SARS-CoV2 infection in symptomatic patients: interest of serological tests and predictors of mortality: experience of DR Congo

Abstract Background In symptomatic patients, the diagnostic approach of COVID-19 should be holistic. We aimed to evaluate the concordance between RT-PCR and serological tests (IgM/IgG), and identify the factors that best predict mortality (clinical stages or viral load). Methods The study included 242 patients referred to the University hospital of Kinshasa for suspected COVID-19, dyspnea or ARDS between June 1st, 2020 and August 02, 2020. Both antibody-SARS-CoV2 IgM/IgG and RT-PCR method were performed on the day of admission to hospital. The clinical stages were established according to the COVID-19 WHO classification. The viral load was expressed by the CtN2 (cycle threshold value of the nucleoproteins) and the CtE (envelope) genes of SARS- CoV-2 detected using GeneXpert. Kappa test and Cox regression were used as appropriate. Results The GeneXpert was positive in 74 patients (30.6%). Seventy two patients (29.8%) had positive IgM and 34 patients (14.0%) had positive IgG. The combination of RT-PCR and serological tests made it possible to treat 104 patients as having COVID-19, which represented an increase in cases of around 41% compared to the result based on GeneXpert alone. The comparison between the two tests has shown that 57 patients (23.5%) had discordant results. The Kappa coefficient was 0.451 (p < 0.001). We recorded 23 deaths (22.1%) among the COVID-19 patients vs 8 deaths (5.8%) among other patients. The severe-critical clinical stage increased the risk of mortality vs. mild-moderate stage (aHR: 26.8, p < 0.001). The values of CtE and CtN2 did not influence mortality significantly. Conclusion In symptomatic patients, serological tests are a support which makes it possible to refer patients to the dedicated COVID-19 units and treat a greater number of COVID-19 patients. WHO Clinical classification seems to predict mortality better than SARS-Cov2 viral load.

Download Full-text

SARS-CoV2 infection in Symptomatic patients: interest of Serological tests and Predictors of Mortality. Experience of DR Congo

10.21203/rs.3.rs-132291/v1 ◽

2020 ◽

Author(s):

Jean-Robert Rissassy Makulo ◽

Madone Ndona Mandina ◽

Placide Kingebeni Mbala ◽

Roger Dimosi Wumba ◽

Pierre Zalagile Akilimali ◽

...

Keyword(s):

Viral Load ◽

Cox Regression ◽

Clinical Stage ◽

Threshold Value ◽

University Hospital ◽

Rt Pcr ◽

Serological Tests ◽

Kappa Test ◽

Clinical Stages ◽

The University

Abstract Background: In symptomatic patients, the diagnostic approach of Covid-19 should be holistic. We aimed to evaluate the concordance between RT-PCR and serological tests (IgM/IgG), and identify the factors that best predict mortality (clinical stages or viral load).Methods: The study included 242 patients referred to the University hospital of Kinshasa for suspected Covid-19, dyspnea or ARDS between June 1st, 2020 and August 02, 2020. Both antibody-SARS-CoV2 IgM/IgG and RT-PCR method were performed on the day of admission to hospital. The clinical stages were established according to the Covid-19 WHO classification. The viral load was expressed by the CtN2 (cycle threshold value of the nucleoproteins) and the CtE (envelope) genes of SARS- CoV-2 detected using GeneXpert. Kappa test and Cox regression were used as appropriate.Results: The GeneXpert was positive in 74 patients (30.6%). Seventy two patients (29.8%) had positive IgM and 34 patients (14.0 %) had positive IgG. The combination of RT-PCR and serological tests made it possible to treat 104 patients as having Covid-19, which represented an increase in cases of around 41% compared to the result based on GeneXpert alone. The comparison between the two tests has shown that 57 patients (23.5 %) had discordant results. The Kappa coefficient was 0.451 (p <0.001). We recorded 23 deaths (22.1 %) among the Covid-19 patients vs 8 deaths (5.8 %) among other patients. The severe-critical clinical stage increased the risk of mortality vs. mild-moderate stage (aHR: 26.8, p < 0.001). The values of CtE and CtN2 did not influence mortality significantly. Conclusion: in symptomatic patients, serological tests are a support which makes it possible to treat a greater number of Covid-19 patients. WHO Clinical classification seems to predict mortality better than SARS-Cov2 viral load.

Download Full-text

Role of SatO2, PaO2/FiO2 Ratio and PaO2 to Predict Adverse Outcome in COVID-19: A Retrospective, Cohort Study

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph182111534 ◽

2021 ◽

Vol 18 (21) ◽

pp. 11534

Author(s):

Stefano Sartini ◽

Laura Massobrio ◽

Ombretta Cutuli ◽

Paola Campodonico ◽

Cristina Bernini ◽

...

Keyword(s):

Respiratory Failure ◽

Adverse Outcome ◽

University Hospital ◽

Rt Pcr ◽

Threatening Condition ◽

Life Threatening ◽

Group A ◽

Group B ◽

The University

COVID-19 respiratory failure is a life-threatening condition. Oxygenation targets were evaluated in a non-ICU setting. In this retrospective, observational study, we enrolled all patients admitted to the University Hospital of Genoa, Italy, between 1 February and 31 May 2020 with an RT-PCR positive for SARS-CoV-2. PaO2, PaO2/FiO2 and SatO2% were collected and analyzed at time 0 and in case of admission, patients who required or not C-PAP (groups A and B) were categorized. Each measurement was correlated to adverse outcome. A total of 483 patients were enrolled, and 369 were admitted to hospital. Of these, 153 required C-PAP and 266 had an adverse outcome. Patients with PaO2 <60 and >100 had a higher rate of adverse outcome at time 0, in groups A and B (OR 2.52, 3.45, 2.01, respectively). About the PaO2/FiO2 ratio, the OR for < 300 was 3.10 at time 0, 4.01 in group A and 4.79 in group B. Similar odds were found for < 200 in any groups and < 100 except for group B (OR 11.57). SatO2 < 94% showed OR 1.34, 3.52 and 19.12 at time 0, in groups A and B, respectively. PaO2 < 60 and >100, SatO2 < 94% and PaO2/FiO2 ratio < 300 showed at least two- to three-fold correlation to adverse outcome. This may provide simple but clear targets for clinicians facing COVID-19 respiratory failure in a non ICU-setting.

Download Full-text

Evaluation of HIV Viral Load Activity at the Bacteriology-Virology Laboratory in the University Hospital Center of Brazzaville

Open Journal of Medical Microbiology ◽

10.4236/ojmm.2019.94017 ◽

2019 ◽

Vol 09 (04) ◽

pp. 178-185

Author(s):

Esther Nina Ontsira Ngoyi ◽

Tanguy Mieret ◽

Roland Bienvenu Ossibi Ibara ◽

Axel Aloumba ◽

Géril Obili Sekangue ◽

...

Keyword(s):

Viral Load ◽

University Hospital ◽

Hiv Viral Load ◽

The University ◽

Hospital Center

Download Full-text

AN EPIDEMIOLOGY-CLINICAL CORRELATION OF VIRAL LOAD AS MEASURED BY CYCLE THRESHOLD VALUE BY RT-PCR IN COVID-1

10.36106/4843504 ◽

2021 ◽

pp. 1-2

Author(s):

Atrikumar P. Patel ◽

Palak Shah ◽

Pavan Acharya ◽

Monila N. Patel

Keyword(s):

Polymerase Chain Reaction ◽

Viral Load ◽

Severe Acute Respiratory Syndrome ◽

Threshold Value ◽

Clinical Correlation ◽

Rt Pcr ◽

Chain Reaction ◽

Oropharyngeal Swab ◽

Polymerase Chain ◽

Novel Coronavirus

The 2019 novel coronavirus [severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)] was rst documented in December 2019 in Wuhan, China, and spread across the globe resulting in [1]. signicant global morbidity and mortality Diagnosis of COVID-19 is mainly done by nasopharyngeal and oropharyngeal swab RT-PCR (Reverse transcriptase - polymerase chain reaction). Real time RT-PCR is of great interest today for detection of SARS- CoV-2 due to its benets as a specic assay.

Download Full-text

Ovarian cancer subtypes and survival in relation to three comprehensive imaging parameters

Journal of Ovarian Research ◽

10.1186/s13048-020-00625-8 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Hanna Sartor ◽

Maria Bjurberg ◽

Mihaela Asp ◽

Anna Kahn ◽

Jenny Brändstedt ◽

...

Keyword(s):

Ovarian Cancer ◽

Peritoneal Carcinomatosis ◽

Surgical Planning ◽

Cox Regression ◽

Clinical Stage ◽

Histological Type ◽

Age At Diagnosis ◽

Mammographic Breast Density ◽

Advanced Clinical Stage ◽

Clinical Stages

Abstract Background Ovarian cancer (OC) is usually detected in late clinical stages, and imaging at diagnosis is crucial. Peritoneal carcinomatosis (PC) and cardio phrenic lymph nodes (CPLN) are pathological findings of computed tomography (CT) and are relevant for surgical planning. Furthermore, mammographic breast density (BD) has shown an association with OC risk and might be prognostically relevant. However, it is not known if PC, CPLN, and BD are associated with aggressive OC subtypes and impaired OC survival. Herein, we investigated associations between three comprehensive image parameters and OC subtypes and survival. Methods The Malmö Diet and Cancer Study is a prospective study that included 17,035 women (1991–1996). Tumor information on 159 OC and information on OC specific survival (last follow-up, 2017-12-31) was registered. The CT and mammography closest to diagnosis were evaluated (Peritoneal Carcinomatosis Index PCI, CPLN, and BD). Associations between CT-PCI, CPLN, and BD vs. clinical stage [stage I vs. advanced stage (II-IV), histological type/grade (high grade serous and endometrioid vs. other subtypes], and OC-specific survival were analyzed by logistic and Cox regression. Results There was a significant association between higher CT-PCI score and advanced clinical stage (adjusted OR 1.26 (1.07–1.49)), adjusted for age at diagnosis and histological type/grade. Increasing CT-PCI was significantly associated with impaired OC specific survival (adjusted HR 1.04 (1.01–1.07)), adjusted for age at diagnosis, histological type/grade, and clinical stage. There was no significant association between PCI and histological type/grade, nor between BD or CPLN vs. the studied outcomes. Conclusions Image PCI score was significantly associated with advanced clinical stages and impaired OC survival. An objective approach (based on imaging) to scoring peritoneal carcinomatosis in ovarian cancer could help surgeons and oncologists to optimize surgical planning, treatment, and care.

Download Full-text

Protracted viral shedding and viral load are associated with ICU mortality in Covid-19 patients with acute respiratory failure

Annals of Intensive Care ◽

10.1186/s13613-020-00783-4 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

L. Bitker ◽

F. Dhelft ◽

L. Chauvelot ◽

E. Frobert ◽

L. Folliet ◽

...

Keyword(s):

Viral Load ◽

Respiratory Failure ◽

Acute Respiratory Failure ◽

Antiviral Treatment ◽

University Hospital ◽

Rt Pcr ◽

Viral Shedding ◽

Icu Discharge ◽

Independent Risk Factors ◽

Lung Ct

Abstract Background Protracted viral shedding is common in hospitalized patients with COVID-19 pneumonia, and up to 40% display signs of pulmonary fibrosis on computed tomography (CT) after hospital discharge. We hypothesized that COVID-19 patients with acute respiratory failure (ARF) who die in intensive care units (ICU) have a lower viral clearance in the respiratory tract than ICU patients discharged alive, and that protracted viral shedding in respiratory samples is associated with patterns of fibroproliferation on lung CT. We, therefore, conducted a retrospective observational study, in 2 ICU of Lyon university hospital. Results 129 patients were included in the study, of whom 44 (34%) died in ICU. 432 RT-PCR for SARS-CoV-2 were performed and 137 CT scans were analyzed. Viral load was significantly higher in patients deceased as compared to patients alive at ICU discharge (p < 0.001), after adjustment for the site of viral sampling and RT-PCR technique. The median time to SARS-CoV-2 negativation on RT-PCR was 19 days [CI95 %:15–21] in patients alive at ICU discharge and 26 days [CI95 %:17-infinity] in non-survivors at ICU discharge. Competitive risk regression identified patients who died in ICU and age as independent risk factors for longer time to SARS-CoV-2 negativation on RT-PCR, while antiviral treatment was independently associated with shorter time. None of the CT scores exploring fibroproliferation (i.e., bronchiectasis and reticulation scores) were significantly associated with time to SARS-CoV-2 negativation. Conclusions Viral load in respiratory samples is significantly lower and viral shedding significantly shorter in ICU survivors of COVID-19 associated acute respiratory failure. Protracted viral shedding is unrelated to occurrence of fibrosis on lung CT.

Download Full-text

Diagnostic Accuracy of SARS-CoV-2 Antigen Detection Test in Children: A Real-Life Study

Frontiers in Pediatrics ◽

10.3389/fped.2021.647274 ◽

2021 ◽

Vol 9 ◽

Author(s):

Camille Jung ◽

Corinne Levy ◽

Emmanuelle Varon ◽

Sandra Biscardi ◽

Christophe Batard ◽

...

Keyword(s):

Real Life ◽

University Hospital ◽

Rt Pcr ◽

Life Study ◽

Mean Delay ◽

Positive Person ◽

The Mean ◽

Real Life Study ◽

The University ◽

Positive Groups

Naso-pharyngeal RT-PCR is the gold standard for the diagnosis of COVID-19, but there is a need for rapid and reliable tests. Some validation studies have used frozen aliquots mainly from adults. The aim of this real-life study was to test the performance of a SARS-CoV-2 rapid antigen test (SC2-RAT) in children. Symptomatic patients aged 0 to 17 years were recruited in the emergency department of the University Hospital of Creteil and in primary care pediatric practices from October 10, 2020 for 7 weeks. Each enrolled child had a SARS-CoV-2 RT-PCR test and a SC2-RAT from two distinct nasopharyngeal swabs. Among the 308 patients (mean [SD] age 4.9 [5.3] years), fever was the main symptom (73.4%), with no difference between COVID-19–negative and –positive groups. The prevalence of COVID-19 was 10.7% (95% CI 7.5–14.7). On the whole cohort, the sensitivity and specificity of the SC2-RAT compared to RT-PCR was 87.9% (95% CI 71.8–96.6) and 98.5% (95% CI 96.3–99.6). Considering samples with cycle threshold >25, the sensibility was lower: 63.6% (95% CI 30.8–89.1) and the specificity 99.6% (95% CI 98.0–100.0). The mean delay to obtain an SC2-RAT result was <15 min but was 3.2 h (SD 5.5) for an RT-PCR result. Contact with a COVID-19–positive person was more frequent for COVID-19–positive than –negative patients (n = 21, 61.6%, vs. n = 64, 24.6%; p < 0.01). In real life, SC2-RAT seems reliable for symptomatic children, allowing to detect contagious children.

Download Full-text

COVID-19 Clinical Characteristics and Outcomes in Children and Adolescents Hospitalized at the University Hospital of the West Indies, Jamaica in 2020-2021

10.1101/2021.11.26.21266916 ◽

2021 ◽

Author(s):

Crista-Lee Shahine Berry ◽

Roxanne Helene Melbourne-Chambers ◽

Abigail Natalie Harrison ◽

Joshua James Anzinger ◽

Kelly-Ann Maxorinthia Gordon-Johnson ◽

...

Keyword(s):

University Hospital ◽

Kawasaki Syndrome ◽

Invasive Ventilation ◽

Rt Pcr ◽

Non Invasive ◽

Non Invasive Ventilation ◽

Organ Systems ◽

Intravenous Gammaglobulin ◽

The University ◽

Inflammatory Syndrome

Objectives: Multisystem inflammatory syndrome of children (MISC) carries a high attributable morbidity. We describe children aged <16 years hospitalised with COVID-19 and/or MISC, April 2020 to June 2021. Methods: All were tested for SARS-CoV-2, infectious disease consultations performed, modified CDC criteria for MISC applied, charts reviewed and data analyzed. Results: Among 79 consecutive children with SARS-CoV-2, 41(52%) were hospitalised; with median age 10.5 years; Afro-Caribbean ethnicity 40(98%); males 21(51%); SARS-CoV-2 RT-PCR positivity 26 (63%), IgG/IgM positivity 7(17%), community exposures 8 (20%). MISC-cases 18 (44%) vs. non-MISC 23(56%) had fever (94% vs. 30%; p<0.01), fatigue/lethargy (41% vs. 4%; p=0.004), rhinorrhoea (28% vs. 4%; p=0.035), elevated neutrophils (100% vs. 87%; p=0.024) and ≥4 abnormal inflammatory biomarkers 13 (72%). MISC-cases had >2 organ/systems (100% vs. 35%; p<0.01), including gastrointestinal (72% vs. 17%; p<0.01), haematological/coagulopathic (67% vs. 4%; p<0.01); dermatologic (56% vs. 0%; p<0.01), cardiac (17% vs. 0%; p=0.042) with Kawasaki Syndrome (44% vs. 0%; p<0.01) and pleural effusions (17% vs. 0%; p=0.042). MISC-cases were treated with intravenous immune gammaglobulin (14, 78%), aspirin (12, 68%), steroids (9, 50%) and intensive care with non-invasive ventilation (2, 11%). One (6%) with pre-morbid illness died, the remainder recovered. Conclusion: MISC was treated successfully with intravenous gammaglobulin, steroids and/or aspirin in 94% before cardiopulmonary decompensation, or need for inotropes, vasopressors, or invasive ventilation.

Download Full-text

Comparing The Viral Load of Severe Acute Respiratory Syndrome Coronavirus 2 in Different Human Specimens

Kurdistan Journal of Applied Research ◽

10.24017/covid.15 ◽

2020 ◽

pp. 131-145

Author(s):

Ali Hattem Hussain

Keyword(s):

Viral Load ◽

Rectal Swab ◽

Throat Swab ◽

Meta Analysis ◽

Threshold Value ◽

Load Cycle ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Load Detection ◽

Respiratory Specimens

This meta-analysis study analyzed the data of 47 recent studies with data related SARS-COV-2 viral load detection in different human specimens. 1099 patients were tested for SARS-COV-2 viral load using up to 19 different respiratory and non-respiratory specimens using RT-PCR by targeting different types of viral genes of which ORF1ab is the most commonly used target gene. 9909 specimens were taken from the patients. The mean of viral load cycle threshold value is 17.8 (±11.7), with a median of 15.95 with minimum value of 0.2 and a maximum value of 36.5. Nasopharyngeal swab has the highest positivity rate (90.5%) for viral load detection followed by Bronchoalveolar lavage, nasal swab, nasopharyngeal aspirate, throat swab and sputum. For the non-respiratory specimen, stool and rectal swab are most appropriate specimens followed by blood. The urine is not appropriate specimen for viral load detection due to very low sensitivity. The sputum was positive up to 23 days in a daily manner since start of symptoms except for the days 19, 21, and 23 that were negative for the virus. Three specimens, the nasopharyngeal swab, throat swab, and rectal swab, showed positive RT-PCR results before the appearance of COVID-19 clinical features. Possible positive results can be present up to 43 days in throat swab, stool, and rectal swab. After negative conversion of respiratory specimens, the viral shedding can continue more than one month from stool and rectal swab. The 3rd day since onset of symptoms is the most day of testing (223/2935). The highest positivity of SARS-COV-2 viral load was recorded in day 16 since the onset of symptoms.

Download Full-text

First report of dasheen mosaic virus infecting taro (Colocasia esculenta) in Louisiana

Plant Disease ◽

10.1094/pdis-04-21-0854-pdn ◽

2021 ◽

Author(s):

Cesar Escalante ◽

David Galo ◽

Rodrigo Diaz ◽

Rodrigo Valverde

Keyword(s):

United States ◽

Mosaic Virus ◽

Consensus Sequence ◽

The United States ◽

Colocasia Esculenta ◽

Rt Pcr ◽

Serological Tests ◽

First Report ◽

Pcr Products ◽

The University

Taro [Colocasia esculenta (L.) Schott], also called dasheen or malanga is an important staple crop in many tropical and subtropical countries (Chaïr et al. 2016). In October 2020, taro plants showing foliar symptoms consisting of mosaic, feathery mottle, and vein clearing patterns were observed in the Hilltop Arboretum, the Bluebonnet Swamp Nature Center, the Louisiana State University Agricultural Center Botanic Gardens, and the University Lake, in Baton Rouge, Louisiana. Unidentified aphids were also observed infesting the plants showing the described symptoms. From each location, two foliar samples from symptomatic and two from asymptomatic plants were collected and tested by ELISA using antiserum for general potyvirus group (Agdia, Elkhart, IN). Seven of eight symptomatic samples tested positive while the asymptomatic samples were negative. The seven positive samples were used to perform an additional ELISA test using antiserum specific for dasheen mosaic virus (DsMV) (Agdia). All seven samples tested positive for DsMV. To confirm the identity of the virus, total RNA was extracted from the seven samples using the PureLink® Plant RNA Reagent Kit (Invitrogen, Carlsbad, CA). After DNA digestion with PerfeCta® DNase I (Qiagen, Beverly, MA), the RNA was used to perform reverse transcription polymerase chain reaction (RT-PCR) with primer set DMV 5708-5731-F/DMV 6131-6154-R which is specific for DsMV (Wang et al. 2017). RT-PCR was performed using the AccessQuickTM RT-PCR System (Promega, Madison, WI) following the reaction conditions described by Wang et al. PCR products of the expected size (~447 bp) were obtained with all seven samples and were Sanger-sequenced. A consensus sequence (MW284936) was obtained with the two sequences from samples collected at the University Lake and aligned with other sequences available in the GenBank using BLASTn. Our isolate of DsMV showed 90.6% nt identity to an isolate of DsMV from Ethiopia (MG602229). Mechanical inoculations to healthy taro plants were conducted using leaf tissue of symptomatic plants as source of inoculum. Inoculated plants exhibited mosaic symptoms three weeks after inoculation and were ELISA-positive for DsMV. Symptomatology, serological tests, RT-PCR testing, and DNA sequencing of RT-PCR products support that the symptomatic taro plants were infected with DsMV. Taro is a crop in Hawaii, but in the contiguous United States, it is mostly grown as an ornamental and is considered an invasive species. Its distribution is restricted to the southern continental states and Hawaii (Cozad et al. 2018). CABI, EPPO (1998) lists the presence of DsMV in several states of the United States, including Louisiana; however, there is no record in the literature of the identification of this virus in Louisiana. The potential impact of DsMV in taro and related ornamental species in southern United States is unknown. To the best of our knowledge, this is the first report documenting DsMV infecting taro in Louisiana.

Download Full-text