Guest Editors
Juliana S. Gularte
Feevale University
Juliana S. Gularte is Biologist, Master, and PhD in Environmental Quality at Feevale University, Brazil, with a period as a guest PhD student at the Mads Clausen Institute, University of Southern Denmark. She has been a member of Feevale University's Molecular Microbiology Lab since 2014. Her main research experience is in environmental virology, working with enteric viruses and their relationship with anthropic impacts on ecosystems. She has a strong background in molecular biology working with molecular approaches as polymerase chain reaction (PCR), real-time PCR (qPCR), digital PCR (dPCR), and next-generation sequencing (NGS). Juliana has also worked with Cell Culture-based Methods as viral isolation and integrated cell culture quantitative PCR (ICC-qPCR), and Immuno-based methods like Immunomagnetic separation (IMS). Currently, she is a researcher at Feevale University's Molecular Microbiology Lab with a scholarship funded by Dimensions Sciences, working especially with SARS-CoV-2 diagnosis and characterization in Southern Brazil.
Paula R. Almeida
Feevale University
Paula R. Almeida is Assistant Professor at the Veterinary School of Feevale University, has a Master Degree in Veterinary Sciences in the area of Veterinary Pathology, currently is a Doctoral Candidate at Feevale University in Environmental Quality, with emphasis in arbovirus diagnosis and surveillance in sylvatic cycles. Her main research interests are emerging infectious diseases, zoonosis, diagnostic pathology, molecular biology, and bioinformatics. She is a member of Feevale University's Molecular Microbiology Lab, where she conducts experiments with Flavivirus including Molecular Diagnosis, high throughput library preparation, and virus isolation. Currently, the Lab has been aiding in diagnostic efforts to fight and characterize SARS-CoV-2 in Brazil. With this new demand, she is now also responsible for RT-dPCR quantification of SARS-CoV-2 samples and controls to be applied in diagnosis of SARS-CoV-2, and for preparing libraries directed to high throughput sequencing of respiratory viruses in Southern Brazilian patients.
Fernando R. Spilki
Feevale University
Fernando R. Spilki is the Coordinator of Veterinary and Biology Schools at Feevale University, he is also President of the Brazilian Society of Virology, Associated Editor of the Brazilian Journal of Microbiology and Academic Editor of PeerJ. He is the leader of Feevale University's Molecular Microbiology Lab, where several aspects of environmental, animal and human virology, diagnosis of viral diseases in animals and humans, detection of viruses in environmental matrices and foods, and development of new molecular diagnostic techniques, antivirals, and vaccines are studied. Currently, he is a member of Brazilian Rede-Virus MCTIC, a network of researchers, laboratories, research centers, research institutes, government funding agencies, and the Ministry of Sciences, Technology, Innovation, and Communications built in an effort to respond to COVID-19 emergency, that will remain active to fight future emerging infectious diseases in Brazil. In face of the concerning COVID-19 outcome, all the infrastructure of Feevale University's Molecular Microbiology Lab has been redirected to SARS-CoV-2 diagnosis and research.
Collection Overview
Diagnostic methods based on amplification of genetic sequences have a broad applicability in diagnosis of several genetic and infectious diseasyes. Digital Polymerase Chain Reaction (dPCR) is a method of target amplification that allows for accurate quantification, detection of small quantities of target molecules, and target copy number variation analysis. Digital PCR relies on fluorescent probe based assays, with chip or microfluidic techniques that are able to distribute reactions in partitions. Proportions of positive and negative partitions and applications of Poisson distribution theory are used in data interpretation and estimation of target copy number present in a sample. With the appropriate number of target molecules in a sample, it is possible to obtain accurate target quantification with very narrow confidence intervals. With the ongoing SARS-CoV-2 pandemics, real-time information is one of the most essential factors helping to control viral spread and assist on experiments that require accurate viral quantification with efficiency. Information about viral titration methods in different samples is required to estimate viral pathogenicity, assess treatment success, and estimate the viral degree of transmissibility and survival. This methods collection gathers experimental methods and information concerning dPCR applicability in SARS-CoV-2 quantification and detection. The resources of this collection aim to assist the use of RT-dPCR for standardization, assessment of assay sensitivity, and comparison of different RT-PCR methods used in SARS-CoV-2 detection, as well as RT-dPCR use in viral quantification in experiments that involve viral resistance and potential drug discovery. Even so, methods described here can be applied to several other potential PCR targets.
Articles
Two-Step Reverse Transcription Droplet Digital PCR Protocols for SARS-CoV-2 Detection and Quantification
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Cited by 4
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2021
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Raphael Nyaruaba1,2,3, Xiaohong Li1, Caroline Mwaliko2,3,4, Changchang Li1, Matilu Mwau5, Nelson Odiwour1,2,3, Elishiba Muturi1,2,3, Caroline Muema1,2,3, Junhua Li1, Junping Yu1, Hongping Wei1
1Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, 2International College, University of Chinese Academy of Sciences, 3Sino-Africa Joint Research Center, 4CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 5Center for Infectious and Parasitic Diseases Control Research, Kenya Medical Research Institute