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Inson JGM, Malla B, Amalin DM, Carvajal TM, Enriquez MLD, Hirai S, Raya S, Rahmani AF, Angga MS, Sthapit N, Shrestha S, Ruti AA, Takeda T, Kitajima M, Alam ZF, Haramoto E. Detection of SARS-CoV-2 and Omicron variant RNA in wastewater samples from Manila, Philippines. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170921. [PMID: 38350577 DOI: 10.1016/j.scitotenv.2024.170921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/26/2024] [Accepted: 02/10/2024] [Indexed: 02/15/2024]
Abstract
Manila, a highly urbanized city, is listed as one of the top cities with the highest recorded number of coronavirus disease 2019 (COVID-19) cases in the Philippines. This study aimed to detect and quantify the RNA of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the Omicron variant in 51 wastewater samples collected from three locations in Manila, namely Estero de Santa Clara, Estero de Pandacan, which are open drainages, and a sewage treatment plant (STP) at De La Salle University-Manila, between July 2022 and February 2023. Using one-step reverse transcription-quantitative polymerase chain reaction, SARS-CoV-2 and Omicron variant RNA were detected in 78 % (40/51; 4.9 ± 0.5 log10 copies/L) and 60 % (24/40; 4.4 ± 0.3 log10 copies/L) of wastewater samples collected from all sampling sites, respectively. SARS-CoV-2 RNA was detected frequently at Estero de Santa Clara (88 %, 15/17); its highest concentration was at the STP (6.3 log10 copies/L). The Omicron variant RNA was present in the samples collected (4.4 ± 0.3 log10 copies/L) from all sampling sites, with the highest concentration at the STP (4.9 log10 copies/L). Regardless of normalization, using concentrations of pepper mild mottle virus RNA, SARS-CoV-2 RNA concentrations exhibited the highest positive correlation with COVID-19 reported cases in Manila 5 days after the clinical report. These findings revealed that wastewater-based epidemiology may aid in identifying and monitoring of the presence of pathogens in open drainages and STPs in the Philippines. This paper provides the first documentation on SARS-CoV-2 and the Omicron variant in wastewater from Manila.
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Affiliation(s)
- Jessamine Gail M Inson
- Department of Biology, De La Salle University, Manila 1004, Philippines; Environmental Biomonitoring Research Unit, Center for Natural Sciences and Environmental Research, De La Salle University, Manila 1004, Philippines.
| | - Bikash Malla
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Divina M Amalin
- Department of Biology, De La Salle University, Manila 1004, Philippines; Biological Control Research Unit, Center for Natural Sciences and Environmental Research, De La Salle University, Manila 1004, Philippines.
| | - Thaddeus M Carvajal
- Department of Biology, De La Salle University, Manila 1004, Philippines; Biological Control Research Unit, Center for Natural Sciences and Environmental Research, De La Salle University, Manila 1004, Philippines.
| | | | - Soichiro Hirai
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
| | - Sunayana Raya
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Aulia Fajar Rahmani
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Made Sandhyana Angga
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Niva Sthapit
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Sadhana Shrestha
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Annisa Andarini Ruti
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Tomoko Takeda
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Masaaki Kitajima
- Division of Environmental Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan.
| | - Zeba F Alam
- Department of Biology, De La Salle University, Manila 1004, Philippines; Environmental Biomonitoring Research Unit, Center for Natural Sciences and Environmental Research, De La Salle University, Manila 1004, Philippines.
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
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Omole A, Affonso de Oliveira JF, Sutorus L, Steinmetz NF. Pharmacology of a Plant Virus Immunotherapy Candidate for Peritoneal Metastatic Ovarian Cancer. ACS Pharmacol Transl Sci 2024; 7:445-455. [PMID: 38357279 PMCID: PMC10863429 DOI: 10.1021/acsptsci.3c00285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 02/16/2024]
Abstract
Due to the increasing incidence of cancer, there is a need to develop new platforms that can combat this disease. Cancer immunotherapy is a platform that takes advantage of the immune system to recognize and eradicate tumors and metastases. Our lab has identified a plant virus nanoparticle, cowpea mosaic virus (CPMV) as a promising approach for cancer immunotherapy. When administered intratumorally, CPMV relieves the immune system of tumor-induced immunosuppression and reprograms the tumor microenvironment into an activated state to launch systemic antitumor immunity. The efficacy of CPMV has been tested in many tumor models and in canine cancer patients with promising results: tumor shrinkage, systemic efficacy (abscopal effect), and immune memory to prevent recurrence. To translate this drug candidate from the bench to the clinic, studies that investigate the safety, pharmacology, and toxicity are needed. In this work, we describe the efficacy of CPMV against a metastatic ovarian tumor model and investigate the biodistribution of CPMV after single or repeated intraperitoneal administration in tumor-bearing and healthy mice. CPMV shows good retention in the tumor nodules and broad bioavailability with no apparent organ toxicity based on histopathology. Data indicate persistence of the viral RNA, which remains detectable 2 weeks post final administration, a phenomenon also observed with some mammalian viral infections. Lastly, while protein was not detected in stool or urine, RNA was shed through excretion from mice; however, there was no evidence that RNA was infectious to plants. Taken together, the data indicate that systemic administration results in broad bioavailability with no apparent toxicity. While RNA is shed from the subjects, data suggest agronomical safety. This data is consistent with prior reports and provides support for translational efforts.
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Affiliation(s)
- Anthony
O. Omole
- Department
of Nanoengineering, University of California, San Diego, La Jolla, California 92093-0021, United
States
- Shu
and K.C. Chien and Peter Farrell Collaboratory, University of California, San Diego, La Jolla, California 92093, United States
- Center
for Nano-ImmunoEngineering, University of
California, San Diego, La Jolla, California 92093-0403, United States
- Moores
Cancer Center, University of California,
San Diego, La Jolla, California 92037, United States
| | - Jessica Fernanda Affonso de Oliveira
- Department
of Nanoengineering, University of California, San Diego, La Jolla, California 92093-0021, United
States
- Shu
and K.C. Chien and Peter Farrell Collaboratory, University of California, San Diego, La Jolla, California 92093, United States
- Center
for Nano-ImmunoEngineering, University of
California, San Diego, La Jolla, California 92093-0403, United States
- Moores
Cancer Center, University of California,
San Diego, La Jolla, California 92037, United States
| | - Lucas Sutorus
- Department
of Nanoengineering, University of California, San Diego, La Jolla, California 92093-0021, United
States
- Shu
and K.C. Chien and Peter Farrell Collaboratory, University of California, San Diego, La Jolla, California 92093, United States
- Center
for Nano-ImmunoEngineering, University of
California, San Diego, La Jolla, California 92093-0403, United States
- Moores
Cancer Center, University of California,
San Diego, La Jolla, California 92037, United States
| | - Nicole F. Steinmetz
- Department
of Nanoengineering, University of California, San Diego, La Jolla, California 92093-0021, United
States
- Shu
and K.C. Chien and Peter Farrell Collaboratory, University of California, San Diego, La Jolla, California 92093, United States
- Center
for Nano-ImmunoEngineering, University of
California, San Diego, La Jolla, California 92093-0403, United States
- Moores
Cancer Center, University of California,
San Diego, La Jolla, California 92037, United States
- Department
of Bioengineering, University of California,
San Diego, La Jolla, California 92093-0412, United States
- Department
of Radiology, University of California,
San Diego, La Jolla, California 92122, United States
- Institute
for Materials Discovery and Design, University
of California, San Diego, La Jolla, California 92093, United States
- Center
for Engineering in Cancer, Institute of Engineering Medicine, University of California, San Diego, La Jolla, California 92093, United States
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Yao Y, Zhu Y, Nogueira R, Klawonn F, Wallner M. Optimal Selection of Sampling Points within Sewer Networks for Wastewater-Based Epidemiology Applications. Methods Protoc 2024; 7:6. [PMID: 38251199 PMCID: PMC10801534 DOI: 10.3390/mps7010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/19/2023] [Accepted: 01/01/2024] [Indexed: 01/23/2024] Open
Abstract
Wastewater-based epidemiology (WBE) has great potential to monitor community public health, especially during pandemics. However, it faces substantial hurdles in pathogen surveillance through WBE, encompassing data representativeness, spatiotemporal variability, population estimates, pathogen decay, and environmental factors. This paper aims to enhance the reliability of WBE data, especially for early outbreak detection and improved sampling strategies within sewer networks. The tool implemented in this paper combines a monitoring model and an optimization model to facilitate the optimal selection of sampling points within sewer networks. The monitoring model utilizes parameters such as feces density and average water consumption to define the detectability of the virus that needs to be monitored. This allows for standardization and simplicity in the process of moving from the analysis of wastewater samples to the identification of infection in the source area. The entropy-based model can select optimal sampling points in a sewer network to obtain the most specific information at a minimum cost. The practicality of our tool is validated using data from Hildesheim, Germany, employing SARS-CoV-2 as a pilot pathogen. It is important to note that the tool's versatility empowers its extension to monitor other pathogens in the future.
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Affiliation(s)
- Yao Yao
- Institute for Information Engineering, Ostfalia University of Applied Sciences, Salzdahlumer Str. 46/48, 38302 Wolfenbüttel, Germany;
| | - Yibo Zhu
- Faculty of Civil and Environmental Engineering, Ostfalia University of Applied Sciences, Herbert-Meyer-Str. 7, 29556 Suderburg, Germany; (Y.Z.); (M.W.)
| | - Regina Nogueira
- Institute of Sanitary Engineering and Waste Management, Leibniz University Hannover, Welfengarten 1, 30167 Hannover, Germany;
| | - Frank Klawonn
- Biostatistics Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Markus Wallner
- Faculty of Civil and Environmental Engineering, Ostfalia University of Applied Sciences, Herbert-Meyer-Str. 7, 29556 Suderburg, Germany; (Y.Z.); (M.W.)
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Piewbang C, Poonsin P, Lohavicharn P, Punyathi P, Kesdangsakonwut S, Kasantikul T, Techangamsuwan S. Natural SARS-CoV-2 infection in dogs: Determination of viral loads, distributions, localizations, and pathology. Acta Trop 2024; 249:107070. [PMID: 37956819 DOI: 10.1016/j.actatropica.2023.107070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/13/2023] [Accepted: 11/10/2023] [Indexed: 11/15/2023]
Abstract
Instances of reverse zoonosis involving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been documented in both controlled experiments and spontaneous cases. Although dogs are susceptible to infection, clinical significance is limited to mild or asymptomatic. Here, we investigate the fatal cases of natural SARS-CoV-2 infection in dogs in Thailand. Pathological findings of SARS-CoV-2-infected dogs reveal severe diffuse alveolar damage, pulmonary hyalinization and fibrosis, and syncytial formation, together with minor lesions in brain and kidney. Employing reverse transcription-digital PCR, substantial viral loads of SARS-CoV-2 were detected in lung, kidney, brain, trachea, tonsil, tracheobronchial lymph node, liver, and intestine, respectively. Localization of SARS-CoV-2 within various tissues was examined through immunohistochemistry (IHC), where the co-localization of the viral spike protein and the angiotensin-converting enzyme 2 (ACE2) receptor was illustrated using double IHC. SARS-CoV-2 localization was markedly identified in the epithelial cells of the lung, trachea, intestine and kidneys, and moderately presented in the salivary gland and gall bladder, where the co-localization with the ACE2 was also evident. Neurons in the brainstem where exhibited lymphocytic perivascular cuffing were also found to be positive for SARS-CoV-2 in IHC testing, despite lacking ACE2 receptor expression. In addition, SARS-CoV-2 replication within the lungs of infected dogs was confirmed by transmission electron microscopy, visualizing free viral particles within the cytosol or the endoplasmic reticulum of syncytial cells within the lung. This study considerably expanded on the knowledge of the pathology associated with natural SARS-CoV-2 infection in dogs, a scenario that is relatively infrequent but occasionally leads to fatal outcome. Furthermore, these findings suggest the potential utility of dogs as a model for studying SARS-CoV-2 infection in humans, warranting further investigation.
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Affiliation(s)
- Chutchai Piewbang
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Panida Poonsin
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pattiya Lohavicharn
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Panitnan Punyathi
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sawang Kesdangsakonwut
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Tanit Kasantikul
- Veterinary Diagnostic Laboratory, Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
| | - Somporn Techangamsuwan
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand.
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Rago V, Bossio S, Lofaro D, Perri A, Di Agostino S. New Insights into the Link between SARS-CoV-2 Infection and Renal Cancer. Life (Basel) 2023; 14:52. [PMID: 38255667 PMCID: PMC10817602 DOI: 10.3390/life14010052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/17/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Cancer has been described as a risk factor for greater susceptibility to SARS-CoV-2 infection and severe COVID-19, mainly for patients with metastatic disease. Conversely, to that reported for most solid and hematological malignancies, the few available clinical studies reported that the infection did not increase the risk of death in renal cancer patients. The expression on proximal tubular renal cells of the key players in cellular viral uptake, ACE2, TMPRSS2, and NRP1, seems to be the mechanism for the direct kidney injury seen in patients with COVID-19. Interestingly, data from The Cancer Genome Atlas and experimental analyses on various renal cancer cell lines demonstrated that the above-reported receptors/cofactors are maintained by renal cancer cells. However, whether SARS-CoV-2 infection directly kills renal cancer cells or generates enhanced immunogenicity is a question worth investigating. In addition, some researchers have further addressed the topic by studying the expression and prognostic significance of gene signatures related to SARS-CoV-2 infection in renal cancer patients. The emerging data highlights the importance of better understanding the existence of a link between renal cancer and COVID-19 since it could lead to the identification of new prognostic factors and the development of new therapeutic targets in the management of renal cancer patients.
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Affiliation(s)
- Vittoria Rago
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy;
| | - Sabrina Bossio
- Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, 88100 Catanzaro, Italy;
| | - Danilo Lofaro
- de-Health Lab, Department of Mechanical, Energy, Management Engineering, University of Calabria, 87036 Rende, Italy;
| | - Anna Perri
- Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, 88100 Catanzaro, Italy;
| | - Silvia Di Agostino
- Department of Health Sciences, Magna Græcia University of Catanzaro, 88100 Catanzaro, Italy;
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Choi BJ, Hoselton S, Njau GN, Idamawatta I, Carson P, McEvoy J. Estimating the prevalence of COVID-19 cases through the analysis of SARS-CoV-2 RNA copies derived from wastewater samples from North Dakota. GLOBAL EPIDEMIOLOGY 2023; 6:100124. [PMID: 37881481 PMCID: PMC10594563 DOI: 10.1016/j.gloepi.2023.100124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/27/2023] Open
Abstract
The SARS-CoV-2 virus was first detected in December 2019, which prompted many researchers to investigate how the virus spreads. SARS-CoV-2 is mainly transmitted through respiratory droplets. Symptoms of the SARS-CoV-2 virus appear after an incubation period. Moreover, the asymptomatic infected individuals unknowingly spread the virus. Detecting infected people requires daily tests and contact tracing, which are expensive. The early detection of infectious diseases, including COVID-19, can be achieved with wastewater-based epidemiology, which is timely and cost-effective. In this study, we collected wastewater samples from wastewater treatment plants in several cities in North Dakota and then extracted viral RNA copies. We used log-RNA copies in the model to predict the number of infected cases using Quantile Regression (QR) and K-Nearest Neighbor (KNN) Regression. The model's performance was evaluated by comparing the Mean Absolute Percentage Error (MAPE). The QR model performs well in cities where the population is >10000 . In addition, the model predictions were compared with the basic Susceptible-Infected-Recovered (SIR) model which is the golden standard model for infectious diseases.
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Affiliation(s)
- Bong-Jin Choi
- Department of Statistics and Department of Public Health, North Dakota State University, United States of America
| | - Scott Hoselton
- Department of Microbiological Sciences, North Dakota State University, United States of America
| | - Grace N. Njau
- North Dakota Department of Health, United States of America
| | - I.G.C.G. Idamawatta
- Department of Statistics, North Dakota State University, United States of America
| | - Paul Carson
- Center for Immunization Research and Education (CIRE), Department of Public Health, North Dakota State University, United States of America
| | - John McEvoy
- Department of Microbiological Sciences, North Dakota State University, United States of America
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Termansen MB, Frische S. Fecal-oral transmission of SARS-CoV-2: A systematic review of evidence from epidemiological and experimental studies. Am J Infect Control 2023; 51:1430-1437. [PMID: 37121473 PMCID: PMC10141930 DOI: 10.1016/j.ajic.2023.04.170] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/21/2023] [Accepted: 04/21/2023] [Indexed: 05/02/2023]
Abstract
BACKGROUND SARS-CoV-2 ribonucleic acid (RNA) has been detected in feces, but RNA is not infectious. This systematic review aims to answer if fecal SARS-CoV-2 is experimentally infectious and if evidence of human fecal-oral SARS-CoV-2 transmission exists. METHODS On September 19, 2022, we searched PubMed, Embase, Web of Science, medRxiv, and bioRxiv. Biomedical studies inoculating SARS-CoV-2 from feces, rectal, or anal swabs in cells, tissue, organoids, or animals were included. Epidemiological studies of groups differing in exposure to fecal SARS-CoV-2 were included. Risk of bias was assessed using standardized tools. Results were summarized by vote counting, tabulation, and a harvest plot. PROSPERO registration no. CRD42020221719. RESULTS A total of 4,874 studies were screened; 26 studies were included; and 13 out of 23 biomedical studies (56.5%) succeeded in infection. Two (66.7%) epidemiological studies found limited evidence suggesting fecal-oral transmission. All studies had concerns about the risk of bias. CONCLUSIONS It is possible to experimentally infect cell cultures, organoids, and animals with fecal SARS-CoV-2. No strong epidemiologic evidence was found to support human fecal-oral transmission. We advise future research to study fecal infectivity at different time points during infection, apply appropriate controls, use in vivo models, and study fecal exposure as a risk factor of transmission in human populations.
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Kononova Y, Adamenko L, Kazachkova E, Solomatina M, Romanenko S, Proskuryakova A, Utkin Y, Gulyaeva M, Spirina A, Kazachinskaia E, Palyanova N, Mishchenko O, Chepurnov A, Shestopalov A. Features of SARS-CoV-2 Replication in Various Types of Reptilian and Fish Cell Cultures. Viruses 2023; 15:2350. [PMID: 38140591 PMCID: PMC10748073 DOI: 10.3390/v15122350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/24/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND SARS-CoV-2 can enter the environment from the feces of COVID-19 patients and virus carriers through untreated sewage. The virus has shown the ability to adapt to a wide range of hosts, so the question of the possible involvement of aquafauna and animals of coastal ecosystems in maintaining its circulation remains open. METHODS the aim of this work was to study the tropism of SARS-CoV-2 for cells of freshwater fish and reptiles, including those associated with aquatic and coastal ecosystems, and the effect of ambient temperature on this process. In a continuous cell culture FHM (fathead minnow) and diploid fibroblasts CGIB (silver carp), SARS-CoV-2 replication was not maintained at either 25 °C or 29 °C. At 29 °C, the continuous cell culture TH-1 (eastern box turtle) showed high susceptibility to SARS-CoV-2, comparable to Vero E6 (development of virus-induced cytopathic effect (CPE) and an infectious titer of 7.5 ± 0.17 log10 TCID50/mL on day 3 after infection), and primary fibroblasts CNI (Nile crocodile embryo) showed moderate susceptibility (no CPE, infectious titer 4.52 ± 0.14 log10 TCID50/mL on day 5 after infection). At 25 °C, SARS-CoV-2 infection did not develop in TH-1 and CNI. CONCLUSIONS our results show the ability of SARS-CoV-2 to effectively replicate without adaptation in the cells of certain reptile species when the ambient temperature rises.
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Affiliation(s)
- Yulia Kononova
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Lyubov Adamenko
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Evgeniya Kazachkova
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Mariya Solomatina
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Svetlana Romanenko
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, Russia; (S.R.); (A.P.); (Y.U.)
| | - Anastasia Proskuryakova
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, Russia; (S.R.); (A.P.); (Y.U.)
| | - Yaroslav Utkin
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, Russia; (S.R.); (A.P.); (Y.U.)
| | - Marina Gulyaeva
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
- The Department of Natural Science, Novosibirsk State University, 2, Pirogova St., Novosibirsk 630090, Russia
| | - Anastasia Spirina
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Elena Kazachinskaia
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Natalia Palyanova
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Oksana Mishchenko
- 48 Central Research Institute of the Ministry of Defense of the Russian Federation, Moscow 141306, Russia;
| | - Alexander Chepurnov
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Alexander Shestopalov
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
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Pepe-Mooney BJ, Smith CJ, Sherman MS, North TE, Padera RF, Goessling W. SARS-CoV-2 viral liver aggregates and scarce parenchymal infection implicate systemic disease as a driver of abnormal liver function. Hepatol Commun 2023; 7:e0290. [PMID: 37889528 PMCID: PMC10615432 DOI: 10.1097/hc9.0000000000000290] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/22/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Liver function tests (LFTs) are elevated in >50% of hospitalized individuals infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), with increased enzyme levels correlating with a more severe COVID-19 course. Despite these observations, evaluations of viral presence within liver parenchyma and viral impact on liver function remain controversial. METHODS AND RESULTS Our work is a comprehensive immunopathological evaluation of liver tissue from 33 patients with severe, and ultimately fatal, cases of SARS-CoV-2 infection. Coupled with clinical data, we reveal the absence of SARS-CoV-2 infection in cholangiocytes and hepatocytes despite dramatic systemic viral presence. Critically, we identify significant focal viral sinusoidal aggregates in 2/33 patients and single viral RNA molecules circulating in the hepatic sinusoids of 15/33 patients. Utilizing co-immunofluorescence, focal viral liver aggregates in patients with COVID-19 were colocalized to platelet and fibrin clots, indicating the presence of virus-containing sinusoidal microthrombi. Furthermore, this patient cohort, from the initial months of the COVID-19 pandemic, demonstrates a general downtrend of LFTs over the course of the study timeline and serves as a remarkable historical time point of unattenuated viral replication within patients. CONCLUSIONS Together, our findings indicate that elevated LFTs found in our patient cohort are not due to direct viral parenchymal infection with SARS-CoV-2 but rather likely a consequence of systemic complications of COVID-19. This work aids in the clinical treatment considerations of patients with SARS-CoV-2 as therapies for these patients may be considered in terms of their direct drug hepatotoxity rather than worsening hepatic function due to direct infection.
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Affiliation(s)
- Brian J. Pepe-Mooney
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Harvard–MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Colton J. Smith
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Marc S. Sherman
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Trista E. North
- Stem Cell Program, Division of Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts, USA
- Developmental and Regenerative Biology Program, Harvard Medical School, Boston, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
| | - Robert F. Padera
- Harvard–MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston Massachusetts, USA
| | - Wolfram Goessling
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Harvard–MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Developmental and Regenerative Biology Program, Harvard Medical School, Boston, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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10
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Khemiri H, Gdoura M, Ben Halima S, Krichen H, Cammà C, Lorusso A, Ancora M, Di Pasquale A, Cherni A, Touzi H, Sadraoui A, Meddeb Z, Hogga N, Ammi R, Triki H, Haddad-Boubaker S. SARS-CoV-2 excretion kinetics in nasopharyngeal and stool samples from the pediatric population. Front Med (Lausanne) 2023; 10:1226207. [PMID: 38020093 PMCID: PMC10643538 DOI: 10.3389/fmed.2023.1226207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 10/02/2023] [Indexed: 12/01/2023] Open
Abstract
Background The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for serious respiratory infections in humans. Even in the absence of respiratory symptoms, gastrointestinal (GI) signs were commonly reported in adults and children. Thus, oral-fecal transmission was suspected as a possible route of infection. The objective of this study was to describe RNA shedding in nasopharyngeal and stool samples obtained from asymptomatic and symptomatic children and to investigate virus viability. Methods This study included 179 stool and 191 nasopharyngeal samples obtained from 71 children, which included symptomatic (n = 64) and asymptomatic (n = 7) ones. They were collected every 7 days from the onset of the infection until negativation. Viral RNA was detected by real-time RT-PCR, targeting the N and ORF1 genes. Whole-genome sequencing was performed for positive cases. Viral isolation was assessed on Vero cells, followed by molecular detection confirmation. Results All cases included in this study (n = 71) were positive in their nasopharyngeal samples. SARS-CoV-2 RNA was detected in 36 stool samples obtained from 15 out of 71 (21.1%) children; 13 were symptomatic and two were asymptomatic. Excretion periods varied from 7 to 21 days and 7 to 14 days in nasopharyngeal and fecal samples, respectively. Four variants were detected: Alpha (n = 3), B.1.160 (n = 3), Delta (n = 7), and Omicron (n = 1). Inoculation of stool samples on cell culture showed no specific cytopathic effect. All cell culture supernatants were negative for RT-qPCR. Conclusion Our study demonstrated nasopharyngeal and fecal shedding of SARS-CoV-2 RNA by children up to 21 and 14 days, respectively. Fecal shedding was recorded in symptomatic and asymptomatic children. Nevertheless, SARS-CoV-2 was not isolated from positive stool samples.
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Affiliation(s)
- Haifa Khemiri
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Mariem Gdoura
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Samar Ben Halima
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Henda Krichen
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Massimo Ancora
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Adriano Di Pasquale
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Asma Cherni
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Henda Touzi
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Amel Sadraoui
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Zina Meddeb
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Nahed Hogga
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Radhia Ammi
- Service of External Consultants, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Henda Triki
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Sondes Haddad-Boubaker
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
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11
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Atoui A, Cordevant C, Chesnot T, Gassilloud B. SARS-CoV-2 in the environment: Contamination routes, detection methods, persistence and removal in wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 881:163453. [PMID: 37059142 PMCID: PMC10091716 DOI: 10.1016/j.scitotenv.2023.163453] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 06/01/2023]
Abstract
The present study reviewed the occurrence of SARS-CoV-2 RNA and the evaluation of virus infectivity in feces and environmental matrices. The detection of SARS-CoV-2 RNA in feces and wastewater samples, reported in several studies, has generated interest and concern regarding the possible fecal-oral route of SARS-CoV-2 transmission. To date, the presence of viable SARS-CoV-2 in feces of COVID-19 infected people is not clearly confirmed although its isolation from feces of six different patients. Further, there is no documented evidence on the infectivity of SARS-CoV-2 in wastewater, sludge and environmental water samples, although the viral genome has been detected in these matrices. Decay data revealed that SARS-CoV-2 RNA persisted longer than infectious particle in all aquatic environment, indicating that genome quantification of SARS-CoV-2 does not imply the presence of infective viral particles. In addition, this review also outlined the fate of SARS-CoV-2 RNA during the different steps in the wastewater treatment plant and focusing on the virus elimination along the sludge treatment line. Studies showed complete removal of SARS-CoV-2 during the tertiary treatment. Moreover, thermophilic sludge treatments present high efficiency in SARS-CoV-2 inactivation. Further studies are required to provide more evidence with respect to the inactivation behavior of infectious SARS-CoV-2 in different environmental matrices and to examine factors affecting SARS-CoV-2 persistence.
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Affiliation(s)
- Ali Atoui
- ANSES, Nancy Laboratory for Hydrology, Water Microbiology Unit, 40, rue Lionnois, 54 000 Nancy, France.
| | - Christophe Cordevant
- ANSES, Strategy and Programs Department, Research and Reference Division, Maisons-Alfort F-94 700, France
| | - Thierry Chesnot
- ANSES, Nancy Laboratory for Hydrology, Water Microbiology Unit, 40, rue Lionnois, 54 000 Nancy, France
| | - Benoît Gassilloud
- ANSES, Nancy Laboratory for Hydrology, Water Microbiology Unit, 40, rue Lionnois, 54 000 Nancy, France
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12
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Tsegaye AT, Sherry C, Oduol C, Otieno J, Rwigi D, Masheti M, Machura I, Liru M, Akuka J, Omedo D, Symekher S, Khamadi SA, Isaaka L, Ogero M, Mumelo L, Berkley JA, Agweyu A, Walson JL, Singa BO, Tickell KD. Clinical epidemiology of COVID-19 among hospitalized children in rural western Kenya. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0002011. [PMID: 37315023 PMCID: PMC10266603 DOI: 10.1371/journal.pgph.0002011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/12/2023] [Indexed: 06/16/2023]
Abstract
The epidemiology of pediatric COVID-19 in sub-Saharan Africa and the role of fecal-oral transmission in SARS-CoV-2 are poorly understood. Among children and adolescents in Kenya, we identify correlates of COVID-19 infection, document the clinical outcomes of infection, and evaluate the prevalence and viability of SARS-CoV-2 in stool. We recruited a prospective cohort of hospitalized children aged two months to 15 years in western Kenya between March 1 and June 30 2021. Children with SARS-CoV-2 were followed monthly for 180-days after hospital discharge. Bivariable logistic regression analysis was used to identify the clinical and sociodemographics correlates of SARS-CoV-2 infection. We also calculated the prevalence of SARS-CoV-2 detection in stool of confirmed cases. Of 355 systematically tested children, 55 (15.5%) were positive and were included in the cohort. The commonest clinical features among COVID-19 cases were fever (42/55, 76%), cough (19/55, 35%), nausea and vomiting (19/55, 35%), and lethargy (19/55, 35%). There were no statistically significant difference in baseline sociodemographic and clinical characteristics between SARS-CoV-2 positive and negative participants. Among positive participants, 8/55 (14.5%, 95%CI: 5.3%-23.9%) died; seven during the inpatient period. Forty-nine children with COVID-19 had stool samples or rectal swabs available at baseline, 9 (17%) had PCR-positive stool or rectal swabs, but none had SARS-CoV-2 detected by culture. Syndromic identification of COVID-19 is particularly challenging among children as the presenting symptoms and signs mirror other common pediatric diseases. Mortality among children hospitalized with COVID-19 was high in this cohort but was comparable to mortality seen with other common illnesses in this setting. Among this small set of children with COVID-19 we detected SARS-CoV-2 DNA, but were not able to culture viable SARs-CoV-2 virus, in stool. This suggests that fecal transmission may not be a substantial risk in children recently diagnosed and hospitalized with COVID-19 infection.
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Affiliation(s)
- Adino Tesfahun Tsegaye
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Christina Sherry
- Departments of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Chrisantus Oduol
- Center for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Joyce Otieno
- Center for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Doreen Rwigi
- Center for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Mary Masheti
- Center for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Meshack Liru
- Homa Bay County Referral Hospital, Homa Bay, Kenya
| | - Joyce Akuka
- Migori County Referral Hospital, Migori, Kenya
| | | | - Samwel Symekher
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Samoel A. Khamadi
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Lynda Isaaka
- KEMRI/Wellcome Trust Research Programme, Nairobi, Kenya
| | - Morris Ogero
- KEMRI/Wellcome Trust Research Programme, Nairobi, Kenya
| | | | - James A. Berkley
- KEMRI/Wellcome Trust Research Programme, Nairobi, Kenya
- The Childhood Acute Illness and Nutrition Network (CHAIN), Nairobi, Kenya
- Centre for Tropical Medicine & Global Health Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Ambrose Agweyu
- KEMRI/Wellcome Trust Research Programme, Nairobi, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Judd L. Walson
- The Childhood Acute Illness and Nutrition Network (CHAIN), Nairobi, Kenya
- Departments of Global Health, Medicine (Infectious Disease), Pediatrics and Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Benson O. Singa
- Center for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Kirkby D. Tickell
- Departments of Global Health, University of Washington, Seattle, Washington, United States of America
- The Childhood Acute Illness and Nutrition Network (CHAIN), Nairobi, Kenya
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13
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Gentry Z, Zhao L, Faust RA, David RE, Norton J, Xagoraraki I. Wastewater surveillance beyond COVID-19: a ranking system for communicable disease testing in the tri-county Detroit area, Michigan, USA. Front Public Health 2023; 11:1178515. [PMID: 37333521 PMCID: PMC10272568 DOI: 10.3389/fpubh.2023.1178515] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/12/2023] [Indexed: 06/20/2023] Open
Abstract
Introduction Throughout the coronavirus disease 2019 (COVID-19) pandemic, wastewater surveillance has been utilized to monitor the disease in the United States through routine national, statewide, and regional monitoring projects. A significant canon of evidence was produced showing that wastewater surveillance is a credible and effective tool for disease monitoring. Hence, the application of wastewater surveillance can extend beyond monitoring SARS-CoV-2 to encompass a diverse range of emerging diseases. This article proposed a ranking system for prioritizing reportable communicable diseases (CDs) in the Tri-County Detroit Area (TCDA), Michigan, for future wastewater surveillance applications at the Great Lakes Water Authority's Water Reclamation Plant (GLWA's WRP). Methods The comprehensive CD wastewater surveillance ranking system (CDWSRank) was developed based on 6 binary and 6 quantitative parameters. The final ranking scores of CDs were computed by summing the multiplication products of weighting factors for each parameter, and then were sorted based on decreasing priority. Disease incidence data from 2014 to 2021 were collected for the TCDA. Disease incidence trends in the TCDA were endowed with higher weights, prioritizing the TCDA over the state of Michigan. Results Disparities in incidences of CDs were identified between the TCDA and state of Michigan, indicating epidemiological differences. Among 96 ranked CDs, some top ranked CDs did not present relatively high incidences but were prioritized, suggesting that such CDs require significant attention by wastewater surveillance practitioners, despite their relatively low incidences in the geographic area of interest. Appropriate wastewater sample concentration methods are summarized for the application of wastewater surveillance as per viral, bacterial, parasitic, and fungal pathogens. Discussion The CDWSRank system is one of the first of its kind to provide an empirical approach to prioritize CDs for wastewater surveillance, specifically in geographies served by centralized wastewater collection in the area of interest. The CDWSRank system provides a methodological tool and critical information that can help public health officials and policymakers allocate resources. It can be used to prioritize disease surveillance efforts and ensure that public health interventions are targeted at the most potentially urgent threats. The CDWSRank system can be easily adopted to geographical locations beyond the TCDA.
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Affiliation(s)
- Zachary Gentry
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, United States
| | - Liang Zhao
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, United States
| | | | - Randy E. David
- Wayne State University School of Medicine, Detroit, MI, United States
| | - John Norton
- Great Lakes Water Authority, Detroit, MI, United States
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, United States
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Costanzo M, De Giglio MAR, Roviello GN. Deciphering the Relationship between SARS-CoV-2 and Cancer. Int J Mol Sci 2023; 24:ijms24097803. [PMID: 37175509 PMCID: PMC10178366 DOI: 10.3390/ijms24097803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/17/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Some viruses are known to be associated with the onset of specific cancers. These microorganisms, oncogenic viruses or oncoviruses, can convert normal cells into cancer cells by modulating the central metabolic pathways or hampering genomic integrity mechanisms, consequently inhibiting the apoptotic machinery and/or enhancing cell proliferation. Seven oncogenic viruses are known to promote tumorigenesis in humans: human papillomavirus (HPV), hepatitis B and C viruses (HBV, HCV), Epstein-Barr virus (EBV), human T-cell leukemia virus 1 (HTLV-1), Kaposi sarcoma-associated herpesvirus (KSHV), and Merkel cell polyomavirus (MCPyV). Recent research indicates that SARS-CoV-2 infection and COVID-19 progression may predispose recovered patients to cancer onset and accelerate cancer development. This hypothesis is based on the growing evidence regarding the ability of SARS-CoV-2 to modulate oncogenic pathways, promoting chronic low-grade inflammation and causing tissue damage. Herein, we summarize the main relationships known to date between virus infection and cancer, providing a summary of the proposed biochemical mechanisms behind the cellular transformation. Mechanistically, DNA viruses (such as HPV, HBV, EBV, and MCPyV) encode their virus oncogenes. In contrast, RNA viruses (like HCV, HTLV-1) may encode oncogenes or trigger host oncogenes through cis-/-trans activation leading to different types of cancer. As for SARS-CoV-2, its role as an oncogenic virus seems to occur through the inhibition of oncosuppressors or controlling the metabolic and autophagy pathways in the infected cells. However, these effects could be significant in particular scenarios like those linked to severe COVID-19 or long COVID. On the other hand, looking at the SARS-CoV-2─cancer relationship from an opposite perspective, oncolytic effects and anti-tumor immune response were triggered by SARS-CoV-2 infection in some cases. In summary, our work aims to recall comprehensive attention from the scientific community to elucidate the effects of SARS-CoV-2 and, more in general, β-coronavirus infection on cancer susceptibility for cancer prevention or supporting therapeutic approaches.
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Affiliation(s)
- Michele Costanzo
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore s.c.ar.l., Via G. Salvatore 486, 80145 Naples, Italy
| | | | - Giovanni Nicola Roviello
- Institute of Biostructures and Bioimaging, Italian National Council for Research (IBB-CNR), Via P. Castellino 111, 80131 Naples, Italy
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15
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Abstract
COVID (Coronavirus disease)-19 is a systemic disease and the kidney is one of the target organs of infection. Kidney injury is common and can occur in up to 40% of patients. Several glomerular diseases have been reported in association with COVID-19. Some are likely related to COVID-19 whereas many are likely coincidental. Glomerular diseases that are frequently reported in COVID-19 and have a plausible mechanistic explanation, are likely to be related to COVID-19. On the other hand, glomerular diseases that are seldom reported and have no known plausible mechanism, are likely to be unrelated. Collapsing glomerulopathy (CG) is by far the most prevalent. Its association with COVID-19, resembling human immunodeficiency virus (HIV) and CG, led to the newly proposed term “COVID-19 associated nephropathy” or “COVAN”. High-risk APOL1 genotypes are the major risk factor in COVAN patients. Podocytopathy, membranous nephropathy, pauci-immune crescentic glomerulonephritis, and thrombotic microangiopathy are also reported. In kidney allografts, CG remains the most common glomerular pathology. Patients typically present with acute kidney injury (AKI) or abnormal urinary findings at the time of or shortly after COVID-19 diagnosis. Treatment of glomerular disease in COVID-19 patients is challenging. Providers should cautiously consider balancing risks and benefit of immunosuppression, particularly in patients with active diseases. Short-term outcomes vary but generally remain poor with high morbidity and mortality. Future study of long-term outcomes is needed to improve our understanding of glomerular disease associated with COVID-19.
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Scott G, Evens N, Porter J, Walker DI. The Inhibition and Variability of Two Different RT-qPCR Assays Used for Quantifying SARS-CoV-2 RNA in Wastewater. FOOD AND ENVIRONMENTAL VIROLOGY 2023; 15:71-81. [PMID: 36790663 PMCID: PMC9930079 DOI: 10.1007/s12560-022-09542-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/01/2022] [Indexed: 06/18/2023]
Abstract
Faecal shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its subsequent detection in wastewater turned the spotlight onto wastewater-based epidemiology (WBE) for monitoring the coronavirus-disease 2019 (COVID-19) pandemic. WBE for SARS-CoV-2 has been deployed in 70 countries, providing insights into disease prevalence, forecasting and the spatiotemporal tracking and emergence of SARS-CoV-2 variants. Wastewater, however, is a complex sample matrix containing numerous reverse transcription quantitative PCR (RT-qPCR) inhibitors whose concentration and diversity are influenced by factors including population size, surrounding industry and agriculture and climate. Such differences in the RT-qPCR inhibitor profile are likely to impact the quality of data produced by WBE and potentially produce erroneous results.To help determine the possible impact of RT-qPCR assay on data quality, two assays employed by different laboratories within the UK's SARS-CoV-2 wastewater monitoring programme were assessed in the Cefas laboratory in Weymouth, UK. The assays were based on Fast Virus (FV) and qScript (qS) chemistries using the same primers and probes, but at different concentrations and under different cycling conditions. Bovine serum albumin and MgSO4 were also added to the FV assay reaction mixture. Two-hundred and eighty-six samples were analysed, and an external control RNA (EC RNA)-based method was used to measure RT-qPCR inhibition. Compared with qS, FV showed a 40.5% reduction in mean inhibition and a 57.0% reduction in inter-sample inhibition variability. A 4.1-fold increase in SARS-CoV-2 quantification was seen for FV relative to qS; partially due (1.5-fold) to differences in reverse transcription efficiency and the use of a dsDNA standard. Analytical variability was reduced by 51.2% using FV while qS increased the number of SARS-CoV-2 negative samples by 2.6-fold. This study indicates the importance of thorough method optimisation for RT-qPCR-based WBE which should be performed using a selection of samples which are representative of the physiochemical properties of wastewater. Furthermore, RT-qPCR inhibition, analytical variability and reverse transcription efficiency should be key considerations during assay optimisation. A standardised framework for the optimisation and validation of WBE procedures should be formed including concessions for emergency response situations that would allow flexibility in the process to address the difficult balance between the urgency of providing data and the availability of resources.
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Affiliation(s)
- George Scott
- Centre for Environment, Fisheries and Aquaculture Science, The Nothe, Barrack Road, Weymouth, DT4 8UB, UK.
| | - Nicholas Evens
- Environment Agency, National Monitoring, Starcross, Exeter, EX6 8FD, UK
| | - Jonathan Porter
- Environment Agency, National Monitoring, Starcross, Exeter, EX6 8FD, UK
| | - David I Walker
- Centre for Environment, Fisheries and Aquaculture Science, The Nothe, Barrack Road, Weymouth, DT4 8UB, UK
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Erdem D, Kayaaslan B, Cakir EY, Dinc B, Asilturk D, Kirca F, Segmen F, Turan IO, Guner R. Investigation of SARS-CoV-2 using RT-PCR in vaginal swab samples of female patients with a diagnosis of severe COVID-19. Taiwan J Obstet Gynecol 2023; 62:270-274. [PMID: 36965894 PMCID: PMC9729648 DOI: 10.1016/j.tjog.2022.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE It is important to determine the presence of SARS-CoV-2 in the vaginal fluid samples of reproductive-aged women with severe disease during the acute stage of the disease and to determine the risks of transmission by sexual or vertical transmission. MATERIAL AND METHODS Adult women with confirmed severe COVID-19 who were admitted to Ankara City Hospital intensive care unit (ICU) between December 1st, 2020, and January 1st, 2021, were enrolled in the study. Vaginal swab samples were collected within 48 h in the ICU using Dacron or rayon swabs and tested for SARS-CoV-2 using reverse transcription real-time polymerase chain reaction (RT PCR). RESULTS Thirty women of reproductive age were included in the study, five (16.7%) of whom were pregnant. The mean age was 44.9 (±10.5) years. The most common symptoms were headache (100%), muscle soreness (86.7%), cough (76.7%), fever (60%), and nausea and vomiting (20%). Nineteen (63.3%) patients had underlying medical conditions. The time interval from obtaining vaginal swab samples to admission to the ICU was 48 h. The time between vaginal sampling and PCR positivity ranged from 2 to 18 days. SARS-CoV-2 was not detected in any vaginal samples. CONCLUSION Our study showed that women with severe COVID-19 did not have SARS-CoV-2 in their vaginal fluids. Investigation of the presence of SARS-CoV-2 in vaginal secretions may help in determining the risks of sexual transmission and vertical transmission from mother to baby. Information on this subject is still limited. Larger studies on comprehensive biological samples are needed.
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Affiliation(s)
- Deniz Erdem
- Department of Intensive Care Unıt, Univeristy of Health Sciences, Ankara City Hospital, Ankara, Turkey.
| | - Bircan Kayaaslan
- Infectious Disease and Clinical Microbiology, Ankara Yildırım Beyazit University, Ankara City Hospital, Ankara, Turkey
| | | | - Bedia Dinc
- Department of Medical Microbiology, University of Health Sciences, Ankara City Hospital, Ankara, Turkey
| | - Dilek Asilturk
- Infectious Disease and Clinical Microbiology, Ankara City Hospital, Ankara, Turkey
| | - Fisun Kirca
- Department of Medical Microbiology, Ankara City Hospital, Ankara, Turkey
| | - Fatih Segmen
- Department of Intensive Care Unıt, Ankara City Hospital, Ankara, Turkey
| | - Isil Ozkocak Turan
- Department of Intensive Care Unıt, Univeristy of Health Sciences, Ankara City Hospital, Ankara, Turkey
| | - Rahmet Guner
- Infectious Disease and Clinical Microbiology, Ankara Yildırım Beyazit University, Ankara City Hospital, Ankara, Turkey
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18
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Mostafa M, Barhoum A, Sehit E, Gewaid H, Mostafa E, Omran MM, Abdalla MS, Abdel-Haleem FM, Altintas Z, Forster RJ. Current trends in COVID-19 diagnosis and its new variants in physiological fluids: Surface antigens, antibodies, nucleic acids, and RNA sequencing. Trends Analyt Chem 2022; 157:116750. [PMID: 36060607 PMCID: PMC9425703 DOI: 10.1016/j.trac.2022.116750] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 06/21/2022] [Accepted: 07/24/2022] [Indexed: 12/15/2022]
Abstract
Rapid, highly sensitive, and accurate virus circulation monitoring techniques are critical to limit the spread of the virus and reduce the social and economic burden. Therefore, point-of-use diagnostic devices have played a critical role in addressing the outbreak of COVID-19 (SARS-CoV-2) viruses. This review provides a comprehensive overview of the current techniques developed for the detection of SARS-CoV-2 in various body fluids (e.g., blood, urine, feces, saliva, tears, and semen) and considers the mutations (i.e., Alpha, Beta, Gamma, Delta, Omicron). We classify and comprehensively discuss the detection methods depending on the biomarker measured (i.e., surface antigen, antibody, and nucleic acid) and the measurement techniques such as lateral flow immunoassay (LFIA), enzyme-linked immunosorbent assay (ELISA), reverse transcriptase-polymerase chain reaction (RT-PCR), reverse transcription loop-mediated isothermal amplification (RT-LAMP), microarray analysis, clustered regularly interspaced short palindromic repeats (CRISPR) and biosensors. Finally, we addressed the challenges of rapidly identifying emerging variants, detecting the virus in the early stages of infection, the detection sensitivity, selectivity, and specificity, and commented on how these challenges can be overcome in the future.
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Affiliation(s)
- Menna Mostafa
- NanoStruc Research Group, Chemistry Department, Faculty of Science, Helwan University, 11795, Cairo, Egypt
| | - Ahmed Barhoum
- National Centre for Sensor Research, School of Chemical Sciences, Dublin City University, D09 V209, Dublin, Ireland
| | - Ekin Sehit
- Institute of Chemistry, Technical University of Berlin, 10623, Berlin, Germany
- Institute of Materials Science, Faculty of Engineering, Kiel University, 24143, Kiel, Germany
| | - Hossam Gewaid
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St, Dublin, D02R590, Ireland
| | - Eslam Mostafa
- Borg Pharmaceutical Industries, Refaat Hassan St, Al Abageyah, El-Khalifa, Cairo Governorate, 16, Egypt
| | - Mohamed M Omran
- Chemistry Department, Faculty of Science, Helwan University, 11795, Cairo, Egypt
| | - Mohga S Abdalla
- Chemistry Department, Faculty of Science, Helwan University, 11795, Cairo, Egypt
| | - Fatehy M Abdel-Haleem
- Chemistry Department, Faculty of Science, Cairo University, 12613, Giza, Egypt
- Center for Hazards Mitigation, Environmental Studies and Research (CHMESR), Cairo University, 12613, Giza, Egypt
| | - Zeynep Altintas
- Institute of Chemistry, Technical University of Berlin, 10623, Berlin, Germany
- Institute of Materials Science, Faculty of Engineering, Kiel University, 24143, Kiel, Germany
| | - Robert J Forster
- National Centre for Sensor Research, School of Chemical Sciences, Dublin City University, D09 V209, Dublin, Ireland
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19
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Sun X, Gao C, Zhao K, Yang Y, Rassadkina Y, Fajnzylber J, Regan J, Li JZ, Lichterfeld M, Yu XG. Immune-profiling of SARS-CoV-2 viremic patients reveals dysregulated innate immune responses. Front Immunol 2022; 13:984553. [DOI: 10.3389/fimmu.2022.984553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 09/01/2022] [Indexed: 11/10/2022] Open
Abstract
SARS-CoV-2 plasma viremia has been associated with severe disease and death in COVID-19. However, the effects of viremia on immune responses in blood cells remain unclear. The current study comprehensively examined transcriptional signatures of PBMCs involving T cells, B cells, NK cells, monocytes, myeloid dendritic cells (mDCs), and plasmacytoid dendritic cells (pDCs) respectively, from three different groups including individuals with moderate (nM), or severe disease with (vS) or without (nS) detectable plasma viral load. Whole transcriptome analysis demonstrated that all seven immune cell subsets were associated with disease severity regardless of cell type. Supervised clustering analysis demonstrated that mDCs and pDCs gene signatures could distinguish disease severity. Notably, transcriptional signatures of the vS group were enriched in pathways related to DNA repair, E2F targets, and G2M checkpoints; in contrast, transcriptional signatures of the nM group were enriched in interferon responses. Moreover, we observed an impaired induction of interferon responses accompanied by imbalanced cell-intrinsic immune sensing and an excessive inflammatory response in patients with severe disease (nS and vS). In sum, our study provides detailed insights into the systemic immune response to SARS-CoV-2 infection and reveals profound alterations in seven major immune cells in COVID-19 patients.
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20
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Liu D, Zhang Y, Chen D, Wang X, Huang F, Long L, Zheng X. Evaluation of the presence of SARS-CoV-2 in vaginal and anal swabs of women with omicron variants of SARS-CoV-2 infection. Front Microbiol 2022; 13:1035359. [DOI: 10.3389/fmicb.2022.1035359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022] Open
Abstract
ObjectivesThe study aimed to determine whether SARS-CoV-2 Omicron variant could be detected in the vaginal fluid and anal swabs of reproductive-aged and postmenopausal women infected with SARS-CoV-2 Omicron variant.MethodsIncluded in this study were 63 women who were laboratory confirmed as having SARS-CoV-2 Omicron variant infection and admitted to the responsible ward of Daping Hospital of at the National Exhibition and Convention Center(Shanghai) Makeshift Hospital from May 1–24, 2022.From them, vaginal and anal swabs were obtained with informed consent. The demographic and baseline clinical characteristics and the swab test results were analyzed.ResultsThe 63 included patients ranged in age from 18 to 72 years with a median of 47.71 ± 15.21 years. Of them, 38 women (60.3%) were in their reproductive years. Most of the participants (77.8%) were healthy without significant underlying diseases. Fourteen patients (22.2%) had asymptomatic infection and the remaining 49 (77.8%) had mild infection. The upper respiratory tract symptoms including cough (40/63.5%) and sore throat (18/28.6%)were the most common clinical manifestations of these mildly infected patients. Only 5 patients (7.8%) had gastrointestinal (GI) symptoms, including simple diarrhea in 4 patients, and diarrhea with vomiting in one patient. Pharyngeal,vaginal and anal swabs were collected simultaneously from all 63 patients 8–16 (mean 11.25 ± 2.23) days after SARS-Cov-2 Omicron variant infection. The vaginal swabs were negative for SARS-CoV-2 in all 63 patients, and the anal swabs were positive in 4 patients (6.5%). The overall median hospitalization duration was 16.73 ± 3.16 days.ConclusionThe results of the present study suggest that there is a low possibility of SARS-Cov-2 Omicron variant transmission via the digestive tract and vaginal fluid. The correlation between the GI symptoms and the presence of viral RNA in anal swabs is uncertain.
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21
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Guo Y, Li X, Luby S, Jiang G. Vertical outbreak of COVID-19 in high-rise buildings: The role of sewer stacks and prevention measures. CURRENT OPINION IN ENVIRONMENTAL SCIENCE & HEALTH 2022; 29:100379. [PMID: 35856009 PMCID: PMC9279164 DOI: 10.1016/j.coesh.2022.100379] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/27/2022] [Accepted: 07/04/2022] [Indexed: 05/25/2023]
Abstract
COVID-19 outbreaks in high-rise buildings suggested the transmission route of fecal-aerosol-inhalation due to the involvement of viral aerosols in sewer stacks. The vertical transmission is likely due to the failure of water traps that allow viral aerosols to spread through sewer stacks. This process can be further facilitated by the chimney effect in vent stack, extract ventilation in bathrooms, or wind-induced air pressure fluctuations. To eliminate the risk of such vertical disease spread, the installation of protective devices is highly encouraged in high-rise buildings. Although the mechanism of vertical pathogen spread through drainage pipeline has been illustrated by tracer gas or microbial experiments and numerical modeling, more research is needed to support the update of regulatory and design standards for sewerage facilities.
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Affiliation(s)
- Ying Guo
- School of Civil, Mining, Environmental and Architectural Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Xuan Li
- School of Civil, Mining, Environmental and Architectural Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Stephen Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA 94305, USA
| | - Guangming Jiang
- School of Civil, Mining, Environmental and Architectural Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW 2522, Australia
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22
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Alkhamis A, Alshamali Y, Chehadeh W, Jasem A, Omar AA, Alghounaim M, Elsaaran H, Al-Youha S, Almazeedi S, Alkhamis MA, Alsabah S. Predictors of intensive care unit admission and mortality in SARS-CoV-2 infection: A cross sectional study at a tertiary care hospital. Ann Med Surg (Lond) 2022; 80:104097. [PMID: 35818560 PMCID: PMC9259005 DOI: 10.1016/j.amsu.2022.104097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 12/15/2022] Open
Abstract
Background The transmissibility and associated morbidity and mortality of severe acute respiratory syndrome-related coronavirus (SARS-Cov-2), have overwhelmed worldwide healthcare systems, resulting in an urgent need to understand this virus and its associated effects. The aim of our study was to identify patient symptoms, clinical characteristics, laboratory, and radiology findings that are associated with serious morbidity and mortality in COVID-19 patients. Methods A cross sectional study was conducted in Jaber Al Ahmad Hospital, the designated COVID-19 center in Kuwait between August 1st, 2020 and January 31st, 2021. The main outcomes measured in this study were to identify variables associated with intensive care unit (ICU) admission, as proxy for serious morbidity, and in hospital mortality. Results Two hundred and seventy-six patients were included in the study. Thirty-six (13%) patients were admitted to intensive care unit (ICU) and 33 (12%) patients expired. On multivariate analysis we found having elevated fibrinogen [OR 1.39, 95% CI 1.08–1.64, P = 0.04], low estimated glomerular filtration rate (eGFR) [OR 0.89, 95% CI 0.81–0.95, P = 0.02], and having bilateral patchy lung shadowing [OR 6.68, 95% CI 1.85–15.28, P < 0.01] to be significantly associated with increase odds of ICU admission. Elevated CRP [OR 1.25, 95% CI 1.10–1.98, P < 0.01], low eGFR [OR 0.95, 95% CI 0.90–0.99, P = 0.05] and having ischemic heart disease [OR 7.03, 95% CI 1.60–46.42, P = 0.04] were independently associated with increased odds of mortality. Conclusion Certain inflammatory and coagulopathy markers, and having certain lung radiological features, in addition to having medical comorbidities, specifically, ischemic heart disease and renal impairment are key predictors for serious morbidity and mortality in patients infected with COVID-19. These should be incorporated into medical institutes risk assessment tools used by physicians and policy makers to instigate, prioritize, and reprioritize care in patients with COVID-19 and instigate preventative strategy to reduce the impact of future outbreak. Understanding risk factors associated with worse outcomes when infected with COVID-19 infection is important. A multifactorial model incorporating certain laboratory blood tests and patient clinical characteristics seems to be the best way to predict morbidity and mortality. Obesity, Cardiovascular and renal deficiencies are predictors of worse outcomes and so should be prioritized in managing COVID-19 patients.
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23
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Kumar M, Jiang G, Kumar Thakur A, Chatterjee S, Bhattacharya T, Mohapatra S, Chaminda T, Kumar Tyagi V, Vithanage M, Bhattacharya P, Nghiem LD, Sarkar D, Sonne C, Mahlknecht J. Lead time of early warning by wastewater surveillance for COVID-19: Geographical variations and impacting factors. CHEMICAL ENGINEERING JOURNAL (LAUSANNE, SWITZERLAND : 1996) 2022; 441:135936. [PMID: 35345777 PMCID: PMC8942437 DOI: 10.1016/j.cej.2022.135936] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/07/2022] [Accepted: 03/19/2022] [Indexed: 05/05/2023]
Abstract
The global data on the temporal tracking of the COVID-19 through wastewater surveillance needs to be comparatively evaluated to generate a proper and precise understanding of the robustness, advantages, and sensitivity of the wastewater-based epidemiological (WBE) approach. We reviewed the current state of knowledge based on several scientific articles pertaining to temporal variations in COVID-19 cases captured via viral RNA predictions in wastewater. This paper primarily focuses on analyzing the WBE-based temporal variation reported globally to check if the reported early warning lead-time generated through environmental surveillance is pragmatic or latent. We have compiled the geographical variations reported as lead time in various WBE reports to strike a precise correlation between COVID-19 cases and genome copies detected through wastewater surveillance, with respect to the sampling dates, separately for WASH and non-WASH countries. We highlighted sampling methods, climatic and weather conditions that significantly affected the concentration of viral SARS-CoV-2 RNA detected in wastewater, and thus the lead time reported from the various climatic zones with diverse WASH situations were different. Our major findings are: i) WBE reports around the world are not comparable, especially in terms of gene copies detected, lag-time gained between monitored RNA peak and outbreak/peak of reported case, as well as per capita RNA concentrations; ii) Varying sanitation facility and climatic conditions that impact virus degradation rate are two major interfering features limiting the comparability of WBE results, and iii) WBE is better applicable to WASH countries having well-connected sewerage system.
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Affiliation(s)
- Manish Kumar
- Sustainability Cluster, School of Engineering, University of Petroleum & Energy Studies, Dehradun, Uttarakhand 248007, India
| | - Guangming Jiang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, Australia
| | - Alok Kumar Thakur
- Discipline of Earth Science, Indian Institute of Technology Gandhinagar, Gujarat 382 355, India
| | - Shreya Chatterjee
- Encore Insoltech Pvt Ltd, Randesan, Gandhinagar, Gujarat 382 307, India
| | - Tanushree Bhattacharya
- Department of Civil and Environmental Engineering, Birla Institute of Technology, Mesra 835215, India
| | - Sanjeeb Mohapatra
- NUS Environmental Research Institute, National University of Singapore, Singapore
| | - Tushara Chaminda
- Department of Civil and Environmental Engineering, University of Ruhuna, Sri Lanka
| | - Vinay Kumar Tyagi
- Environmental BioTechnology Group (EBiTG), Department of Civil Engineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Meththika Vithanage
- Sustainability Cluster, School of Engineering, University of Petroleum & Energy Studies, Dehradun, Uttarakhand 248007, India
- Ecosphere Resilience Research Center, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka
| | - Prosun Bhattacharya
- COVID-19 Research@KTH, Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology,SE-100 44, Stockholm, Sweden
| | - Long D Nghiem
- Centre for Technology in Water & Wastewater, University of Technology Sydney, Ultimo 2007, Australia
| | - Dibyendu Sarkar
- Department of Civil, Environmental and Ocean Engineering, Stevens Institute of Technology, NJ 07030, USA
| | - Christian Sonne
- Sustainability Cluster, School of Engineering, University of Petroleum & Energy Studies, Dehradun, Uttarakhand 248007, India
- Department of Ecoscience, Aarhus University, Roskilde DK-4000, Denmark
| | - Jürgen Mahlknecht
- Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Campus Monterey, Monterrey 64849, Nuevo Leon, Mexico
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24
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Amahmid O, El Guamri Y, Rakibi Y, Ouizat S, Yazidi M, Razoki B, Kaid Rassou K, Asmama S, Bouhoum K, Belghyti D. Occurrence of SARS-CoV-2 in excreta, sewage, and environment: epidemiological significance and potential risks. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2022; 32:1686-1706. [PMID: 33752527 DOI: 10.1080/09603123.2021.1901865] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/08/2021] [Indexed: 05/23/2023]
Abstract
The detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in patients' excreta raises the issue of its occurrence and fate in sewage. This review has focused on the presence of the SARS-CoV-2 in human excreta, wastewater, sewage sludge, and river waters. It explored the potential use of the wastewater-based epidemiology approach to report on the situation of current and eventual future SARS-CoV-2 outbreaks. The main concern of the occurrence of SARS-CoV-2 in the environment is the public health risks at sites of sewage products disposal and reuse, especially in low-income countries with inadequate sanitation, where direct discharge and reuse of raw sewage are common practices. The review also addressed the role sewage-irrigated agriculture can have in SARS-CoV-2 spread in the environmental compartments reached through sewage products application. An overview was made on the interest of sewage management, water safety, and hygienic practices for controlling the environmental dissemination of SARS-CoV-2.
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Affiliation(s)
- Omar Amahmid
- Department of Life and Earth Sciences, (Biology/geology Research Units), Regional Centre for Careers of Education and Training CRMEF Marrakech-Safi, Marrakesh, Morocco
- Department of Biology, Laboratory of Water, Biodiversity and Climatic Change, Faculty of Sciences Semlalia, Cadi Ayyad Univesity, Marrakesh, Morocco
- Department of Biology, Laboratory of Natural Resources and Sustainable Development, University Ibn Tofail, Kenitra, Morocco
| | - Youssef El Guamri
- Department of Life and Earth Sciences, (Biology/geology Research Units), Regional Centre for Careers of Education and Training CRMEF Marrakech-Safi, Marrakesh, Morocco
- Department of Biology, Laboratory of Natural Resources and Sustainable Development, University Ibn Tofail, Kenitra, Morocco
| | - Youness Rakibi
- Department of Life and Earth Sciences, (Biology/geology Research Units), Regional Centre for Careers of Education and Training CRMEF Marrakech-Safi, Marrakesh, Morocco
- Engineering Laboratory of Organometallic, Molecular Materials and Environment (LIMOME), Sidi Mohammed Ben Abdellah University, Fez, Morocco
| | - Saadia Ouizat
- Chemistry and Didactics Unit, Regional Centre for Careers of Education and Training CRMEF Marrakech-Safi, Marrakesh, Morocco
| | - Mohamed Yazidi
- Department of Life and Earth Sciences, (Biology/geology Research Units), Regional Centre for Careers of Education and Training CRMEF Marrakech-Safi, Marrakesh, Morocco
| | - Bouchra Razoki
- Department of Life and Earth Sciences, (Biology/geology Research Units), Regional Centre for Careers of Education and Training CRMEF Marrakech-Safi, Marrakesh, Morocco
| | - Khadija Kaid Rassou
- Department of Life and Earth Sciences, (Biology/geology Research Units), Regional Centre for Careers of Education and Training CRMEF Marrakech-Safi, Marrakesh, Morocco
| | - Souad Asmama
- Laboratory of Biomedical Analysis, University Hospital Centre Mohammad VI, Marrakech, Morocco
| | - Khadija Bouhoum
- Department of Biology, Laboratory of Water, Biodiversity and Climatic Change, Faculty of Sciences Semlalia, Cadi Ayyad Univesity, Marrakesh, Morocco
| | - Driss Belghyti
- Department of Biology, Laboratory of Natural Resources and Sustainable Development, University Ibn Tofail, Kenitra, Morocco
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25
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El-Malah SS, Saththasivam J, Jabbar KA, K K A, Gomez TA, Ahmed AA, Mohamoud YA, Malek JA, Abu Raddad LJ, Abu Halaweh HA, Bertollini R, Lawler J, Mahmoud KA. Application of human RNase P normalization for the realistic estimation of SARS-CoV-2 viral load in wastewater: A perspective from Qatar wastewater surveillance. ENVIRONMENTAL TECHNOLOGY & INNOVATION 2022; 27:102775. [PMID: 35761926 PMCID: PMC9220754 DOI: 10.1016/j.eti.2022.102775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/30/2022] [Accepted: 06/19/2022] [Indexed: 05/06/2023]
Abstract
The apparent uncertainty associated with shedding patterns, environmental impacts, and sample processing strategies have greatly influenced the variability of SARS-CoV-2 concentrations in wastewater. This study evaluates the use of a new normalization approach using human RNase P for the logic estimation of SARS-CoV-2 viral load in wastewater. SARS-CoV-2 variants outbreak was monitored during the circulating wave between February and August 2021. Sewage samples were collected from five major wastewater treatment plants and subsequently analyzed to determine the viral loads in the wastewater. SARS-CoV-2 was detected in all the samples where the wastewater Ct values exhibited a similar trend as the reported number of new daily positive cases in the country. The infected population number was estimated using a mathematical model that compensated for RNA decay due to wastewater temperature and sewer residence time, and which indicated that the number of positive cases circulating in the population declined from 765,729 ± 142,080 to 2,303 ± 464 during the sampling period. Genomic analyses of SARS-CoV-2 of thirty wastewater samples collected between March 2021 and April 2021 revealed that alpha (B.1.1.7) and beta (B.1.351) were among the dominant variants of concern (VOC) in Qatar. The findings of this study imply that the normalization of data allows a more realistic assessment of incidence trends within the population.
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Affiliation(s)
- Shimaa S El-Malah
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, P.O. Box 34110, Doha, Qatar
| | - Jayaprakash Saththasivam
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, P.O. Box 34110, Doha, Qatar
| | - Khadeeja Abdul Jabbar
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, P.O. Box 34110, Doha, Qatar
| | - Arun K K
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, P.O. Box 34110, Doha, Qatar
| | - Tricia A Gomez
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, P.O. Box 34110, Doha, Qatar
| | - Ayeda A Ahmed
- Genomics Laboratory, Weill Cornell Medicine-Qatar (WCM-Q), Cornell University, Doha, Qatar
| | - Yasmin A Mohamoud
- Genomics Laboratory, Weill Cornell Medicine-Qatar (WCM-Q), Cornell University, Doha, Qatar
| | - Joel A Malek
- Genomics Laboratory, Weill Cornell Medicine-Qatar (WCM-Q), Cornell University, Doha, Qatar
| | - Laith J Abu Raddad
- Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar
| | - Hussein A Abu Halaweh
- Drainage Network Operation & Maintenance Department, Public Works Authority, Doha, Qatar
| | | | - Jenny Lawler
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, P.O. Box 34110, Doha, Qatar
| | - Khaled A Mahmoud
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, P.O. Box 34110, Doha, Qatar
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26
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Concas G, Barone M, Francavilla R, Cristofori F, Dargenio VN, Giorgio R, Dargenio C, Fanos V, Marcialis MA. Twelve Months with COVID-19: What Gastroenterologists Need to Know. Dig Dis Sci 2022; 67:2771-2791. [PMID: 34333726 PMCID: PMC8325547 DOI: 10.1007/s10620-021-07158-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 07/06/2021] [Indexed: 02/07/2023]
Abstract
Corona virus disease-19 (COVID-19) is the latest global pandemic. COVID-19 is mainly transmitted through respiratory droplets and, apart from respiratory symptoms, patients often present with gastrointestinal symptoms and liver involvement. Given the high percentage of COVID-19 patients that present with gastrointestinal symptoms (GIS), in this review, we report a practical up-to-date reference for the physician in their clinical practice with patients affected by chronic gastrointestinal (GI) diseases (inflammatory bowel disease, coeliac disease, chronic liver disease) at the time of COVID-19. First, we summarised data on the origin and pathogenetic mechanism of SARS-CoV-2. Then, we performed a literature search up to December 2020 examining clinical manifestations of GI involvement. Next, we illustrated and summarised the most recent guidelines on how to adhere to GI procedures (endoscopy, liver biopsy, faecal transplantation), maintaining social distance and how to deal with immunosuppressive treatment. Finally, we focussed on some special conditions such as faecal-oral transmission and gut microbiota. The rapid accumulation of information relating to this condition makes it particularly essential to revise the literature to take account of the most recent publications for medical consultation and patient care.
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Affiliation(s)
- Giulia Concas
- School of Paediatrics, University of Cagliari, 09124 Cagliari, Italy
| | - Michele Barone
- Gastroenterology Unit, Department of Emergency and Organ Transplantation, University of Bari, University Hospital “Policlinico”, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Ruggiero Francavilla
- Department of Biomedical Science and Human Oncology, Children’s Hospital “Giovanni XXIII”, University of Bari, 70126 Bari, Italy
| | - Fernanda Cristofori
- Department of Biomedical Science and Human Oncology, Children’s Hospital “Giovanni XXIII”, University of Bari, 70126 Bari, Italy
| | - Vanessa Nadia Dargenio
- Department of Biomedical Science and Human Oncology, Children’s Hospital “Giovanni XXIII”, University of Bari, 70126 Bari, Italy
| | - Rossella Giorgio
- Department of Biomedical Science and Human Oncology, Children’s Hospital “Giovanni XXIII”, University of Bari, 70126 Bari, Italy
| | - Costantino Dargenio
- Department of Biomedical Science and Human Oncology, Children’s Hospital “Giovanni XXIII”, University of Bari, 70126 Bari, Italy
| | - Vassilios Fanos
- Neonatal Intensive Care Unit, Azienda Ospedaliero Universitaria, University of Cagliari, Cagliari, 09124 Cagliari, Italy
| | - Maria Antonietta Marcialis
- Neonatal Intensive Care Unit, Azienda Ospedaliero Universitaria, University of Cagliari, Cagliari, 09124 Cagliari, Italy
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Jiang G, Wu J, Weidhaas J, Li X, Chen Y, Mueller J, Li J, Kumar M, Zhou X, Arora S, Haramoto E, Sherchan S, Orive G, Lertxundi U, Honda R, Kitajima M, Jackson G. Artificial neural network-based estimation of COVID-19 case numbers and effective reproduction rate using wastewater-based epidemiology. WATER RESEARCH 2022; 218:118451. [PMID: 35447417 PMCID: PMC9006161 DOI: 10.1016/j.watres.2022.118451] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/02/2022] [Accepted: 04/10/2022] [Indexed: 05/06/2023]
Abstract
As a cost-effective and objective population-wide surveillance tool, wastewater-based epidemiology (WBE) has been widely implemented worldwide to monitor the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA concentration in wastewater. However, viral concentrations or loads in wastewater often correlate poorly with clinical case numbers. To date, there is no reliable method to back-estimate the coronavirus disease 2019 (COVID-19) case numbers from SARS-CoV-2 concentrations in wastewater. This greatly limits WBE in achieving its full potential in monitoring the unfolding pandemic. The exponentially growing SARS-CoV-2 WBE dataset, on the other hand, offers an opportunity to develop data-driven models for the estimation of COVID-19 case numbers (both incidence and prevalence) and transmission dynamics (effective reproduction rate). This study developed artificial neural network (ANN) models by innovatively expanding a conventional WBE dataset to include catchment, weather, clinical testing coverage and vaccination rate. The ANN models were trained and evaluated with a comprehensive state-wide wastewater monitoring dataset from Utah, USA during May 2020 to December 2021. In diverse sewer catchments, ANN models were found to accurately estimate the COVID-19 prevalence and incidence rates, with excellent precision for prevalence rates. Also, an ANN model was developed to estimate the effective reproduction number from both wastewater data and other pertinent factors affecting viral transmission and pandemic dynamics. The established ANN model was successfully validated for its transferability to other states or countries using the WBE dataset from Wisconsin, USA.
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Affiliation(s)
- Guangming Jiang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia; Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, Australia.
| | - Jiangping Wu
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia
| | - Jennifer Weidhaas
- University of Utah, Civil and Environmental Engineering, 110 Central Campus Drive, Suite 2000, Salt Lake City, UT, USA
| | - Xuan Li
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia
| | - Yan Chen
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia
| | - Jochen Mueller
- Queensland Alliance for Environmental Health Sciences, The University of Queensland, Australia
| | - Jiaying Li
- Queensland Alliance for Environmental Health Sciences, The University of Queensland, Australia
| | - Manish Kumar
- Sustainability Cluster, School of Engineering, University of Petroleum & Energy Studies, Dehradun, Uttarakhand 248007, India
| | - Xu Zhou
- Shenzhen Engineering Laboratory of Microalgal Bioenergy, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Sudipti Arora
- Dr. B. Lal Institute of Biotechnology, Jaipur, India
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, Kofu, Japan
| | - Samendra Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA, USA
| | - Gorka Orive
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country UPV/EHU, Paseo de la Universidad 7, Vitoria-Gasteiz 01006, Spain; Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Vitoria-Gasteiz, Spain
| | - Unax Lertxundi
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country UPV/EHU, Paseo de la Universidad 7, Vitoria-Gasteiz 01006, Spain; Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Vitoria-Gasteiz, Spain
| | - Ryo Honda
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa 920-1192, Japan
| | - Masaaki Kitajima
- Division of Environmental Engineering, Hokkaido University, Hokkaido 060-8628, Japan
| | - Greg Jackson
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, 4102, Brisbane, Australia
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28
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Li X, Kulandaivelu J, Guo Y, Zhang S, Shi J, O'Brien J, Arora S, Kumar M, Sherchan SP, Honda R, Jackson G, Luby SP, Jiang G. SARS-CoV-2 shedding sources in wastewater and implications for wastewater-based epidemiology. JOURNAL OF HAZARDOUS MATERIALS 2022; 432:128667. [PMID: 35339834 PMCID: PMC8908579 DOI: 10.1016/j.jhazmat.2022.128667] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 05/21/2023]
Abstract
Wastewater-based epidemiology (WBE) approach for COVID-19 surveillance is largely based on the assumption of SARS-CoV-2 RNA shedding into sewers by infected individuals. Recent studies found that SARS-CoV-2 RNA concentration in wastewater (CRNA) could not be accounted by the fecal shedding alone. This study aimed to determine potential major shedding sources based on literature data of CRNA, along with the COVID-19 prevalence in the catchment area through a systematic literature review. Theoretical CRNA under a certain prevalence was estimated using Monte Carlo simulations, with eight scenarios accommodating feces alone, and both feces and sputum as shedding sources. With feces alone, none of the WBE data was in the confidence interval of theoretical CRNA estimated with the mean feces shedding magnitude and probability, and 63% of CRNA in WBE reports were higher than the maximum theoretical concentration. With both sputum and feces, 91% of the WBE data were below the simulated maximum CRNA in wastewater. The inclusion of sputum as a major shedding source led to more comparable theoretical CRNA to the literature WBE data. Sputum discharging behavior of patients also resulted in great fluctuations of CRNA under a certain prevalence. Thus, sputum is a potential critical shedding source for COVID-19 WBE surveillance.
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Affiliation(s)
- Xuan Li
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia
| | | | - Ying Guo
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia
| | - Shuxin Zhang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia
| | - Jiahua Shi
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia; Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, Australia
| | - Jake O'Brien
- Queensland Alliance for Environmental Health Sciences, The University of Queensland, Woollongabba, Queensland 4072, Australia
| | - Sudipti Arora
- Dr. B. Lal Institute of Biotechnology, 6E, Malviya Industrial Area, Malviya Nagar, Jaipur 302017, India
| | - Manish Kumar
- Sustainability Cluster, School of Engineering, University of Petroleum & Energy Studies, Dehradun, Uttarakhand 248007, India
| | - Samendra P Sherchan
- Department of Environmental health sciences, Tulane University, New Orleans, LA 70112, USA; Bioenvironmental Science Program, Morgan Staate University, Baltimore, MD 21251, USA
| | - Ryo Honda
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa 920-1192, Japan
| | - Greg Jackson
- Queensland Alliance for Environmental Health Sciences, The University of Queensland, Woollongabba, Queensland 4072, Australia
| | - Stephen P Luby
- Stanford Center for Innovation in Global Health, and Stanford Woods Institute for the Environment, Stanford University, Stanford, CA 94305, USA
| | - Guangming Jiang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia; Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, Australia.
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29
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SARS-CoV-2 Viral Load in the Pulmonary Compartment of Critically Ill COVID-19 Patients Correlates with Viral Serum Load and Fatal Outcomes. Viruses 2022; 14:v14061292. [PMID: 35746764 PMCID: PMC9228931 DOI: 10.3390/v14061292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/10/2022] [Indexed: 02/07/2023] Open
Abstract
While SARS-CoV-2 detection in sputum and swabs from the upper respiratory tract has been used as a diagnostic tool, virus quantification showed poor correlation to disease outcome and thus, poor prognostic value. Although the pulmonary compartment represents a relevant site for viral load analysis, limited data exploring the lower respiratory tract is available, and its association to clinical outcomes is relatively unknown. Using bronchoalveolar lavage (BAL) and serum samples, we quantified SARS-CoV-2 copy numbers in the pulmonary and systemic compartments of critically ill patients admitted to the intensive care unit of a COVID-19 referral hospital in Croatia during the second and third pandemic waves. Clinical data, including 30-day survival after ICU admission, were included. We found that elevated SARS-CoV-2 copy numbers in both BAL and serum samples were associated with fatal outcomes. Remarkably, the highest and earliest viral loads after initiation of mechanical ventilation support were increased in the non-survival group. Our results imply that viral loads in the lungs contribute to COVID-19 disease severity, while blood titers correlate with lung virus titers, albeit at a lower level. Moreover, they suggest that BAL SARS-CoV-2 copy number quantification at ICU admission may provide a predictive parameter of clinical COVID-19 outcomes.
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30
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Possible Cross-Reactivity of Feline and White-Tailed Deer Antibodies against the SARS-CoV-2 Receptor Binding Domain. J Virol 2022; 96:e0025022. [PMID: 35352999 PMCID: PMC9044950 DOI: 10.1128/jvi.00250-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In late 2019, a novel coronavirus began circulating within humans in central China. It was designated SARS-CoV-2 because of its genetic similarities to the 2003 SARS coronavirus (SARS-CoV). Now that SARS-CoV-2 has spread worldwide, there is a risk of it establishing new animal reservoirs and recombination with native circulating coronaviruses. To screen local animal populations in the United States for exposure to SARS-like coronaviruses, we developed a serological assay using the receptor binding domain (RBD) from SARS-CoV-2. SARS-CoV-2's RBD is antigenically distinct from common human and animal coronaviruses, allowing us to identify animals previously infected with SARS-CoV or SARS-CoV-2. Using an indirect enzyme-linked immunosorbent assay (ELISA) for SARS-CoV-2's RBD, we screened serum from wild and domestic animals for the presence of antibodies against SARS-CoV-2's RBD. Surprisingly prepandemic feline serum samples submitted to the University of Tennessee Veterinary Hospital were ∼50% positive for anti-SARS RBD antibodies. Some of these samples were serologically negative for feline coronavirus (FCoV), raising the question of the etiological agent generating anti-SARS-CoV-2 RBD cross-reactivity. We also identified several white-tailed deer from South Carolina with anti-SARS-CoV-2 antibodies. These results are intriguing, as cross-reactive antibodies toward SARS-CoV-2 RBD have not been reported to date. The etiological agent responsible for seropositivity was not readily apparent, but finding seropositive cats prior to the current SARS-CoV-2 pandemic highlights our lack of information about circulating coronaviruses in other species. IMPORTANCE We report cross-reactive antibodies from prepandemic cats and postpandemic South Carolina white-tailed deer that are specific for that SARS-CoV RBD. There are several potential explanations for this cross-reactivity, each with important implications to coronavirus disease surveillance. Perhaps the most intriguing possibility is the existence and transmission of an etiological agent (such as another coronavirus) with similarity to SARS-CoV-2's RBD region. However, we lack conclusive evidence of prepandemic transmission of a SARS-like virus. Our findings provide impetus for the adoption of a One Health Initiative focusing on infectious disease surveillance of multiple animal species to predict the next zoonotic transmission to humans and future pandemics.
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Zandi M, Soltani S, Tabibzadeh A, Nasimzadeh S, Behboudi E, Zakeri A, Erfani Y, Salmanzadeh S, Abbasi S. Partial sequence conservation of SARS-CoV-2 NSP-2, NSP-12, and Spike in stool samples from Abadan, Iran. Biotechnol Appl Biochem 2022; 70:201-209. [PMID: 35396867 PMCID: PMC9082511 DOI: 10.1002/bab.2343] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/28/2022] [Indexed: 11/09/2022]
Abstract
Since the onset of the coronavirus disease 2019 (COVID-19) pandemic, the clinical manifestations of the virus have undergone many changes. Recently, there have been many reports on gastrointestinal symptoms in COVID-19 patients. This study is aimed to perform a detailed phylogenetic study and assessment of different SNVs in the RNA genome of viruses isolated from fecal samples of patients with COVID-19 who have gastrointestinal symptoms, which can help better understand viral pathogenesis. In the present study, 20 fecal samples were collected by written consent from COVID-19 patients. According to the manufacturer's protocol, virus nucleic acid was extracted from stool samples and the SARS-CoV-2 genome presence in stool samples was confirmed by RT-PCR assay. Three viral genes, S, nsp12, and nsp2, were amplified using the reverse transcription polymerase chain reaction (RT-PCR) method and specific primers. Multiple sequencing alignment (MSA) was performed in the CLC word bench, and a phylogenetic tree was generated by MEGA X based on the neighbor-joining method. Of all cases, 11 (55%) were males. The mean age of the patients was 33.6 years. Diabetes (70%) and blood pressure (55%) were the most prevalent comorbidities. All 20 patients were positive for SARS-CoV-2 infection in respiratory samples. Molecular analysis investigation among 20 stool samples revealed that the SARS-CoV-2 genome was found among 10 stool samples; only three samples were used for sequencing. The polymorphism and phylogenetic analysis in SARS-CoV-2 showed great similarity among all of the evaluated genes with the Wuhan reference sequence and all of the current variants of concern (VOCs). The current study represents a great similarity in polymorphism and phylogenetic analysis of the SARS-CoV-2 isolates with the Wuhan reference sequence and all of the current VOC in the particular evaluated partial sequences of S, nsp12, and nsp2.
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Affiliation(s)
- Milad Zandi
- Department of VirologySchool of Public HealthTehran University of Medical SciencesTehranIran
| | - Saber Soltani
- Department of VirologySchool of Public HealthTehran University of Medical SciencesTehranIran
| | | | - Sepideh Nasimzadeh
- Department of Medical VirologySchool of MedicineAhvaz Jundishapur University of Medical SciencesAhvazIran
| | - Emad Behboudi
- Department of MicrobiologyGolestan University of Medical SciencesGorganIran
| | - Armin Zakeri
- Department of HematologyFaculty of Medical SciencesTarbiat Modares UniversityTehranIran
| | - Yousef Erfani
- Department of Medical Laboratory SciencesSchool of Allied Medical SciencesTehran University Medical SciencesTehranIran
| | - Shokrollah Salmanzadeh
- Health Research InstituteInfectious and Tropical Diseases Research CenterAhvaz Jundishapur University of Medical SciencesAhvazIran
| | - Samaneh Abbasi
- Department of MicrobiologySchool of MedicineAbadan University of Medical SciencesAbadanIran
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32
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Monteiro S, Rente D, Cunha MV, Marques TA, Cardoso E, Vilaça J, Coelho N, Brôco N, Carvalho M, Santos R. Discrimination and surveillance of infectious severe acute respiratory syndrome Coronavirus 2 in wastewater using cell culture and RT-qPCR. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152914. [PMID: 34999067 PMCID: PMC8733236 DOI: 10.1016/j.scitotenv.2022.152914] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/10/2021] [Accepted: 12/31/2021] [Indexed: 05/04/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA has been extensively detected in raw wastewater in studies exploring wastewater-based epidemiology (WBE) for early warning purposes. Nonetheless, only a few limited studies investigated the presence of SARS-CoV-2 in treated wastewaters to determine the potential health risks across the water cycle. The detection of SARS-CoV-2 has been done mostly by RT-qPCR and ddPCR, which only provides information on the presence of nucleic acids rather than information on potential infectivity. In this study, we set to develop and evaluate the use of viability RT-qPCR for the selective discrimination and surveillance of infectious SARS-CoV-2 in secondary-treated wastewater. Enzymatic (nuclease) and viability dye (Reagent D) pretreatments were applied to infer infectivity through RT-qPCR using porcine epidemic diarrhea virus (PEDV) as a CoV surrogate. Infectivity tests were first performed on PEDV purified RNA, then on infectious and heat-inactivated PEDV, and finally on heat inactivated PEDV spiked in concentrated secondary-treated wastewater. The two viability RT-qPCR methods were then applied to 27 secondary-treated wastewater samples positive for SARS-CoV-2 RNA at the outlet of five large urban wastewater treatment plants in Portugal. Reagent D pretreatment showed similar behavior to cell culture for heat-inactivated PEDV and both viability RT-qPCR methods performed comparably to VERO E6 cell culture for SARS-CoV-2 present in secondary-treated wastewater, eliminating completely the RT-qPCR signal. Our study demonstrated the lack of infectious SARS-CoV-2 viral particles on secondary-treated wastewater through the application of two pretreatment methods for the rapid inference of infectivity through RT-qPCR, showing their potential application in environmental screening. This study addressed a knowledge gap on the public health risks of SARS-CoV-2 across the water cycle.
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Affiliation(s)
- Silvia Monteiro
- Laboratorio de Análises, Tecnico Lisboa, Universidade de Lisboa, Lisboa, Portugal.
| | - Daniela Rente
- Laboratorio de Análises, Tecnico Lisboa, Universidade de Lisboa, Lisboa, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Tiago A Marques
- Centre for Research into Ecological and Environmental Modelling, The Observatory, University of St Andrews, St Andrews KY16 9LZ, Scotland; Centro de Estatística e Aplicações, Departamento de Biologia Ambiental, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Eugénia Cardoso
- Águas do Tejo Atlântico, Fábrica de Águas de Alcântara, Avenida de Ceuta, 1300-254 Lisboa, Portugal
| | - João Vilaça
- SIMDOURO, ETAR de Gaia Litoral, 4400-356 Canidelo, Portugal
| | | | - Nuno Brôco
- AdP VALOR, Serviços Ambientais, S.A., Rua Visconde de Seabra, 3, 1700-421 Lisboa, Portugal
| | - Marta Carvalho
- AdP VALOR, Serviços Ambientais, S.A., Rua Visconde de Seabra, 3, 1700-421 Lisboa, Portugal
| | - Ricardo Santos
- Laboratorio de Análises, Tecnico Lisboa, Universidade de Lisboa, Lisboa, Portugal
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33
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Abayomi-Alli OO, Damaševičius R, Maskeliūnas R, Misra S. An Ensemble Learning Model for COVID-19 Detection from Blood Test Samples. SENSORS 2022; 22:s22062224. [PMID: 35336395 PMCID: PMC8955536 DOI: 10.3390/s22062224] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/28/2022] [Accepted: 03/10/2022] [Indexed: 02/04/2023]
Abstract
Current research endeavors in the application of artificial intelligence (AI) methods in the diagnosis of the COVID-19 disease has proven indispensable with very promising results. Despite these promising results, there are still limitations in real-time detection of COVID-19 using reverse transcription polymerase chain reaction (RT-PCR) test data, such as limited datasets, imbalance classes, a high misclassification rate of models, and the need for specialized research in identifying the best features and thus improving prediction rates. This study aims to investigate and apply the ensemble learning approach to develop prediction models for effective detection of COVID-19 using routine laboratory blood test results. Hence, an ensemble machine learning-based COVID-19 detection system is presented, aiming to aid clinicians to diagnose this virus effectively. The experiment was conducted using custom convolutional neural network (CNN) models as a first-stage classifier and 15 supervised machine learning algorithms as a second-stage classifier: K-Nearest Neighbors, Support Vector Machine (Linear and RBF), Naive Bayes, Decision Tree, Random Forest, MultiLayer Perceptron, AdaBoost, ExtraTrees, Logistic Regression, Linear and Quadratic Discriminant Analysis (LDA/QDA), Passive, Ridge, and Stochastic Gradient Descent Classifier. Our findings show that an ensemble learning model based on DNN and ExtraTrees achieved a mean accuracy of 99.28% and area under curve (AUC) of 99.4%, while AdaBoost gave a mean accuracy of 99.28% and AUC of 98.8% on the San Raffaele Hospital dataset, respectively. The comparison of the proposed COVID-19 detection approach with other state-of-the-art approaches using the same dataset shows that the proposed method outperforms several other COVID-19 diagnostics methods.
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Affiliation(s)
- Olusola O. Abayomi-Alli
- Department of Software Engineering, Kaunas University of Technology, 51368 Kaunas, Lithuania;
| | - Robertas Damaševičius
- Department of Software Engineering, Kaunas University of Technology, 51368 Kaunas, Lithuania;
- Correspondence:
| | - Rytis Maskeliūnas
- Department of Multimedia Engineering, Kaunas University of Technology, 51368 Kaunas, Lithuania;
| | - Sanjay Misra
- Department of Computer Science and Communication, Ostfold University College, 3001 Halden, Norway;
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34
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Xiao F, Wan P, Wei Q, Wei G, Yu Y. Prolonged fecal shedding of SARS-CoV-2 in a young immunocompetent COVID-19 patient: a case report and literature overview. J Med Virol 2022; 94:3133-3137. [PMID: 35274321 PMCID: PMC9088484 DOI: 10.1002/jmv.27694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 02/02/2022] [Accepted: 03/02/2022] [Indexed: 12/02/2022]
Abstract
Clinicians are facing several challenges in tackling coronavirus disease 2019 (COVID‐19); one issue is prolonged detection of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) RNA. Here, we describe a case of SARS‐CoV‐2 infection in a young immunocompetent patient with a virological course lasting for 71 days. Following antiviral treatment, but no additional glucocorticoid or interferon therapy, the patient recovered from COVID‐19 pneumonia (moderate). Detection of viral RNA via throat swabs showed negative results. However, the viral RNA reappeared and persisted in stool samples for an additional 27 days, while the patient remained asymptomatic and exhibited no abnormal signs. This case indicates that SARS‐CoV‐2 can result in a prolonged fecal RNA shedding, even in an immunocompetent patient with zero exposure to immunosuppressive therapies.
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Affiliation(s)
- Fang Xiao
- Department of Infectious Disease, The First Affiliated Hospital of Guangxi Medical University
| | - Peiqi Wan
- Department of Infectious Disease, The First Affiliated Hospital of Guangxi Medical University
| | - Qiuling Wei
- Department of Infectious Disease, Guangxi Duan Yao Autonomous County People's Hospital
| | - Guiyang Wei
- Department of Infectious Disease, Guangxi Duan Yao Autonomous County People's Hospital
| | - Yanhong Yu
- Department of Infectious Disease, The First Affiliated Hospital of Guangxi Medical University
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35
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Li YS, Ren HC, Cao JH. Correlation of SARS‑CoV‑2 to cancer: Carcinogenic or anticancer? (Review). Int J Oncol 2022; 60:42. [PMID: 35234272 PMCID: PMC8923649 DOI: 10.3892/ijo.2022.5332] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 12/15/2021] [Indexed: 11/05/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly infectious and pathogenic. Among patients with severe SARS-CoV-2-caused by corona virus disease 2019 (COVID-19), those complicated with malignant tumor are vulnerable to COVID-19 due to compromised immune function caused by tumor depletion, malnutrition and anti-tumor treatment. Cancer is closely related to the risk of severe illness and mortality in patients with COVID-19. SARS-CoV-2 could promote tumor progression and stimulate metabolism switching in tumor cells to initiate tumor metabolic modes with higher productivity efficiency, such as glycolysis, for facilitating the massive replication of SARS-CoV-2. However, it has been shown that infection with SARS-CoV-2 leads to a delay in tumor progression of patients with natural killer cell (NK cell) lymphoma and Hodgkin's lymphoma, while SARS-CoV-2 elicited anti-tumor immune response may exert a potential oncolytic role in lymphoma patients. The present review briefly summarized potential carcinogenicity and oncolytic characteristics of SARS-CoV-2 as well as strategies to protect patients with cancer during the COVID-19 pandemic.
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Affiliation(s)
- Ying-Shuang Li
- Intravenous Drug Administration Center, Department of Pharmacy, The Third People's Hospital of Qingdao, Qingdao, Shandong 266041, P.R. China
| | - Hua-Cheng Ren
- Intravenous Drug Administration Center, Department of Pharmacy, The Third People's Hospital of Qingdao, Qingdao, Shandong 266041, P.R. China
| | - Jian-Hua Cao
- Intravenous Drug Administration Center, Department of Pharmacy, The Third People's Hospital of Qingdao, Qingdao, Shandong 266041, P.R. China
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36
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Yavarian J, Javaherian M, Malekshahi SS, Ahmadinejad Z, Ghiasvand F, Ahmadi E, Abbasian L, Malihe Hasannezhad MH, Dabaghipour N, Shafiei-Jandaghi NZ, Mokhtari-Azad T, Hajiabdolbaghi M. The Persistence Time of SARS-CoV-2 RNA in hospitalized COVID-19 Patients: A prospective Study. Infect Disord Drug Targets 2022; 22:56-61. [PMID: 35209824 DOI: 10.2174/1871526522666220223162445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/06/2021] [Accepted: 12/02/2021] [Indexed: 01/08/2023]
Abstract
BACKGROUND In the late December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), the causative agent of coronavirus disease 2019 (COVID-19), spreads to almost all countries worldwide. The outbreak of this virus has also been confirmed since 19 February 2020 in Iran. OBJECTIVE The aim of this study was to investigate the time of viral RNA clearance in swab and serum samples of COVID-19 patients who received different medications. We also evaluated different factors that may be affected viral RNA persistence in patients infected by SARS-CoV-2. METHODS In March 2020, twenty-one hospitalized COVID-19 patients were participated in this prospective study. All patients received antiviral agents in their routine care. Throat swabs and blood samples were obtained from all patients in different intervals including day 3 or 5, day 7, day 10 and finally 14 days after the first positive real time RT-PCR (rRT-PCT) test Results: The median time from the SO to first negative rRT-PCR results for throat swabs and serum samples of COVID-19 patients were 18 and 14 days, respectively. These times were more significant in patients with lymphopenia, oxygen saturation ≤ 90% and comorbidity. CONCLUSION This preliminary study highlights that SASR-CoV-2 RNA was not detectable in the upper respiratory tract longer than three weeks. In addition, SARS-CoV may persist for a long period of time in the respiratory than the serum samples. This study support the idea that in the settings of limited resources the patients should cease to be tested earlier than three weeks for discharge management.
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Affiliation(s)
- Jila Yavarian
- Virology department Tehran University of Medical Sciences Iran
| | - Mohammad Javaherian
- Liver Transplantation Research Center Tehran University of Medical Sciences Iran
| | | | - Zahra Ahmadinejad
- Department of infectious diseases, Tehran University of Medical Sciences iran
| | - Fatemeh Ghiasvand
- Department of infectious diseases, Tehran University of Medical Sciences iran
| | | | - Ladan Abbasian
- Department of infectious diseases, Tehran University of Medical Sciences Iran
| | | | - Narges Dabaghipour
- Tehran University of Medical Sciences Liver Transplantation Research Center Iran
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Kidney Injury in COVID-19: Epidemiology, Molecular Mechanisms, and Potential Therapeutic Targets. Int J Mol Sci 2022; 23:ijms23042242. [PMID: 35216358 PMCID: PMC8877127 DOI: 10.3390/ijms23042242] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 01/08/2023] Open
Abstract
As of December 2021, SARS-CoV-2 had caused over 250 million infections and 5 million deaths worldwide. Furthermore, despite the development of highly effective vaccines, novel variants of SARS-CoV-2 continue to sustain the pandemic, and the search for effective therapies for COVID-19 remains as urgent as ever. Though the primary manifestation of COVID-19 is pneumonia, the disease can affect multiple organs, including the kidneys, with acute kidney injury (AKI) being among the most common extrapulmonary manifestations of severe COVID-19. In this article, we start by reflecting on the epidemiology of kidney disease in COVID-19, which overwhelmingly demonstrates that AKI is common in COVID-19 and is strongly associated with poor outcomes. We also present emerging data showing that COVID-19 may result in long-term renal impairment and delve into the ongoing debate about whether AKI in COVID-19 is mediated by direct viral injury. Next, we focus on the molecular pathogenesis of SARS-CoV-2 infection by both reviewing previously published data and presenting some novel data on the mechanisms of cellular viral entry. Finally, we relate these molecular mechanisms to a series of therapies currently under investigation and propose additional novel therapeutic targets for COVID-19.
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Development of an in vitro model for animal species susceptibility to SARS-CoV-2 replication based on expression of ACE2 and TMPRSS2 in avian cells. Virology 2022; 569:1-12. [PMID: 35217403 PMCID: PMC8837912 DOI: 10.1016/j.virol.2022.01.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/26/2022] [Accepted: 01/26/2022] [Indexed: 01/06/2023]
Abstract
The SARS-CoV-2 (SARS-CoV-2) virus has caused a worldwide pandemic because of the virus's ability to transmit efficiently human-to-human. A key determinant of infection is the attachment of the viral spike protein to the host receptor angiotensin-converting enzyme 2 (ACE2). Because of the presumed zoonotic origin of SARS-CoV-2, there is no practical way to assess the susceptibility of every species to SARS-CoV-2 by direct challenge studies. In an effort to have a better predictive model of animal host susceptibility to SARS-CoV-2, we expressed the ACE2 and/or transmembrane serine protease 2 (TMPRSS2) genes from humans and other animal species in the avian fibroblast cell line, DF1, that is not permissive to infection. We demonstrated that expression of both human ACE2 and TMPRSS2 genes is necessary to support SARS-CoV-2 infection and replication in DF1 and a non-permissive sub-lineage of MDCK cells. Titers of SARS-CoV-2 in these cell lines were comparable to those observed in control Vero cells. To further test the model, we developed seven additional transgenic cell lines expressing the ACE2 and TMPRSS2 derived from Felis catus (cat), Equus caballus (horse), Sus domesticus (pig), Capra hircus (goat), Mesocricetus auratus (Golden hamster), Myotis lucifugus (Little Brown bat) and Hipposideros armiger (Great Roundleaf bat) in DF1 cells. Results demonstrate permissive replication of SARS-CoV-2 in cat, Golden hamster, and goat species, but not pig or horse, which correlated with the results of reported challenge studies. Cells expressing genes from either bat species tested demonstrated temporal replication of SARS-CoV-2 that peaked early and was not sustained. The development of this cell culture model allows for more efficient testing of the potential susceptibility of many different animal species for SARS-CoV-2 and emerging variant viruses.
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SARS-CoV-2 loads in urine, sera and stool specimens in association with clinical features of COVID-19 patients. JOURNAL OF CLINICAL VIROLOGY PLUS 2022; 2:100059. [PMID: 35262032 PMCID: PMC8673951 DOI: 10.1016/j.jcvp.2021.100059] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/30/2021] [Accepted: 12/13/2021] [Indexed: 12/19/2022] Open
Abstract
Background Study design Results Conclusion
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40
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Zanchettin AM, Facciotti F. A collaborative robotic solution to partly automate SARS-CoV-2 serological tests in small facilities. SLAS Technol 2022; 27:100-106. [PMID: 35058214 PMCID: PMC8545608 DOI: 10.1016/j.slast.2021.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The outbreak of COVID-19 has introduced a significant stress on the healthcare systems of many countries. The availability of quick and reliable screening methodologies can be regarded as the keystone approach to mitigate the spread of the infection until mass vaccination campaigns will be made available to the population. In this scenario, robotics technology can serve as a substantial help in clinical laboratories to speed up the activities. This work describes in the details a collaborative robotics application developed in partnership with a clinical hospital and a robot manufacturer to partly automate SARS-CoV-2 quantitative serological tests. This technology can be particularly beneficial for small laboratory facilities to alleviate technicians from performing repetitive operations. By automating part of the operations, the overall throughput can be increased of 66%, while the amount of possibly harmful pipetting activities performed by the human can be reduced of 62%.
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Affiliation(s)
- Andrea Maria Zanchettin
- Politecnico di Milano, Dipartimento di Elettronica, Informazione e Bioingegneria, Piazza Leonardo Da Vinci 32, Milano, Italy.
| | - Federica Facciotti
- Istituto Europeo di Oncologia IRCCS, Dipartimento di Oncologia Sperimentale, via Ripamonti 435, Milano, Italy.
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41
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Sobsey MD. Absence of virological and epidemiological evidence that SARS-CoV-2 poses COVID-19 risks from environmental fecal waste, wastewater and water exposures. JOURNAL OF WATER AND HEALTH 2022; 20:126-138. [PMID: 35100160 DOI: 10.2166/wh.2021.182] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This review considers evidence for infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presence and COVID-19 infection and illness resulting from exposure to environmental fecal wastes and waters. There is no documented evidence that (1) infectious, replication-capable SARS-CoV-2 is present in environmental fecal wastes, wastewater or water, and (2) well-documented epidemiological evidence of COVID-19 infection, illness or death has never been reported for these exposure media. COVID-19 is transmitted mainly by direct personal contact and respiratory secretions as airborne droplets and aerosols, and less so by respiratory-secreted fomites via contact (touch) exposures. While SARS-CoV-2 often infects the gastrointestinal tract of infected people, its presence as infectious, replication-capable virus in environmental fecal wastes and waters has never been documented. There is only rare and unquantified evidence of infectious, replication-capable SARS-CoV-2 in recently shed feces of COVID-19 hospital patients. The human infectivity dose-response relationship of SARS-CoV-2 is unknown, thereby making it impossible to estimate evidence-based quantitative health effects assessments by quantitative microbial risk assessment methods requiring both known exposure assessment and health effects assessment data. The World Health Organization, Water Environment Federation, US Centers for Disease Control and Prevention and others do not consider environmental fecal wastes and waters as sources of exposure to infectious SARS-CoV-2 causing COVID-19 infection and illness.
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Affiliation(s)
- Mark D Sobsey
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599-7431, USA E-mail:
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42
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Helms L, Marchiano S, Stanaway IB, Hsiang TY, Juliar BA, Saini S, Zhao YT, Khanna A, Menon R, Alakwaa F, Mikacenic C, Morrell ED, Wurfel MM, Kretzler M, Harder JL, Murry CE, Himmelfarb J, Ruohola-Baker H, Bhatraju PK, Gale M, Freedman BS. Cross-validation of SARS-CoV-2 responses in kidney organoids and clinical populations. JCI Insight 2021; 6:e154882. [PMID: 34767537 PMCID: PMC8783682 DOI: 10.1172/jci.insight.154882] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/10/2021] [Indexed: 11/17/2022] Open
Abstract
Kidneys are critical target organs of COVID-19, but susceptibility and responses to infection remain poorly understood. Here, we combine SARS-CoV-2 variants with genome-edited kidney organoids and clinical data to investigate tropism, mechanism, and therapeutics. SARS-CoV-2 specifically infects organoid proximal tubules among diverse cell types. Infections produce replicating virus, apoptosis, and disrupted cell morphology, features of which are revealed in the context of polycystic kidney disease. Cross-validation of gene expression patterns in organoids reflects proteomic signatures of COVID-19 in the urine of critically ill patients indicating interferon pathway upregulation. SARS-CoV-2 viral variants alpha, beta, gamma, kappa, and delta exhibit comparable levels of infection in organoids. Infection is ameliorated in ACE2-/- organoids and blocked via treatment with de novo-designed spike binder peptides. Collectively, these studies clarify the impact of kidney infection in COVID-19 as reflected in organoids and clinical populations, enabling assessment of viral fitness and emerging therapies.
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Affiliation(s)
- Louisa Helms
- Department of Medicine
- Division of Nephrology
- Kidney Research Institute
- Institute for Stem Cell and Regenerative Medicine
- Department of Laboratory Medicine and Pathology
| | - Silvia Marchiano
- Department of Medicine
- Institute for Stem Cell and Regenerative Medicine
- Department of Laboratory Medicine and Pathology
- Division of Cardiology
- Center for Cardiovascular Biology
| | - Ian B. Stanaway
- Department of Medicine
- Division of Nephrology
- Kidney Research Institute
| | - Tien-Ying Hsiang
- Center for Innate Immunity and Immune Disease, Department of Immunology
| | - Benjamin A. Juliar
- Department of Medicine
- Division of Nephrology
- Kidney Research Institute
- Institute for Stem Cell and Regenerative Medicine
| | - Shally Saini
- Institute for Stem Cell and Regenerative Medicine
- Department of Biochemistry; and
| | - Yan Ting Zhao
- Institute for Stem Cell and Regenerative Medicine
- Department of Biochemistry; and
- Department of Oral Health Sciences, School of Dentistry, University of Washington School of Medicine, Seattle, Washington, USA
| | - Akshita Khanna
- Institute for Stem Cell and Regenerative Medicine
- Department of Laboratory Medicine and Pathology
- Center for Cardiovascular Biology
| | - Rajasree Menon
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Fadhl Alakwaa
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Carmen Mikacenic
- Department of Medicine
- Translational Research, Benaroya Research Institute, Seattle, Washington, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Eric D. Morrell
- Department of Medicine
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Mark M. Wurfel
- Department of Medicine
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Jennifer L. Harder
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Charles E. Murry
- Department of Medicine
- Institute for Stem Cell and Regenerative Medicine
- Department of Laboratory Medicine and Pathology
- Division of Cardiology
- Center for Cardiovascular Biology
- Sana Biotechnology, Seattle, Washington, USA
| | | | - Hannele Ruohola-Baker
- Institute for Stem Cell and Regenerative Medicine
- Department of Biochemistry; and
- Department of Oral Health Sciences, School of Dentistry, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Pavan K. Bhatraju
- Department of Medicine
- Kidney Research Institute
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Michael Gale
- Center for Innate Immunity and Immune Disease, Department of Immunology
| | - Benjamin S. Freedman
- Department of Medicine
- Division of Nephrology
- Kidney Research Institute
- Institute for Stem Cell and Regenerative Medicine
- Department of Laboratory Medicine and Pathology
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
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Ferreira BIDS, da Silva-Gomes NL, Coelho WLDCNP, da Costa VD, Carneiro VCDS, Kader RL, Amaro MP, Villar LM, Miyajima F, Alves-Leon SV, de Paula VS, Leon LAA, Moreira OC. Validation of a novel molecular assay to the diagnostic of COVID-19 based on real time PCR with high resolution melting. PLoS One 2021; 16:e0260087. [PMID: 34807915 PMCID: PMC8608302 DOI: 10.1371/journal.pone.0260087] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/03/2021] [Indexed: 01/12/2023] Open
Abstract
The emergence of the COVID-19 pandemic resulted in an unprecedented need for RT-qPCR-based molecular diagnostic testing, placing a strain on the supply chain and the availability of commercially available PCR testing kits and reagents. The effect of limited molecular diagnostics-related supplies has been felt across the globe, disproportionally impacting molecular diagnostic testing in developing countries where acquisition of supplies is limited due to availability. The increasing global demand for commercial molecular diagnostic testing kits and reagents has made standard PCR assays cost prohibitive, resulting in the development of alternative approaches to detect SARS-CoV-2 in clinical specimens, circumventing the need for commercial diagnostic testing kits while mitigating the high-demand for molecular diagnostics testing. The timely availability of the complete SARS-CoV-2 genome in the beginning of the COVID-19 pandemic facilitated the rapid development and deployment of specific primers and standardized laboratory protocols for the molecular diagnosis of COVID-19. An alternative method offering a highly specific manner of detecting and genotyping pathogens within clinical specimens is based on the melting temperature differences of PCR products. This method is based on the melting temperature differences between purine and pyrimidine bases. Here, RT-qPCR assays coupled with a High Resolution Melting analysis (HRM-RTqPCR) were developed to target different regions of the SARS-CoV-2 genome (RdRp, E and N) and an internal control (human RNAse P gene). The assays were validated using synthetic sequences from the viral genome and clinical specimens (nasopharyngeal swabs, serum and saliva) of sixty-five patients with severe or moderate COVID-19 from different states within Brazil; a larger validation group than that used in the development to the commercially available TaqMan RT-qPCR assay which is considered the gold standard for COVID-19 testing. The sensitivity of the HRM-RTqPCR assays targeting the viral N, RdRp and E genes were 94.12, 98.04 and 92.16%, with 100% specificity to the 3 SARS-CoV-2 genome targets, and a diagnostic accuracy of 95.38, 98.46 and 93.85%, respectively. Thus, HRM-RTqPCR emerges as an attractive alternative and low-cost methodology for the molecular diagnosis of COVID-19 in restricted-budget laboratories.
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Affiliation(s)
- Beatriz Iandra da Silva Ferreira
- Real Time PCR Platform RPT09A, Laboratory of Molecular Biology and Endemic Diseases, Oswaldo Cruz Institute/ Fiocruz, Rio de Janeiro, Brazil
| | - Natália Lins da Silva-Gomes
- Real Time PCR Platform RPT09A, Laboratory of Molecular Biology and Endemic Diseases, Oswaldo Cruz Institute/ Fiocruz, Rio de Janeiro, Brazil
| | | | | | | | - Rafael Lopes Kader
- University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marisa Pimentel Amaro
- University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lívia Melo Villar
- Laboratory of Viral Hepatitis, Oswaldo Cruz Institute/ Fiocruz, Rio de Janeiro, Brazil
| | - Fábio Miyajima
- Oswaldo Cruz Foundation (Fiocruz), Branch Ceará, Eusebio, Brazil
| | - Soniza Vieira Alves-Leon
- University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Luciane Almeida Amado Leon
- Laboratory of Technological Development in Virology, Oswaldo Cruz Institute/ Fiocruz, Rio de Janeiro, Brazil
| | - Otacilio Cruz Moreira
- Real Time PCR Platform RPT09A, Laboratory of Molecular Biology and Endemic Diseases, Oswaldo Cruz Institute/ Fiocruz, Rio de Janeiro, Brazil
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Chiem C, Alghamdi K, Nguyen T, Han JH, Huo H, Jackson D. The Impact of COVID-19 on Blood Transfusion Services: A Systematic Review and Meta-Analysis. Transfus Med Hemother 2021; 30:1-12. [PMID: 34934412 PMCID: PMC8678226 DOI: 10.1159/000519245] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 08/08/2021] [Indexed: 01/28/2023] Open
Abstract
Introduction While SARS-CoV-2's main transmission route is through respiratory droplets, research has found that viral RNA could be detected in blood samples, causing concerns over the safety of blood donations and blood products. This paper therefore aims to systematically search for studies that have addressed their country's lack of donations and analyse the risk of blood transfusion-transmission. As such, it will answer the question "should blood services focus more on donation vigilance or worry more about the risks of transmission through blood products?" Methods 38 articles were identified through a systematic review adopting the PRISMA and STROBE guidelines. Meta-analysis was conducted using OpenMeta software. Results The average decrease in blood donations was found to be 38%, with some regions showing up to 67% decrease. To assess the risk of actual blood transfusion-transmission, three datasets were analysed. Firstly, the viral load in COVID-19 patients was studied and found to have less than 1% detection rate (ARD = -0.831, 95% -0.963, -0.699). Secondly, the prevalence of finding viral RNA in a pool of donations was nearly -1.503 (ARD = -1.538, -1.468). Lastly, recipients who were given blood products of positive donors were found to be -0.911 (ARD 95% = -1.247, -0.575). Discussion/Conclusion Blood centres should focus more on launching initiatives and policies that would increase their countries' blood supply as the virus has no direct threat to blood safety.
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Affiliation(s)
- Cindy Chiem
- Laboratory Medicine, School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
| | - Khader Alghamdi
- Laboratory Medicine, School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
| | - Thao Nguyen
- Laboratory Medicine, School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
| | - Joon Hee Han
- Laboratory Medicine, School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
| | - Hongzhao Huo
- Laboratory Medicine, School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
| | - Denise Jackson
- Laboratory Medicine, School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
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45
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Guaman-Bautista LP, Moreta-Urbano E, Oña-Arias CG, Torres-Arias M, Kyriakidis NC, Malcı K, Jonguitud-Borrego N, Rios-Solis L, Ramos-Martinez E, López-Cortés A, Barba-Ostria C. Tracking SARS-CoV-2: Novel Trends and Diagnostic Strategies. Diagnostics (Basel) 2021; 11:1981. [PMID: 34829328 PMCID: PMC8621220 DOI: 10.3390/diagnostics11111981] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/18/2021] [Accepted: 09/23/2021] [Indexed: 12/26/2022] Open
Abstract
The COVID-19 pandemic has had an enormous impact on economies and health systems globally, therefore a top priority is the development of increasingly better diagnostic and surveillance alternatives to slow down the spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In order to establish massive testing and contact tracing policies, it is crucial to have a clear view of the diagnostic options available and their principal advantages and drawbacks. Although classical molecular methods such as RT-qPCR are broadly used, diagnostic alternatives based on technologies such as LAMP, antigen, serological testing, or the application of novel technologies such as CRISPR-Cas for diagnostics, are also discussed. The present review also discusses the most important automation strategies employed to increase testing capability. Several serological-based diagnostic kits are presented, as well as novel nanotechnology-based diagnostic methods. In summary, this review provides a clear diagnostic landscape of the most relevant tools to track COVID-19.
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Affiliation(s)
- Linda P. Guaman-Bautista
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito 170147, Ecuador; (L.P.G.-B.); (E.M.-U.); (C.G.O.-A.)
| | - Erick Moreta-Urbano
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito 170147, Ecuador; (L.P.G.-B.); (E.M.-U.); (C.G.O.-A.)
| | - Claudia G. Oña-Arias
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito 170147, Ecuador; (L.P.G.-B.); (E.M.-U.); (C.G.O.-A.)
| | - Marbel Torres-Arias
- Immunology and Virology Laboratory, Department of Life Science and Agriculture, Universidad de las Fuerzas Armadas, Quito 171103, Ecuador;
| | - Nikolaos C. Kyriakidis
- Grupo de Investigación en Biotecnología Aplicada a Biomedicina (BIOMED), Universidad de Las Américas, Quito 170125, Ecuador;
- One Health Research Group, Faculty of Medicine, Universidad de Las Américas (UDLA), Quito 170125, Ecuador
| | - Koray Malcı
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH8 9LE, UK; (K.M.); (N.J.-B.); (L.R.-S.)
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh EH8 9LE, UK
| | - Nestor Jonguitud-Borrego
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH8 9LE, UK; (K.M.); (N.J.-B.); (L.R.-S.)
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh EH8 9LE, UK
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH8 9LE, UK; (K.M.); (N.J.-B.); (L.R.-S.)
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh EH8 9LE, UK
| | - Espiridion Ramos-Martinez
- Experimental Medicine Research Unit, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 4510, Mexico;
| | - Andrés López-Cortés
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito 170147, Ecuador;
| | - Carlos Barba-Ostria
- Escuela de Medicina, Colegio de Ciencias de la Salud Quito, Universidad San Francisco de Quito USFQ, Quito 170901, Ecuador
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Basit A, Karim AM, Asif M, Ali T, Lee JH, Jeon JH, Rehman SU, Lee SH. Designing Short Peptides to Block the Interaction of SARS-CoV-2 and Human ACE2 for COVID-19 Therapeutics. Front Pharmacol 2021; 12:731828. [PMID: 34512357 PMCID: PMC8430035 DOI: 10.3389/fphar.2021.731828] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/17/2021] [Indexed: 12/18/2022] Open
Abstract
To date, the current COVID-19 pandemic caused by SARS-CoV-2 has infected 99.2 million while killed 2.2 million people throughout the world and is still spreading widely. The unavailability of potential therapeutics against this virus urges to search and develop new drugs. SARS-CoV-2 enters human cells by interacting with human angiotensin-converting enzyme 2 (ACE2) receptor expressed on human cell surface through utilizing receptor-binding domain (RBD) of its spike glycoprotein. The RBD is highly conserved and is also a potential target for blocking its interaction with human cell surface receptor. We designed short peptides on the basis of our previously reported truncated ACE2 (tACE2) for increasing the binding affinity as well as the binding interaction network with RBD. These peptides can selectively bind to RBD with much higher affinities than the cell surface receptor. Thus, these can block all the binding residues required for binding to cell surface receptor. We used selected amino acid regions (21–40 and 65–75) of ACE2 as scaffold for the de novo peptide design. Our designed peptide Pep1 showed interactions with RBD covering almost all of its binding residues with significantly higher binding affinity (−13.2 kcal mol−1) than the cell surface receptor. The molecular dynamics (MD) simulation results showed that designed peptides form a stabilized complex with RBD. We suggest that blocking the RBD through de novo designed peptides can serve as a potential candidate for COVID-19 treatment after further clinical investigations.
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Affiliation(s)
- Abdul Basit
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Asad Mustafa Karim
- Department of Bioscience and Biotechnology, The University of Suwon, Hwaseong, South Korea
| | - Muhammad Asif
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Tanveer Ali
- Department of Host Defense, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Jung Hun Lee
- National Leading Research Laboratory, Department of Biological Sciences, Myongji University, Yongin, South Korea
| | - Jeong Ho Jeon
- National Leading Research Laboratory, Department of Biological Sciences, Myongji University, Yongin, South Korea
| | - Shafiq Ur Rehman
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Sang Hee Lee
- National Leading Research Laboratory, Department of Biological Sciences, Myongji University, Yongin, South Korea
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Mencacci A, Gili A, Gidari A, Schiaroli E, Russo C, Cenci E, Camilloni B, Graziani A, Melelli-Roia A, Francisci D, Stracci F. Role of Nucleocapsid Protein Antigen Detection for Safe End of Isolation of SARS-CoV-2 Infected Patients with Long Persistence of Viral RNA in Respiratory Samples. J Clin Med 2021; 10:jcm10184037. [PMID: 34575147 PMCID: PMC8469917 DOI: 10.3390/jcm10184037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 12/23/2022] Open
Abstract
Background. In SARS-CoV-2 infection, viral RNA may persist in respiratory samples for several weeks after the resolution of symptoms. Criteria to assess the end of infectivity are not unequivocally defined. In some countries, time from diagnosis is the unique criterion used, in addition to symptom cessation. This study evaluates the role of the Lumipulse® Antigen Assay (LAA) for the safe end of isolation of patients ≥21 days after the diagnosis of infection. Methods. A total of 671 nasopharyngeal swabs from patients diagnosed with infection at least 21 days before were assessed by RT-PCR and LAA, and the role of LAA in predicting the absence of infectivity was evaluated by virus cell culture. Results. Viable virus was present in 10/138 cultured samples. Eight out of ten infective patients suffered from a concomitant disease, predisposing them to long-term shedding of infective virus. In particular, infectious virus was isolated from 10/20 RT-PCR+/LAA+ cultured samples, whereas no viable virus was found in all 118 RT-PCR+/LAA– cultured swabs. LLA and RT-PCR agreed in 484/671 (72.1%) samples, with 100% and 26.7% concordance in RT-PCR negative and positive samples, respectively. Conclusions. Viable virus can be found ≥21 days after diagnosis in immunocompromised or severely ill patients. LAA better than RT-PCR predicts non-infectivity of patients and can be safely used to end isolation in cases with long persistence of viral RNA in the respiratory tract.
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Affiliation(s)
- Antonella Mencacci
- Department of Medicine and Surgery, Microbiology and Clinical Microbiology, Santa Maria Della Misericordia” Hospital, University of Perugia, 06129 Perugia, Italy; (C.R.); (E.C.); (B.C.); (A.G.); (A.M.-R.)
- Correspondence: (A.M.); (A.G.); Tel.: +39-0755784277 (A.M.); +39-0755858033 (A.G.)
| | - Alessio Gili
- Public Health Section, Department of Medicine and Surgery, University of Perugia, 06129 Perugia, Italy;
- Correspondence: (A.M.); (A.G.); Tel.: +39-0755784277 (A.M.); +39-0755858033 (A.G.)
| | - Anna Gidari
- Department of Medicine and Surgery, Infectious Diseases Clinic, “Santa Maria della Misericordia” Hospital, University of Perugia, 06129 Perugia, Italy; (A.G.); (E.S.); (D.F.)
| | - Elisabetta Schiaroli
- Department of Medicine and Surgery, Infectious Diseases Clinic, “Santa Maria della Misericordia” Hospital, University of Perugia, 06129 Perugia, Italy; (A.G.); (E.S.); (D.F.)
| | - Carla Russo
- Department of Medicine and Surgery, Microbiology and Clinical Microbiology, Santa Maria Della Misericordia” Hospital, University of Perugia, 06129 Perugia, Italy; (C.R.); (E.C.); (B.C.); (A.G.); (A.M.-R.)
| | - Elio Cenci
- Department of Medicine and Surgery, Microbiology and Clinical Microbiology, Santa Maria Della Misericordia” Hospital, University of Perugia, 06129 Perugia, Italy; (C.R.); (E.C.); (B.C.); (A.G.); (A.M.-R.)
| | - Barbara Camilloni
- Department of Medicine and Surgery, Microbiology and Clinical Microbiology, Santa Maria Della Misericordia” Hospital, University of Perugia, 06129 Perugia, Italy; (C.R.); (E.C.); (B.C.); (A.G.); (A.M.-R.)
| | - Alessandro Graziani
- Department of Medicine and Surgery, Microbiology and Clinical Microbiology, Santa Maria Della Misericordia” Hospital, University of Perugia, 06129 Perugia, Italy; (C.R.); (E.C.); (B.C.); (A.G.); (A.M.-R.)
| | - Arduino Melelli-Roia
- Department of Medicine and Surgery, Microbiology and Clinical Microbiology, Santa Maria Della Misericordia” Hospital, University of Perugia, 06129 Perugia, Italy; (C.R.); (E.C.); (B.C.); (A.G.); (A.M.-R.)
| | - Daniela Francisci
- Department of Medicine and Surgery, Infectious Diseases Clinic, “Santa Maria della Misericordia” Hospital, University of Perugia, 06129 Perugia, Italy; (A.G.); (E.S.); (D.F.)
| | - Fabrizio Stracci
- Public Health Section, Department of Medicine and Surgery, University of Perugia, 06129 Perugia, Italy;
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48
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Hayden A, Kuentzel M, Chittur SV. Rapid, Affordable, and Scalable SARS-CoV-2 Detection From Saliva. J Biomol Tech 2021; 32:148-157. [PMID: 35027872 DOI: 10.7171/jbt.21-3203-010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Here we present an inexpensive, rapid, and robust reverse-transcription loop-mediated isothermal amplification (RT-LAMP)-based severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection method that is easily scalable, enabling point-of-care facilities and clinical labs to determine results from patients' saliva directly in 30 minutes for less than $2 per reaction. The method uses a novel combination of widely available reagents that can be prepared in bulk, plated, and frozen and remain stable until samples are received. This innovation dramatically reduces preparation time, enabling high-throughput automation and testing with time to results (including setup) in less than 1 hour for 96 patient samples simultaneously when using a 384-well format. By using a dual reporter (phenol red pH indicator for end-point detection and SYTO-9 fluorescent dye for real time), the assay also provides internal validation of results and redundancy in the event of an instrument malfunction.
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Affiliation(s)
- Andrew Hayden
- Center for Functional Genomics, University at Albany, Rensselaer, New York, USA
| | - Marcy Kuentzel
- Center for Functional Genomics, University at Albany, Rensselaer, New York, USA
| | - Sridar V Chittur
- Center for Functional Genomics, University at Albany, Rensselaer, New York, USA.,Department of Biomedical Sciences, School of Public Health, University at Albany, Rensselaer, New York, USA
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Moore KJM, Cahill J, Aidelberg G, Aronoff R, Bektaş A, Bezdan D, Butler DJ, Chittur SV, Codyre M, Federici F, Tanner NA, Tighe SW, True R, Ware SB, Wyllie AL, Afshin EE, Bendesky A, Chang CB, Dela Rosa R, Elhaik E, Erickson D, Goldsborough AS, Grills G, Hadasch K, Hayden A, Her SY, Karl JA, Kim CH, Kriegel AJ, Kunstman T, Landau Z, Land K, Langhorst BW, Lindner AB, Mayer BE, McLaughlin LA, McLaughlin MT, Molloy J, Mozsary C, Nadler JL, D'Silva M, Ng D, O'Connor DH, Ongerth JE, Osuolale O, Pinharanda A, Plenker D, Ranjan R, Rosbash M, Rotem A, Segarra J, Schürer S, Sherrill-Mix S, Solo-Gabriele H, To S, Vogt MC, Yu AD, Mason CE. Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications. J Biomol Tech 2021; 32:228-275. [PMID: 35136384 PMCID: PMC8802757 DOI: 10.7171/jbt.21-3203-017] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As the second year of the COVID-19 pandemic begins, it remains clear that a massive increase in the ability to test for SARS-CoV-2 infections in a myriad of settings is critical to controlling the pandemic and to preparing for future outbreaks. The current gold standard for molecular diagnostics is the polymerase chain reaction (PCR), but the extraordinary and unmet demand for testing in a variety of environments means that both complementary and supplementary testing solutions are still needed. This review highlights the role that loop-mediated isothermal amplification (LAMP) has had in filling this global testing need, providing a faster and easier means of testing, and what it can do for future applications, pathogens, and the preparation for future outbreaks. This review describes the current state of the art for research of LAMP-based SARS-CoV-2 testing, as well as its implications for other pathogens and testing. The authors represent the global LAMP (gLAMP) Consortium, an international research collective, which has regularly met to share their experiences on LAMP deployment and best practices; sections are devoted to all aspects of LAMP testing, including preanalytic sample processing, target amplification, and amplicon detection, then the hardware and software required for deployment are discussed, and finally, a summary of the current regulatory landscape is provided. Included as well are a series of first-person accounts of LAMP method development and deployment. The final discussion section provides the reader with a distillation of the most validated testing methods and their paths to implementation. This review also aims to provide practical information and insight for a range of audiences: for a research audience, to help accelerate research through sharing of best practices; for an implementation audience, to help get testing up and running quickly; and for a public health, clinical, and policy audience, to help convey the breadth of the effect that LAMP methods have to offer.
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Affiliation(s)
- Keith J M Moore
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | | | - Guy Aidelberg
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
| | - Rachel Aronoff
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
- Action for Genomic Integrity Through Research! (AGiR!), Lausanne, Switzerland
- Association Hackuarium, Lausanne, Switzerland
| | - Ali Bektaş
- Oakland Genomics Center, Oakland, CA 94609, USA
| | - Daniela Bezdan
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, 72076 Tübingen, Germany
- Poppy Health, Inc, San Francisco, CA 94158, USA
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital, 72076 Tübingen, Germany
| | - Daniel J Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sridar V Chittur
- Center for Functional Genomics, Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Rensselaer, 12222, USA
| | - Martin Codyre
- GiantLeap Biotechnology Ltd, Wicklow A63 Kv91, Ireland
| | - Fernan Federici
- ANID, Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | | | | | - Randy True
- FloodLAMP Biotechnologies, San Carlos, CA 94070, USA
| | - Sarah B Ware
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
- BioBlaze Community Bio Lab, 1800 W Hawthorne Ln, Ste J-1, West Chicago, IL 60185, USA
- Blossom Bio Lab, 1800 W Hawthorne Ln, Ste K-2, West Chicago, IL 60185, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Evan E Afshin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andres Bendesky
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY 10027, USA
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Connie B Chang
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, 59717, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, 59717, USA
| | - Richard Dela Rosa
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | - Eran Elhaik
- Department of Biology, Lund University, Sölvegatan 35, Lund, Sweden
| | - David Erickson
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY 14850, USA
| | | | - George Grills
- Department of Microbiology, University of Pennsylvania, Philadelphia, 19104, USA
| | - Kathrin Hadasch
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
- Department of Biology, Membrane Biophysics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
- Lab3 eV, Labspace Darmstadt, 64295 Darmstadt, Germany
- IANUS Verein für Friedensorientierte Technikgestaltung eV, 64289 Darmstadt, Germany
| | - Andrew Hayden
- Center for Functional Genomics, Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Rensselaer, 12222, USA
| | | | - Julie A Karl
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | | | | | | | - Zeph Landau
- Department of Computer Science, University of California, Berkeley, Berkeley, 94720, USA
| | - Kevin Land
- Mologic, Centre for Advanced Rapid Diagnostics, (CARD), Bedford Technology Park, Thurleigh MK44 2YA, England
- Department of Electrical, Electronic and Computer Engineering, University of Pretoria, 0028 Pretoria, South Africa
| | | | - Ariel B Lindner
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
| | - Benjamin E Mayer
- Department of Biology, Membrane Biophysics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
- Lab3 eV, Labspace Darmstadt, 64295 Darmstadt, Germany
| | | | - Matthew T McLaughlin
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | - Jenny Molloy
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, England
| | - Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jerry L Nadler
- Department of Pharmacology, New York Medical College, Valhalla, 10595, USA
| | - Melinee D'Silva
- Department of Pharmacology, New York Medical College, Valhalla, 10595, USA
| | - David Ng
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | - Jerry E Ongerth
- University of Wollongong, Environmental Engineering, Wollongong NSW 2522, Australia
| | - Olayinka Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Ilara Mokin, Nigeria
| | - Ana Pinharanda
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Dennis Plenker
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Ravi Ranjan
- Genomics Resource Laboratory, Institute for Applied Life Sciences, University of Massachusetts, Amherst, 01003, USA
| | - Michael Rosbash
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | | | | | | | - Scott Sherrill-Mix
- Department of Microbiology, University of Pennsylvania, Philadelphia, 19104, USA
| | | | - Shaina To
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | - Merly C Vogt
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Albert D Yu
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA
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50
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Soleimani M, Merajikhah A, Beigi-khoozani A. The risk of transmitting the coronavirus to the perioperative team through aerosols produced in the operating room bathrooms. PERIOPERATIVE CARE AND OPERATING ROOM MANAGEMENT 2021; 24:100179. [PMID: 34036186 PMCID: PMC8137350 DOI: 10.1016/j.pcorm.2021.100179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/25/2022]
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