared to other blood groups, and patients with blood type O have a lower risk of infection, suggesting that blood type O may be a protective factor against COVID-19 mortality. Multivariate logistic regression test indicated that higher COVID-19 mortality rates were linked with alkaline phosphatase, alanine aminotransferase, high density lipoprotein, low-density lipoprotein, fasting blood glucose, uric acid, creatinine, erythrocyte sedimentation rate, C-reactive protein, 25-hydroxyvitamin D, real-time PCR Ct values, ABO blood groups, and ABO rs657152 AA genotype. In conclusion, the AA genotype of ABO rs657152 and blood type A were associated with a considerably increased frequency of COVID-19 mortality. Further research is necessary to validate the obtained results.

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.

An assessment on loss of workforce due to COVID-19 among healthcare personnel: A university hospital experience.

Healthcare personnel are among the COVID-19 risk groups. For this reason, increased absence from work affects the loss of labor. This study aimed to evaluate the workforce loss amongst health personnel working in our hospital due to COVID-19 in a one-year period. Workforce loss of healthcare workers was assessed via absenteeism and life expectancy. Loss of workforce for COVID-19 PCR positive or PCR negative but CT findings compatible with COVID-19 and personnel with high-risk exposure for COVID-19 were determined with absenteeism. Healthcare personnel who passed away due to COVID-19 was determined with the consideration of the retirement age and expected life years. Total lost time from work was 14635 days (excluding deaths). Loss of workforce rates resulting from COVID-19 positivity for male employees was greater in comparison to the results for females (p = 0.018). High-risk exposure of healthcare personnel working in clinical sciences was higher than those in other departments (p < 0.001). Total loss in workforce for 3 people passed away was 14 years 5 months, and total life expectancy was 64 years. Healthcare personnel under the age of 40 had less absenteeism than those over 40 years (p < 0.001). It was observed that all occupational groups working at the hospital were impacted by COVID-19. The two most important factors that influenced absenteeism were the reason for being affected (positivity and high risk) and age. Absenteeism and daily case tracing of healthcare personnel working on the frontlines will aid in both the pandemic control and management of workload for those left behind.

Viral cultures for assessing fomite transmission of SARS-CoV-2: a systematic review and meta-analysis

IntroductionThe role of fomites in the transmission of SARS-CoV-2 is unclear. Our objective was to assess whether SARS-CoV-2 can be transmitted through fomites, using evidence from viral culture studies.MethodsWe conducted searches in the WHO Covid-19 Database, PubMed, LitCovid, medRxiv, and Google Scholar to 31 December 2021. We included studies that investigated fomite transmission and performed viral culture to assess the cytopathic effect (CPE) of positive fomite samples and confirmation of SARS-CoV-2 as the cause of the CPE. We assessed the risk of bias using a checklist modified from the QUADAS-2 criteria.ResultsWe included 23 studies. The overall risk of bias was moderate. Five studies demonstrated replication-competent virus from fomite cultures and three used genome sequencing to match fomite samples with human clinical specimens. The mean Ct of samples with positive viral culture was significantly lower compared with cultured samples that returned negative results: SMD -1.45, 95%CI -2.00 to -0.90, I2=0%; P<0.00001. The likelihood of isolating replication-competent virus was significantly greater when the Ct was <30: RR 3.10 (95%CI 1.32 to 7.31, I2=71%, P=0.01). Infectious specimens were mostly detected within 7 days of symptom onset. One study showed possible transmission of SARS-CoV-2 from fomites to humans.ConclusionThe evidence from published studies suggests that replication-competent SARS-CoV-2 is present on fomites. Replication-competent SARS-CoV-2 is significantly more likely when the PCR Ct for clinical specimens and fomite samples is <30. Further studies should investigate the duration of infectiousness of SARS-CoV-2 and the frequency of transmission from fomites.

Angiotensin-converting enzyme 2 rs2285666 polymorphism and clinical parameters as the determinants of COVID-19 severity in Iranian population.

Host genetic factors may be correlated with the severity of coronavirus disease 2019 (COVID‐19). Angiotensin‐converting enzyme 2 (ACE2) plays a vital role in viral cell entrance. The current study aimed to evaluate the association of ACE2 rs2285666 polymorphism and clinical parameters with COVID‐19 mortality. The ACE2 rs2285666 polymorphism was genotyped using the polymerase chain reaction‐restriction fragment length polymorphism in 556 recovered and 522 dead patients. In this study, the frequency of ACE2 rs2285666 CC was significantly higher than TT genotype in dead patients. The multivariate logistic regression analysis results showed that the higher levels of alanine aminotransferase, alkaline phosphatase, creatinine, erythrocyte sedimentation rate, and C‐reactive protein and the low levels of uric acid, cholesterol, low density lipoprotein, 25‐hydroxyvitamin D, real‐time PCR Ct values, and ACE2 rs2285666 CC genotype were associated with increased mortality rates after COVID‐19. In conclusion, our findings demonstrated a possible link between COVID‐19 mortality, clinical parameters, and ACE2 rs2285666 CC. Further research is required to confirm these results.

Prediction and Classification of COVID-19 Admissions to Intensive Care Units (ICU) Using Weighted Radial Kernel SVM Coupled with Recursive Feature Elimination (RFE).

Healthcare systems have been under immense pressure since the beginning of the COVID-19 pandemic; hence, studies on using machine learning (ML) methods for classifying ICU admissions and resource allocation are urgently needed. We investigated whether ML can propose a useful classification model for predicting the ICU admissions of COVID-19 patients. In this retrospective study, the clinical characteristics and laboratory findings of 100 patients with laboratory-confirmed COVID-19 tests were retrieved between May 2020 and January 2021. Based on patients’ demographic and clinical data, we analyzed the capability of the proposed weighted radial kernel support vector machine (SVM), coupled with (RFE). The proposed method is compared with other reference methods such as linear discriminant analysis (LDA) and kernel-based SVM variants including the linear, polynomial, and radial kernels coupled with REF for predicting ICU admissions of COVID-19 patients. An initial performance assessment indicated that the SVM with weighted radial kernels coupled with REF outperformed the other classification methods in discriminating between ICU and non-ICU admissions in COVID-19 patients. Furthermore, applying the Recursive Feature Elimination (RFE) with weighted radial kernel SVM identified a significant set of variables that can predict and statistically distinguish ICU from non-ICU COVID-19 patients. The patients’ weight, PCR Ct Value, CCL19, INF-β, BLC, INR, PT, PTT, CKMB, HB, platelets, RBC, urea, creatinine and albumin results were found to be the significant predicting features. We believe that weighted radial kernel SVM can be used as an assisting ML approach to guide hospital decision makers in resource allocation and mobilization between intensive care and isolation units. We model the data retrospectively on a selected subset of patient-derived variables based on previous knowledge of ICU admission and this needs to be trained in order to forecast prospectively.