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, Efrat Bucris, Oran Erster, Michal Mandelboim, Amos Adler, Saar Burstein, Noam Protter, Moran Szwarcwort-Cohen, Ella Mendelson,
Published: 5 August 2021
Abstract:
Accurate and timely diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is clinically essential, and is required also to monitor confirmed cases aiming to prevent further spread. Positive real-time PCR results at late time points following initial diagnosis may be clinically misleading as this methodology cannot account for the infection capabilities and the existence of whole genome sequences. In this study, 47 serial respiratory samples were tested by Allplex-nCoV test (Seegene), a triplex of three assays targeting the SARS-CoV-2 RdRP, E and N genes and subsequently assessed by next generation sequencing (NGS). COVID19 patients were tested at an early stage of the disease, when all these viral gene targets were positive, and at an advanced stage, when only the N gene target was positive in the Allplex-nCoV test. The corresponding NGS results showed the presence of complete viral genome copies at both early and advanced stages of the disease, although the total number of mapped sequences was lower in samples from advanced disease stages. We conclude that reduced viral transmission at this late disease stage may result from the low quantities of complete viral sequences and not solely from transcription favoring the N gene.
Published: 13 July 2021
by BMJ
Case Reports, Volume 14; https://doi.org/10.1136/bcr-2021-244507

Abstract:
We describe the case of a 63-year-old man who is reported to have the first confirmed case of COVID-19 reinfection in Campania Region, Italy. We found that the two episodes were caused by virus strains with clearly different genome sequences. The patient, a retired nurse, had a very low level of antibodies IgG directed against the spike protein 14 days after his first Pfizer/BioNTek vaccine shot.
Published: 8 July 2021
by MDPI
Viruses, Volume 13; https://doi.org/10.3390/v13071321

Abstract:
Real-time reverse transcription polymerase chain reaction (RT-qPCR) is the most sensitive and specific assay and, therefore, is the “gold standard” diagnostic method for the diagnosis of SARS-CoV-2 infection. The aim of this study was to compare and analyze the detection performance of three different commercially available SARS-CoV-2 nucleic acid detection kits: Sansure Biotech, GeneFinderTM, and TaqPathTM on 354 randomly selected samples from hospitalized COVID-19 patients. All PCR reactions were performed using the same RNA isolates and one real-time PCR machine. The final result of the three evaluated kits was not statistically different (p = 0.107), and also had a strong positive association and high Cohen’s κ coefficient. In contrast, the average Ct values that refer to the ORF1ab and N gene amplification were significantly different (p< 0.001 and p< 0.001, respectively), with the lowest obtained by the TaqPathTM for the ORF1ab and by the Sansure Biotech for the N gene. The results show a high similarity in the analytical sensitivities for SARS-CoV-2 detection, which indicates that the diagnostic accuracy of the three assays is comparable. However, the SanSure Biotech kit showed a bit better diagnostic performance. Our findings suggest that the imperative for improvement should address the determination of cut-off Ct values and rapid modification of the primer sets along with the appearance of new variants.
Bogdan C. Pană, Henrique Lopes, , Diogo Franco, Anca Rapcea, Mihai Stanca, Alina Tănase, Anca Coliţă
Frontiers in Public Health, Volume 9; https://doi.org/10.3389/fpubh.2021.672698

Abstract:
Background: The COVID-19 pandemic forced health-related organizations to rapidly launch country-wide procedures that were easy to use and inexpensive. Body temperature measurement with non-contact infrared thermometers (NCITs) is among the most common procedures, both in hospital settings and in many other entities. However, practical hospital experiences have raised great doubts about the procedure's validity. Aim: This study aimed to evaluate the validity of the body temperature measured using NCITs among oncological and transplant patients who took the polymerase chain reaction test for SARS-Cov-2 PCR+ and PCR- in a Romanian Hospital. Methods: Body temperature was measured for 5,231 inpatients using NCITs. The cutoff point for fever was equal to or above 37.3°C. Patients then completed a questionnaire about their symptoms, contact, and travel history. Findings: Fever was detected in five of 53 persons with PCR+, resulting in a sensitivity of 9.43% (95% CI, 3.13–20.66%). No fever was verified in 5,131 of 5,171 persons with PCR-, resulting in a specificity of 99.15% (95% CI, 98.86–99.38%). A defensive vision of NCIT procedure (maximum standard error only in favor) had a sensitivity of 15.09% (95% CI, 6.75–27.59%). Conclusions: The use of NCITs in a triage provides little value for detection of COVID-19. Moreover, it provides a false sense of protection against the disease while possibly discriminating individuals that could present fever due to other reasons, such as oncologic treatments, where fever is a common therapeutical consequence. The consumption of qualified human resources should be considered, especially in the context of the shortage of healthcare professionals worldwide.
Abiu Sempere-González, Jordi Llaneras-Artigues, Iago Pinal-Fernández, , Olimpia Orozco-Gálvez, Eva Domingo-Baldrich, , Beatriz Meza, , Albert Gil-Vila, et al.
Published: 16 June 2021
The publisher has not yet granted permission to display this abstract.
Byron Freire-Paspuel,
Frontiers in Cellular and Infection Microbiology, Volume 11; https://doi.org/10.3389/fcimb.2021.630552

Abstract:
Background Multiple RT-qPCR kits are available in the market for SARS-CoV-2 diagnosis, some of them with Emergency Use Authorization (EUA) by FDA or their country of origin agency, but many of them lack of proper clinical evaluation. Objective We evaluated the clinical performance of two Korean SARS-CoV-2 RT-PCR kits available in South America, AccuPower SARS-CoV-2 Multiplex RT-PCR kit (Bioneer, South Korea) and Allplex 2019-nCoV Assay (Seegene, South Korea), for RT-qPCR SARS-CoV-2 diagnosis using the CDC protocol as a gold standard. Results We found strong differences among both kits clinical performance and analytical sensitivity; while the Allplex 2019-nCoV Assay has sensitivity of 96.5% and an estimated limit of detection of 4,000 copies/ml, the AccuPower SARS-CoV-2 Multiplex RT-PCR kit has a sensitivity of 75.5% and limit of detection estimated to be bigger than 20,000 copies/ml. Conclusions AccuPower SARS-CoV-2 Multiplex RT-PCR kit and Allplex 2019-nCoV Assay are both made in South Korea but EUA by Korean CDC was only granted to the later. Our results support that Korean CDC EUA should be considered as a quality control proxy for Korean SARS-CoV-2 RT-PCR kits prior to importation by developing countries to guarantee high sensitivity diagnosis.
Science, Volume 372, pp 815-821; https://doi.org/10.1126/science.abh2644

Abstract:
Unmitigated spread in Brazil: Despite an extensive network of primary care availability, Brazil has suffered profoundly during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Using daily data from state health offices, Castro et al. analyzed the pattern of spread of COVID-19 cases and deaths in the country from February to October 2020. Clusters of deaths before cases became apparent indicated unmitigated spread. SARS-CoV-2 circulated undetected in Brazil for more than a month as it spread north from Sã o Paulo. In Manaus, transmission reached unprecedented levels after a momentary respite in mid-2020. Faria et al. tracked the evolution of a new, more aggressive lineage called P.1, which has 17 mutations, including three (K417T, E484K, and N501Y) in the spike protein. After a period of accelerated evolution, this variant emerged in Brazil during November 2020. Coupled with the emergence of P.1, disease spread was accelerated by stark local inequalities and political upheaval, which compromised a prompt federal response. Science , abh1558 and abh2644, this issue p. 821 and p. 815
, Emilia Vaccaro, Roberta Sciorio, Pietro Torre, Antonio Della Vecchia, Andrea Aglitti, Rita Caliulo, Anna Borrelli,
Published: 10 May 2021
by BMJ
Abstract:
Background The SARS-CoV-2 pandemic has infected millions of people and has caused more than 2.30 million deaths worldwide to date. Several doubts arise about the role of asymptomatic carriers in virus transmission. During the first epidemic outbreak in Italy a large screening with nasopharyngeal swab (NS) was performed in those who were considered ‘suspect’ for infection. Aims To report the results of the SARS-CoV-2 screening in a province in Southern Italy and to provide data on the COVID-19 epidemic and the burden of asymptomatic subjects. Patients and methods A retrospective cohort study was set up in all healthcare facilities of the province (12 hospitals and 13 sanitary districts: primary, secondary and tertiary centres) with the aim to analyse the results of NS performed on all subjects suspected to be infected with SARS-CoV-2, either because they presented symptoms suggestive of SARS-CoV-2 infection, they were ‘contacts’ of positive subjects, they came from areas with high prevalence or they were healthcare workers. NS were performed and managed as indicated by international guidelines. The specimens were processed for SARS-CoV-2 detection by real-time PCR. Results A total of 20 325 NS were performed from 13 March to 9 May 2020. Of these, 638 (3.14%) were positive. 470 were asymptomatic, or 75.3% of persons who were positive. They were mostly among ‘contacts’ of symptomatic cases (428 of 470, 91%) and were in domiciliary isolation. Expression of three SARS-CoV-2 genes did not differ between asymptomatic and symptomatic subjects. The strict measures with regard to social distancing led to a continuous decrease in cases during phase 1. Conclusions In a large area in Southern Italy, 3.14% (638 of 20 325) of the total subjects tested were positive for SARS-CoV-2. Most of them were asymptomatic (470 of 624, 75.3%), and of these 91% (428 of 470) were ‘close contacts’ of symptomatic subjects. The combination of social distancing together with the systematic screening of close contacts of COVID-19-positive symptomatic subjects seems to be an efficacious approach to limit the spread of the epidemic.
, M Asso-Bonnet, M Vasse, SARS-CoV-2 Foch Hospital study group
Abstract:
The ID NOW COVID-19 assay is a promising tool for the rapid identification of COVID-19 patients. However, its performances were questioned. We evaluate the ID NOW COVID-19 in comparison to a reference RT-PCR using a collection of 48 fresh nasopharyngeal swabs sampled on universal transport media (UTM). Only 2 false negatives of the ID NOW COVID-19 were identified. They display PCR cycle threshold values of 37.5 and 39.2. The positive percent agreement and the negative percent agreement were 94.9% and 100%, respectively. The Kappa value was 0.88. The ID NOW COVID-19 combines high-speed and accurate processing. Using UTM, the ID NOW COVID-19 could be repeated in the case of invalid result. Further analyses, such as screening of genetic variants or genome sequencing, could also be performed with the same sample. As for all tests, the results should be interpreted according to clinical and epidemiological context.
, Dongju Won, Chang-Ki Kim, Jinwoo Ahn, Youngkee Lee, Hyeongkyun Na, Yun-Tae Kim, Mi-Kyeong Lee, Jong Rak Choi, Hwan-Sub Lim, et al.
Published: 19 March 2021
Virus Research, Volume 297, pp 198398-198398; https://doi.org/10.1016/j.virusres.2021.198398

The publisher has not yet granted permission to display this abstract.
, Thomas A. Mellan, Charles Whittaker, Ingra M. Claro, Darlan Da S. Candido, Swapnil Mishra, Myuki A. E. Crispim, Flavia C. Sales, Iwona Hawryluk, John T. McCrone, et al.
Published: 3 March 2021
Abstract:
Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite high levels of previous infection there. Through genome sequencing of viruses sampled in Manaus between November 2020 and January 2021, we identified the emergence and circulation of a novel SARS-CoV-2 variant of concern, lineage P.1, that acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around early November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.4–2.2 times more transmissible and 25-61% more likely to evade protective immunity elicited by previous infection with non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness. One-Sentence Summary We report the evolution and emergence of a SARS-CoV-2 lineage of concern associated with rapid transmission in Manaus.
Andrea Piana, Maria Eugenia Colucci, Federica Valeriani, Adriano Marcolongo, Giovanni Sotgiu, Cesira Pasquarella, Lory Marika Margarucci, Andrea Petrucca, Gianluca Gianfranceschi, Sergio Babudieri, et al.
Published: 24 February 2021
Abstract:
Several studies evaluated the presence of SARS-CoV-2 in the environment. Saliva and nasopharyngeal droplets can land on objects and surfaces, creating fomites.
Hanan Al Suwaidi, , Rupa Varghese, Zulfa Deesi, Hamda Khansaheb, Sabeel Pokasirakath, Bino Chacko, Ibrahim Abufara, Tom Loney, Alawi Alsheikh-Ali
Published: 19 February 2021
Clinical Microbiology and Infection, Volume 27, pp 1330-1335; https://doi.org/10.1016/j.cmi.2021.02.009

The publisher has not yet granted permission to display this abstract.
, Małgorzata Sateja, Tomasz Maciejewski, Tadeusz Issat
Published: 8 February 2021
Medical Science Monitor, Volume 27; https://doi.org/10.12659/msm.929123

Abstract:
BACKGROUND Between April and September 2020, there were <10 000 reported cases of COVID-19 in the Masovia district, Poland, and <1000 new cases daily in Poland. During this period, all new hospital admissions to a maternity unit of a teaching hospital in Warsaw were screened for the COVID-19 infection. This retrospective study presents the findings from the reverse transcription-polymerase chain reaction (RT-PCR) test for COVID-19. MATERIAL AND METHODS This study included 838 women admitted for delivery between April 20 and September 20, 2020. All the admitted women were assigned to a low-risk or a high-risk group for COVID-19 and underwent RT-PCR nasopharyngeal swab tests (GeneFinder™-COVID-19-Plus-RealAmpKit. OSANG Healthcare Co., Ltd., Gyeonggi-do, Korea) for COVID-19. The testing protocol included repeated testing in case of inconclusive results or negative results in the symptomatic patients. The maternal and neonatal data from these cases were collected and analyzed. RESULTS All of the 838 women tested negative for COVID-19. Two women (0.24%) were classified as high risk for COVID-19. For 4 (0.48%) women, the results were initially inconclusive and negative when repeated. One hundred and eighty-one (21.5%) women presented with comorbidities, and 60 (7.2%) women were ≥40 years old. CONCLUSIONS The findings from this study show that between April and September 2020, there were no cases of COVID-19 infections at the maternity unit of a teaching hospital in Warsaw, Poland. However, the infection rates for COVID-19 across Europe continue to change. Testing protocols have been developed and established for all hospital admissions and it is anticipated that testing methods will become more rapid and accurate.
, Angela (Hong Tian) Dong, Aaron Jones, Jessica Kapralik, Sonya Cui, Jasmine Mah, Wryan Helmeczi, Johnny Su, Vivek Patel, Zaka Zia, et al.
Canadian Journal of Kidney Health and Disease, Volume 8; https://doi.org/10.1177/20543581211027759

Abstract:
Background: The incidence of acute kidney injury (AKI) in patients with COVID-19 and its association with mortality and disease severity is understudied in the Canadian population. Objective: To determine the incidence of AKI in a cohort of patients with COVID-19 admitted to medicine and intensive care unit (ICU) wards, its association with in-hospital mortality, and disease severity. Our aim was to stratify these outcomes by out-of-hospital AKI and in-hospital AKI. Design: Retrospective cohort study from a registry of patients with COVID-19. Setting: Three community and 3 academic hospitals. Patients: A total of 815 patients admitted to hospital with COVID-19 between March 4, 2020, and April 23, 2021. Measurements: Stage of AKI, ICU admission, mechanical ventilation, and in-hospital mortality. Methods: We classified AKI by comparing highest to lowest recorded serum creatinine in hospital and staged AKI based on the Kidney Disease: Improving Global Outcomes (KDIGO) system. We calculated the unadjusted and adjusted odds ratio for the stage of AKI and the outcomes of ICU admission, mechanical ventilation, and in-hospital mortality. Results: Of the 815 patients registered, 439 (53.9%) developed AKI, 253 (57.6%) presented with AKI, and 186 (42.4%) developed AKI in-hospital. The odds of ICU admission, mechanical ventilation, and death increased as the AKI stage worsened. Stage 3 AKI that occurred during hospitalization increased the odds of death (odds ratio [OR] = 7.87 [4.35, 14.23]). Stage 3 AKI that occurred prior to hospitalization carried an increased odds of death (OR = 5.28 [2.60, 10.73]). Limitations: Observational study with small sample size limits precision of estimates. Lack of nonhospitalized patients with COVID-19 and hospitalized patients without COVID-19 as controls limits causal inferences. Conclusions: Acute kidney injury, whether it occurs prior to or after hospitalization, is associated with a high risk of poor outcomes in patients with COVID-19. Routine assessment of kidney function in patients with COVID-19 may improve risk stratification. Trial registration: The study was not registered on a publicly accessible registry because it did not involve any health care intervention on human participants.
, , Paola Checconi, , , Maurizio Capannari, Carlo Tomino, Massimo Fini, Enrico Garaci, Anna Teresa Palamara, et al.
Published: 4 November 2020
Journal of Virological Methods, Volume 287, pp 114008-114008; https://doi.org/10.1016/j.jviromet.2020.114008

The publisher has not yet granted permission to display this abstract.
Katharina Ziegler, Philipp Steininger, Renate Ziegler, Jörg Steinmann, Klaus Korn,
Abstract:
We found that a single nucleotide polymorphism (SNP) in the nucleoprotein gene of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from a patient interfered with detection in a widely used commercial assay. Some 0.2% of the isolates in the EpiCoV database contain this SNP. Although SARS-CoV-2 was still detected by the other probe in the assay, this underlines the necessity of targeting two independent essential regions of a pathogen for reliable detection.
Pilar Díaz-Corvillón, Max Mönckeberg, Antonia Barros, Sebastián E. Illanes, Arturo Soldati, Jyh-Kae Nien, Manuel Schepeler,
Published: 29 September 2020
Abstract:
South America has become the epicenter of coronavirus pandemic. It seems that asymptomatic population may contribute importantly to the spread of the disease. Transmission from asymptomatic pregnant patients’ needs to be characterized in larger population cohorts and symptom assessment needs to be standardized. To assess the prevalence of SARS CoV-2 infection in an unselected obstetrical population and to describe their presentation and clinical evolution. A cross-sectional study was designed. Medical records of pregnant women admitted at the Obstetrics & Gynecology department of Clínica Dávila for labor & delivery, between April 27th and June 7th, 2020 were reviewed. All patients were screened with RT-PCR for SARS CoV-2 at admission. After delivery, positive cases were inquired by the researchers for clinical symptoms presented before admission and clinical evolution. All neonates born from mothers with confirmed SARS CoV-2 were isolated and tested for SARS CoV-2 infection. A total of 586 patients were tested for SARS CoV-2 during the study period. Outcomes were obtained from 583 patients which were included in the study. Thirty-seven pregnant women had a positive test for SARS CoV-2 at admission. Cumulative prevalence of confirmed SARS CoV-2 infection was 6.35% (37/583) [CI 95%: 4.63–8.65]. From confirmed cases, 43.2% (16/37) were asymptomatic. From symptomatic patients 85.7% (18/21) had mild symptoms and evolved without complications and 14.3% (3/21) presented severe symptoms requiring admission to intensive care unit. Only 5.4% (2/37) of the neonates born to mothers with a positive test at admission had a positive RT-PCR for SARS CoV-2. In our study nearly half of pregnant patients with SARS CoV-2 were asymptomatic at the time of delivery. Universal screening, in endemic areas, is necessary for adequate patient isolation, prompt neonatal testing and targeted follow-up.
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