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11 pages, 882 KiB

Open AccessArticle

The Time-Dependent Association of Torque Teno Virus Load with the Level of SARS-CoV-2 S1 IgG Antibodies Following COVID-19 Vaccination in Kidney Transplant Recipients

by Céline Imhof, Lianne Messchendorp, Debbie van Baarle, Ron T. Gansevoort, Coretta Van Leer-Buter and Jan-Stephan F. Sanders

Viruses 2023, 15(11), 2189; https://doi.org/10.3390/v15112189 - 31 Oct 2023

Cited by 1 | Viewed by 1141

Abstract

Kidney transplant recipients (KTR) show an impaired humoral immune response to COVID-19 vaccination due to their immunocompromised status. Torque teno virus (TTV) is a possible marker of immune function. This marker may be helpful in predicting the immune response after COVID-19 vaccination in [...] Read more.

Kidney transplant recipients (KTR) show an impaired humoral immune response to COVID-19 vaccination due to their immunocompromised status. Torque teno virus (TTV) is a possible marker of immune function. This marker may be helpful in predicting the immune response after COVID-19 vaccination in order to decide which vaccination strategy should be applied. We therefore investigated whether TTV load is associated with the humoral response after COVID-19 vaccination. Of the KTR who participated in two prospective vaccination studies and received two to four doses of the mRNA-1273 COVID-19 vaccine, 122 were included. TTV load was measured prior to vaccination, and S1 IgG antibody levels were measured 28 days after vaccination. TTV load was independently inversely associated with S1 IgG antibodies after COVID-19 vaccination (B: −2.19 (95% CI: −3.6–−0.8), p = 0.002). Interestingly, we found a significant interaction between TTV load and time after transplantation (p = 0.005). When patients were longer after transplantation, TTV load was less predictive for S1 IgG antibody response after vaccination compared to patients that were shorter after transplantation. Our data suggest that TTV load is a good marker in predicting COVID-19 vaccination antibody response and may be helpful in selecting a strategy shortly after transplantation. However, this marker should be handled with caution longer after transplantation. Full article

(This article belongs to the Special Issue COVID-19 Diagnostics in Clinical Applications and Pandemic Controls 2023)

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11 pages, 2058 KiB

Open AccessArticle

Colorimetric RT-LAMP Detection of Multiple SARS-CoV-2 Variants and Lineages of Concern Direct from Nasopharyngeal Swab Samples without RNA Isolation

by Santiago Werbajh, Luciana Larocca, Carolina Carrillo, Fabiana Stolowicz, Lorena Ogas, Sergio Pallotto, Solange Cassará, Liliana Mammana, Inés Zapiola, María Belén Bouzas and Adrian A. Vojnov

Viruses 2023, 15(9), 1910; https://doi.org/10.3390/v15091910 - 12 Sep 2023

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Abstract

Since, during the Coronavirus disease 19 (COVID-19) pandemic, a large part of the human population has become infected, a rapid and simple diagnostic method has been necessary to detect its causative agent, the Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2), and control its spread. [...] Read more.

Since, during the Coronavirus disease 19 (COVID-19) pandemic, a large part of the human population has become infected, a rapid and simple diagnostic method has been necessary to detect its causative agent, the Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2), and control its spread. Thus, in the present study, we developed a colorimetric reverse transcription-loop-mediated isothermal amplification (RT-LAMP) kit that allows the detection of SARS-CoV-2 from nasopharyngeal swab samples without the need for RNA extraction. The kit utilizes three sets of LAMP primers targeting two regions of ORF1ab and one region in the E gene. The results are based on the colorimetric change of hydroxynaphthol blue, which allows visual interpretation without needing an expensive instrument. The kit demonstrated sensitivity to detect between 50 and 100 copies of the viral genome per reaction. The kit was authorized by the National Administration of Drugs, Food and Technology (ANMAT) of Argentina after validation using samples previously analyzed by the gold standard RT-qPCR. The results showed a sensitivity of 90.6% and specificity of 100%, consistent with conventional RT-qPCR. In silico analysis confirmed the recognition of SARS-CoV-2 variants of concern (B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.427, and B.1.429), and lineages of the Omicron variant (B.1.1.529) with 100% homology. This rapid, simple, and sensitive RT-LAMP method paves the way for a large screening strategy to be carried out at locations lacking sophisticated instrumental and trained staff, as it particularly happens in regional hospitals and medical centers from rural areas. Full article

(This article belongs to the Special Issue COVID-19 Diagnostics in Clinical Applications and Pandemic Controls 2023)

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12 pages, 728 KiB

Open AccessArticle

Acquisition of Humoral Immune Responses in Convalescent Japanese People with SARS-CoV-2 (COVID-19) Infection in 2021

by Koshiro Monzen, Takanori Watanabe, Toshihiro Okabe, Hisakuni Sekino, Hironori Nakagami and Ryuichi Morishita

Viruses 2023, 15(9), 1842; https://doi.org/10.3390/v15091842 - 30 Aug 2023

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Abstract

We investigated humoral immune responses in 222 unvaccinated Japanese people after recovery from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in 2021. Anti-spike-protein IgG antibody levels and neutralizing antibody titers were measured in serum samples obtained within 20–180 days after diagnosis. The [...] Read more.

We investigated humoral immune responses in 222 unvaccinated Japanese people after recovery from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in 2021. Anti-spike-protein IgG antibody levels and neutralizing antibody titers were measured in serum samples obtained within 20–180 days after diagnosis. The geometric mean of antibody titers was 1555 ELU/mL (95% confidence interval (CI) = 1257–1923), and the neutralizing activity (50% inhibitory dilution) was 253 (95% CI = 204–313). The antibody titer and neutralizing activity both increased with increasing disease severity, and both values were approximately fourfold higher for hospitalized patients than for non-hospitalized patients. However, these differences were smaller in older patients. The humoral immune response, which increased with increasing disease severity, gradually decreased over time after SARS-CoV-2 infection. Most patients with mild or moderate symptoms sustained neutralizing activity for up to 180 days after the infection; the decay of the neutralizing activity in the asymptomatic patients was rather faster than in the other groups. Around 11.7% (26/222) of patients had very low neutralizing activity, and half of these were aged in their 20s. Our study’s results show the importance of measuring the neutralizing activity to confirm the immune status and to estimate the timing of vaccines. Full article

(This article belongs to the Special Issue COVID-19 Diagnostics in Clinical Applications and Pandemic Controls 2023)

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12 pages, 1909 KiB

Open AccessArticle

Lung Ultrasound in Predicting Outcomes in Patients with COVID-19 Treated with Extracorporeal Membrane Oxygenation

by Valentin Sebastian Schäfer, Florian Recker, Edgar Kretschmer, Christian Putensen, Stefan Felix Ehrentraut, Christian Staerk, Tobias Fleckenstein, Andreas Mayr, Armin Seibel, Jens-Christian Schewe and Simon Michael Petzinna

Viruses 2023, 15(9), 1796; https://doi.org/10.3390/v15091796 - 24 Aug 2023

Cited by 1 | Viewed by 1010

Abstract

Pulmonary involvement due to SARS-CoV-2 infection can lead to acute respiratory distress syndrome in patients with COVID-19. Consequently, pulmonary imaging is crucial for management of COVID-19. This study aimed to evaluate the prognostic value of lung ultrasound (LUS) with a handheld ultrasound device [...] Read more.

Pulmonary involvement due to SARS-CoV-2 infection can lead to acute respiratory distress syndrome in patients with COVID-19. Consequently, pulmonary imaging is crucial for management of COVID-19. This study aimed to evaluate the prognostic value of lung ultrasound (LUS) with a handheld ultrasound device (HHUD) in patients with COVID-19 treated with extracorporeal membrane oxygenation (ECMO). Therefore, patients underwent LUS with a HHUD every two days until they were either discharged from the intensive care unit or died. The study was conducted at the University Hospital of Bonn’s anesthesiological intensive care ward from December 2020 to August 2021. A total of 33 patients (median [IQR]: 56.0 [53–60.5] years) were included. A high LUS score was associated with a decreased P/F ratio (repeated measures correlation [rmcorr]: −0.26; 95% CI: −0.34, −0.15; p < 0.001), increased extravascular lung water, defined as fluid accumulation in the pulmonary interstitium and alveoli (rmcorr: 0.11; 95% CI: 0.01, 0.20; p = 0.030), deteriorated electrolyte status (base excess: rmcorr: 0.14; 95% CI: 0.05, 0.24; p = 0.004; pH: rmcorr: 0.12; 95% CI: 0.03, 0.21; p = 0.001), and decreased pulmonary compliance (rmcorr: −0.10; 95% CI: −0.20, −0.01; p = 0.034). The maximum LUS score was lower in survivors (median difference [md]: −0.35; 95% CI: −0.55, −0.06; p = 0.006). A cutoff value for non-survival was calculated at a LUS score of 2.63. At the time of maximum LUS score, P/F ratio (md: 1.97; 95% CI: 1.12, 2.76; p < 0.001) and pulmonary compliance (md: 18.67; 95% CI: 3.33, 37.15; p = 0.018) were higher in surviving patients. In conclusion, LUS with a HHUD enables continuous evaluation of cardiopulmonary function in COVID-19 patients receiving ECMO support therapy and provides prognostic value in determining the patients’ likelihood of survival. Full article

(This article belongs to the Special Issue COVID-19 Diagnostics in Clinical Applications and Pandemic Controls 2023)

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23 pages, 2915 KiB

Open AccessArticle

Molecular and Clinical Epidemiology of SARS-CoV-2 Infection among Vaccinated and Unvaccinated Individuals in a Large Healthcare Organization from New Jersey

by José R. Mediavilla, Tara Lozy, Annie Lee, Justine Kim, Veronica W. Kan, Elizabeth Titova, Ashish Amin, Michael C. Zody, André Corvelo, Dayna M. Oschwald, Amy Baldwin, Samantha Fennessey, Jerry M. Zuckerman, Thomas Kirn, Liang Chen, Yanan Zhao, Kar Fai Chow, Tom Maniatis, David S. Perlin and Barry N. Kreiswirth

Viruses 2023, 15(8), 1699; https://doi.org/10.3390/v15081699 - 05 Aug 2023

Cited by 3 | Viewed by 2115

Abstract

New Jersey was among the first states impacted by the COVID-19 pandemic, with one of the highest overall death rates in the nation. Nevertheless, relatively few reports have been published focusing specifically on New Jersey. Here we report on molecular, clinical, and epidemiologic [...] Read more.

New Jersey was among the first states impacted by the COVID-19 pandemic, with one of the highest overall death rates in the nation. Nevertheless, relatively few reports have been published focusing specifically on New Jersey. Here we report on molecular, clinical, and epidemiologic observations, from the largest healthcare network in the state, in a cohort of vaccinated and unvaccinated individuals with laboratory-confirmed SARS-CoV-2 infection. We conducted molecular surveillance of SARS-CoV-2-positive nasopharyngeal swabs collected in nine hospitals from December 2020 through June 2022, using both whole genome sequencing (WGS) and a real-time RT-PCR screening assay targeting spike protein mutations found in variants of concern (VOCs) within our region. De-identified clinical data were obtained retrospectively, including demographics, COVID-19 vaccination status, ICU admission, ventilator support, mortality, and medical history. Statistical analyses were performed to identify associations between SARS-CoV-2 variants, vaccination status, clinical outcomes, and medical risk factors. A total of 5007 SARS-CoV-2-positive nasopharyngeal swabs were successfully screened and/or sequenced. Variant screening identified three predominant VOCs, including Alpha (n = 714), Delta (n = 1877), and Omicron (n = 1802). Omicron isolates were further sub-typed as BA.1 (n = 899), BA.2 (n = 853), or BA.4/BA.5 (n = 50); the remaining 614 isolates were classified as “Other”. Approximately 31.5% (1577/5007) of the samples were associated with vaccine breakthrough infections, which increased in frequency following the emergence of Delta and Omicron. Severe clinical outcomes included ICU admission (336/5007 = 6.7%), ventilator support (236/5007 = 4.7%), and mortality (430/5007 = 8.6%), with increasing age being the most significant contributor to each (p < 0.001). Unvaccinated individuals accounted for 79.7% (268/336) of ICU admissions, 78.3% (185/236) of ventilator cases, and 74.4% (320/430) of deaths. Highly significant (p < 0.001) increases in mortality were observed in individuals with cardiovascular disease, hypertension, cancer, diabetes, and hyperlipidemia, but not with obesity, thyroid disease, or respiratory disease. Significant differences (p < 0.001) in clinical outcomes were also noted between SARS-CoV-2 variants, including Delta, Omicron BA.1, and Omicron BA.2. Vaccination was associated with significantly improved clinical outcomes in our study, despite an increase in breakthrough infections associated with waning immunity, greater antigenic variability, or both. Underlying comorbidities contributed significantly to mortality in both vaccinated and unvaccinated individuals, with increasing risk based on the total number of comorbidities. Real-time RT-PCR-based screening facilitated timely identification of predominant variants using a minimal number of spike protein mutations, with faster turnaround time and reduced cost compared to WGS. Continued evolution of SARS-CoV-2 variants will likely require ongoing surveillance for new VOCs, with real-time assessment of clinical impact. Full article

(This article belongs to the Special Issue COVID-19 Diagnostics in Clinical Applications and Pandemic Controls 2023)

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25 pages, 1405 KiB

Open AccessArticle

The Prospective COVID-19 Post-Immunization Serological Cohort in Munich (KoCo-Impf): Risk Factors and Determinants of Immune Response in Healthcare Workers

by Christina Reinkemeyer, Yeganeh Khazaei, Maximilian Weigert, Marlene Hannes, Ronan Le Gleut, Michael Plank, Simon Winter, Ivan Noreña, Theresa Meier, Lisa Xu, Raquel Rubio-Acero, Simon Wiegrebe, Thu Giang Le Thi, Christiane Fuchs, Katja Radon, Ivana Paunovic, Christian Janke, Andreas Wieser, Helmut Küchenhoff, Michael Hoelscher and Noemi Castelletti Show full author list Hide full author list

Viruses 2023, 15(7), 1574; https://doi.org/10.3390/v15071574 - 18 Jul 2023

Cited by 1 | Viewed by 1866

Abstract

Antibody studies analyze immune responses to SARS-CoV-2 vaccination and infection, which is crucial for selecting vaccination strategies. In the KoCo-Impf study, conducted between 16 June and 16 December 2021, 6088 participants aged 18 and above from Munich were recruited to monitor antibodies, particularly [...] Read more.

Antibody studies analyze immune responses to SARS-CoV-2 vaccination and infection, which is crucial for selecting vaccination strategies. In the KoCo-Impf study, conducted between 16 June and 16 December 2021, 6088 participants aged 18 and above from Munich were recruited to monitor antibodies, particularly in healthcare workers (HCWs) at higher risk of infection. Roche Elecsys^® Anti-SARS-CoV-2 assays on dried blood spots were used to detect prior infections (anti-Nucleocapsid antibodies) and to indicate combinations of vaccinations/infections (anti-Spike antibodies). The anti-Spike seroprevalence was 94.7%, whereas, for anti-Nucleocapsid, it was only 6.9%. HCW status and contact with SARS-CoV-2-positive individuals were identified as infection risk factors, while vaccination and current smoking were associated with reduced risk. Older age correlated with higher anti-Nucleocapsid antibody levels, while vaccination and current smoking decreased the response. Vaccination alone or combined with infection led to higher anti-Spike antibody levels. Increasing time since the second vaccination, advancing age, and current smoking reduced the anti-Spike response. The cumulative number of cases in Munich affected the anti-Spike response over time but had no impact on anti-Nucleocapsid antibody development/seropositivity. Due to the significantly higher infection risk faced by HCWs and the limited number of significant risk factors, it is suggested that all HCWs require protection regardless of individual traits. Full article

(This article belongs to the Special Issue COVID-19 Diagnostics in Clinical Applications and Pandemic Controls 2023)

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21 pages, 3234 KiB

Open AccessArticle

The Cornell COVID-19 Testing Laboratory: A Model to High-Capacity Testing Hubs for Infectious Disease Emergency Response and Preparedness

by Melissa Laverack, Rebecca L. Tallmadge, Roopa Venugopalan, Daniel Sheehan, Scott Ross, Rahim Rustamov, Casey Frederici, Kim S. Potter, François Elvinger, Lorin D. Warnick, Gary A. Koretzky, Robert Lawlis, Elizabeth Plocharczyk and Diego G. Diel

Viruses 2023, 15(7), 1555; https://doi.org/10.3390/v15071555 - 15 Jul 2023

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Abstract

The unprecedented COVID-19 pandemic posed major challenges to local, regional, and global economies and health systems, and fast clinical diagnostic workflows were urgently needed to contain the spread of SARS-CoV-2. Here, we describe the platform and workflow established at the Cornell COVID-19 Testing [...] Read more.

The unprecedented COVID-19 pandemic posed major challenges to local, regional, and global economies and health systems, and fast clinical diagnostic workflows were urgently needed to contain the spread of SARS-CoV-2. Here, we describe the platform and workflow established at the Cornell COVID-19 Testing Laboratory (CCTL) for the high-throughput testing of clinical samples from the university and the surrounding community. This workflow enabled efficient and rapid detection and the successful control of SARS-CoV-2 infection on campus and its surrounding communities. Our cost-effective and fully automated workflow enabled the testing of over 8000 pooled samples per day and provided results for over 2 million samples. The automation of time- and effort-intensive sample processing steps such as accessioning and pooling increased laboratory efficiency. Customized software applications were developed to track and store samples, deconvolute positive pools, track and report results, and for workflow integration from sample receipt to result reporting. Additionally, quality control dashboards and turnaround-time tracking applications were built to monitor assay and laboratory performance. As infectious disease outbreaks pose a constant threat to both human and animal health, the highly effective workflow implemented at CCTL could be modeled to establish regional high-capacity testing hubs for infectious disease preparedness and emergency response. Full article

(This article belongs to the Special Issue COVID-19 Diagnostics in Clinical Applications and Pandemic Controls 2023)

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11 pages, 897 KiB

Open AccessArticle

Comparative Assessment of the Kinetics of Cellular and Humoral Immune Responses to COVID-19 Vaccination in Cancer Patients

by Lina Souan, Hikmat Abdel-Razeq, Muna Al Zughbieh, Sara Al Badr and Maher A. Sughayer

Viruses 2023, 15(7), 1439; https://doi.org/10.3390/v15071439 - 26 Jun 2023

Cited by 1 | Viewed by 1144

Abstract

Objective: The kinetics of immune responses to various SARS-CoV-2 vaccines in cancer patients were investigated. Methods: In total, 57 cancer patients who received BNT162b2-RNA or BBIBP-CorV vaccines were enrolled. Cellular and humoral immunity were assessed at three-time points, before the first vaccine dose [...] Read more.

Objective: The kinetics of immune responses to various SARS-CoV-2 vaccines in cancer patients were investigated. Methods: In total, 57 cancer patients who received BNT162b2-RNA or BBIBP-CorV vaccines were enrolled. Cellular and humoral immunity were assessed at three-time points, before the first vaccine dose and 14–21 days after the first and second doses. Chemiluminescent microparticle immunoassay was used to evaluate SARS-CoV-2 anti-spike IgG response, and QuantiFERON^® SARS-CoV-2 kit assessed T-cell response. Results: Data showed that cancer patients’ CD4⁺ and CD8⁺ T cell-median IFN-γ secretion of SARS-CoV-2 antigens increased after the first and second vaccine doses (p = 0.027 and p = 0.042). BNT162b2 vaccinees had significantly higher IFN-γ levels to CD4⁺ and CD8⁺ T cell epitopes than BBIBP-CorV vaccinees (p = 0.028). There was a positive correlation between IgG antibody titer and T cell response regardless of vaccine type (p < 0.05). Conclusions: This study is one of the first to investigate cellular and humoral immune responses to SARS-CoV-2 immunization in cancer patients on active therapy after each vaccine dose. COVID-19 immunizations helped cancer patients develop an effective immune response. Understanding the cellular and humoral immune response to COVID-19 in cancer patients undergoing active treatment is necessary to improve vaccines and avoid future SARS pandemics. Full article

(This article belongs to the Special Issue COVID-19 Diagnostics in Clinical Applications and Pandemic Controls 2023)

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9 pages, 1853 KiB

Open AccessCommunication

Subjective Perception of Recovery and Measured Olfactory Function in COVID-19 Patients

by Emilia Cancellieri, Anna Kristina Hernandez, Helena Degkwitz, Elisabeth Kahre, Judith Blankenburg, Theresa S. Horst, Paula Czyborra, Paolo Boscolo-Rizzo and Thomas Hummel

Viruses 2023, 15(7), 1418; https://doi.org/10.3390/v15071418 - 23 Jun 2023

Cited by 1 | Viewed by 1129

Abstract

This cross-sectional study aimed to investigate self-rated olfactory dysfunction in relation to measured olfactory function after partial or complete subjective recovery in individuals with a history of coronavirus disease 2019 (COVID-19) infection. A total of 186 individuals (aged 5–62 years) with a history [...] Read more.

This cross-sectional study aimed to investigate self-rated olfactory dysfunction in relation to measured olfactory function after partial or complete subjective recovery in individuals with a history of coronavirus disease 2019 (COVID-19) infection. A total of 186 individuals (aged 5–62 years) with a history of COVID-19 infection were included. Visual analogue scale (VAS) ratings for olfactory function (before, during, and after infection) and age-appropriate psychophysical olfactory test scores (odor threshold and odor identification: “Sniffin’ Sticks” for adults and both “Sniffin’ Sticks” and “U-Sniff” for children) were determined. Participants were assigned to four “age groups” and three “recovery classes” (incomplete recovery, complete recovery, no smell loss). Surprisingly, there were no significant differences in odor threshold and adult identification scores between the “recovery classes”. However, children with “incomplete recovery” had lower identification scores than those with “complete recovery” (p = 0.033) and those with “no smell loss” (p = 0.022). The pediatric age groups had significantly higher VAS ratings during and after COVID-19 compared to older participants. Older individuals experienced greater magnitude of changes in their sense of smell after COVID-19 infection, but those with parosmia were 3.5 times more likely to report “incomplete recovery" of olfaction after COVID-19. The general prognosis for olfactory recovery after COVID-19 is good but appears to be particularly confounded by the presence of parosmia, leading patients to subjectively report incomplete olfactory recovery. Although it is of high significance to monitor recovery using validated psychophysical olfactory tests, subjective measures of olfaction help provide specific insight, especially for qualitative olfactory dysfunction. Full article

(This article belongs to the Special Issue COVID-19 Diagnostics in Clinical Applications and Pandemic Controls 2023)

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11 pages, 280 KiB

Open AccessArticle

Influence of SARS-CoV-2 Status and Aging on the Nasal and Fecal Immunological Profiles of Elderly Individuals Living in Nursing Homes

by Claudio Alba, Marta Mozota, Rebeca Arroyo, Natalia Gómez-Torres, Irma Castro and Juan Miguel Rodríguez

Viruses 2023, 15(6), 1404; https://doi.org/10.3390/v15061404 - 20 Jun 2023

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Abstract

In the frame of SARS-CoV-2 infection, studies regarding cytokine profiling of mucosal-related samples are scarce despite being the primary infection sites. The objective of this study was to compare the nasal and fecal inflammatory profiles of elderly individuals living in a nursing home [...] Read more.

In the frame of SARS-CoV-2 infection, studies regarding cytokine profiling of mucosal-related samples are scarce despite being the primary infection sites. The objective of this study was to compare the nasal and fecal inflammatory profiles of elderly individuals living in a nursing home highly affected by COVID-19 (ELD1) with those of elderly individuals living in a nursing home with no cases of SARS-CoV-2 infection (ELD2) and, also, with those of healthy SARS-CoV-2-negative younger adults (YHA). BAFF/TNFSF13B, IL6, IL10 and TNF-α (immunological hallmarks of SARS-CoV-2 infection) were the only immune factors whose concentrations were different in the three groups. Their highest concentrations were achieved in the ELD1 group. Nasal and fecal concentrations of a wide number of pro-inflammatory cytokines were similar in the ELD1 and ELD2 groups but higher than those found in the YHA samples. These results reinforce the hypothesis that immunosenescence and inflammaging rendered the elderly as a highly vulnerable population to a neo-infection, such as COVID-19, which was evidenced during the first pandemic waves. Full article

(This article belongs to the Special Issue COVID-19 Diagnostics in Clinical Applications and Pandemic Controls 2023)

11 pages, 326 KiB

Open AccessArticle

Impact of Dexamethasone on the Pathogen Profile of Critically Ill COVID-19 Patients

by Cathrin Kodde, Finja Timmen, Sven Hohenstein, Andreas Bollmann, Marzia Bonsignore, Ralf Kuhlen, Irit Nachtigall and Selcuk Tasci

Viruses 2023, 15(5), 1076; https://doi.org/10.3390/v15051076 - 28 Apr 2023

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Abstract

Background: Even though several therapeutic options are available, COVID-19 is still lacking a specific treatment regimen. One potential option is dexamethasone, which has been established since the early beginnings of the pandemic. The aim of this study was to determine its effects on [...] Read more.

Background: Even though several therapeutic options are available, COVID-19 is still lacking a specific treatment regimen. One potential option is dexamethasone, which has been established since the early beginnings of the pandemic. The aim of this study was to determine its effects on the microbiological findings in critically ill COVID-19 patients. Methods: A multi-center, retrospective study was conducted, in which all the adult patients who had a laboratory-confirmed (PCR) SARS-CoV-2 infection and were treated on intensive care units in one of twenty hospitals of the German Helios network between February 2020–March 2021 were included. Two cohorts were formed: patients who received dexamethasone and those who did not, followed by two subgroups according to the application of oxygen: invasive vs. non-invasive. Results: The study population consisted of 1.776 patients, 1070 of whom received dexamethasone, and 517 (48.3%) patients with dexamethasone were mechanically ventilated, compared to 350 (49.6%) without dexamethasone. Ventilated patients with dexamethasone were more likely to have any pathogen detection than those without (p < 0.026; OR = 1.41; 95% CI 1.04–1.91). A significantly higher risk for the respiratory detection of Klebsiella spp. (p = 0.016; OR = 1.68 95% CI 1.10–2.57) and for Enterobacterales (p = 0.008; OR = 1.57; 95% CI 1.12–2.19) was found for the dexamethasone cohort. Invasive ventilation was an independent risk factor for in-hospital mortality (p < 0.01; OR = 6.39; 95% CI 4.71–8.66). This risk increased significantly in patients aged 80 years or older by 3.3-fold (p < 0.01; OR = 3.3; 95% CI 2.02–5.37) when receiving dexamethasone. Conclusion: Our results show that the decision to treat COVID-19 patients with dexamethasone should be a matter of careful consideration as it involves risks and bacterial shifts. Full article

(This article belongs to the Special Issue COVID-19 Diagnostics in Clinical Applications and Pandemic Controls 2023)

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11 pages, 583 KiB

Open AccessArticle

Molecular Epidemiology of SARS-CoV-2 Omicron Sub-Lineages Isolated from Turkish Patients Infected with COVID-19

by Murat Sayan, Ayse Arikan and Erdal Sanlidag

Viruses 2023, 15(5), 1066; https://doi.org/10.3390/v15051066 - 27 Apr 2023

Cited by 1 | Viewed by 1528

Abstract

Early detection and characterization of new variants and their impacts enable improved genomic surveillance. This study aims to evaluate the subvariant distribution of Omicron strains isolated from Turkish cases to determine the rate of antiviral resistance of RdRp and 3CLpro inhibitors. The Stanford [...] Read more.

Early detection and characterization of new variants and their impacts enable improved genomic surveillance. This study aims to evaluate the subvariant distribution of Omicron strains isolated from Turkish cases to determine the rate of antiviral resistance of RdRp and 3CLpro inhibitors. The Stanford University Coronavirus Antiviral & Resistance Database online tool was used for variant analyses of the strains uploaded to GISAID as Omicron (n = 20.959) between January 2021 and February,2023. Out of 288 different Omicron subvariants, B.1, BA.1, BA.2, BA.4, BE.1, BF.1, BM.1, BN.1, BQ.1, CK.1, CL.1, and XBB.1 were the main determined subvariants, and BA.1 (34.7%), BA.2 (30.8%), and BA.5 (23.6%) were reported most frequently. RdRp and 3CLPro-related resistance mutations were determined in n = 150, 0.72% sequences, while the rates of resistance against RdRp and 3CLpro inhibitors were reported at 0.1% and 0.6%, respectively. Mutations that were previously associated with a reduced susceptibility to remdesivir, nirmatrelvir/r, and ensitrelvir were most frequently detected in BA.2 (51.3%). The mutations detected at the highest rate were A449A/D/G/V (10.5%), T21I (10%), and L50L/F/I/V (6%). Our findings suggest that continuous monitoring of variants, due to the diversity of Omicron lineages, is necessary for global risk assessment. Although drug-resistant mutations do not pose a threat, the tracking of drug mutations will be necessary due to variant heterogenicity. Full article

(This article belongs to the Special Issue COVID-19 Diagnostics in Clinical Applications and Pandemic Controls 2023)

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16 pages, 7169 KiB

Open AccessTechnical Note

Rapid Detection of SARS-CoV-2 RNA Using Reverse Transcription Recombinase Polymerase Amplification (RT-RPA) with Lateral Flow for N-Protein Gene and Variant-Specific Deletion–Insertion Mutation in S-Protein Gene

by Jose L. Malaga, Monica J. Pajuelo, Michiko Okamoto, Emmanuel Kagning Tsinda, Kanako Otani, Pablo Tsukayama, Lucero Mascaro, Diego Cuicapuza, Masamichi Katsumi, Kazuhisa Kawamura, Hidekazu Nishimura, Akie Sakagami, Yo Ueki, Suguru Omiya, Satoshi Okamoto, Asami Nakayama, Shin-ichi Fujimaki, Chuyao Yu, Sikandar Azam, Eiichi Kodama, Clyde Dapat, Hitoshi Oshitani and Mayuko Saito Show full author list Hide full author list

Viruses 2023, 15(6), 1254; https://doi.org/10.3390/v15061254 - 26 May 2023

Cited by 2 | Viewed by 2291

Abstract

Rapid molecular testing for severe acute respiratory coronavirus 2 (SARS-CoV-2) variants may contribute to the development of public health measures, particularly in resource-limited areas. Reverse transcription recombinase polymerase amplification using a lateral flow assay (RT-RPA-LF) allows rapid RNA detection without thermal cyclers. In [...] Read more.

Rapid molecular testing for severe acute respiratory coronavirus 2 (SARS-CoV-2) variants may contribute to the development of public health measures, particularly in resource-limited areas. Reverse transcription recombinase polymerase amplification using a lateral flow assay (RT-RPA-LF) allows rapid RNA detection without thermal cyclers. In this study, we developed two assays to detect SARS-CoV-2 nucleocapsid (N) gene and Omicron BA.1 spike (S) gene-specific deletion–insertion mutations (del211/ins214). Both tests had a detection limit of 10 copies/µL in vitro and the detection time was approximately 35 min from incubation to detection. The sensitivities of SARS-CoV-2 (N) RT-RPA-LF by viral load categories were 100% for clinical samples with high (>9015.7 copies/µL, cycle quantification (Cq): < 25) and moderate (385.5–9015.7 copies/µL, Cq: 25–29.9) viral load, 83.3% for low (16.5–385.5 copies/µL, Cq: 30–34.9), and 14.3% for very low (<16.5 copies/µL, Cq: 35–40). The sensitivities of the Omicron BA.1 (S) RT-RPA-LF were 94.9%, 78%, 23.8%, and 0%, respectively, and the specificity against non-BA.1 SARS-CoV-2-positive samples was 96%. The assays seemed more sensitive than rapid antigen detection in moderate viral load samples. Although implementation in resource-limited settings requires additional improvements, deletion–insertion mutations were successfully detected by the RT-RPA-LF technique. Full article

(This article belongs to the Special Issue COVID-19 Diagnostics in Clinical Applications and Pandemic Controls 2023)

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COVID-19 Diagnostics in Clinical Applications and Pandemic Controls 2023

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