Taylor & Francis

In Part 3 of our COVID-19 diagnostics and detection miniseries, supported by Roche, we explore the contribution PCR has made towards diagnosis during the pandemic. Providing me with an insight into the world of PCR diagnostics is Tyler Miller, Clinical Pathology Resident and Research Fellow at Massachusetts General Hospital, where he was instrumental in setting up the testing regimen for the Hospital.

Ty details the attributes of PCR that lead to it becoming the gold standard for diagnostic tests, before explaining the variance in clinical detection rate during a patient's disease course and how this variation correlates with the infectivity of the patient. Ty also delves into the variety of sample collection methods available, how each of these methods compares in terms of sensitivity and their ability to be integrated into exciting novel PCR techniques.

We also look at the work of the Broad Institute in establishing a mass testing effort that involved automation, workflow optimization and hundreds of new staff, which lead to the delivery of 100,000 tests a day, 5% of the USA's COVID-19 testing at the time. All of this rapid work has led to dramatic changes in the PCR technique and process. These changes are perhaps exemplified by PCR testing without RNA extraction and purification, which Ty explains was partly developed due to the limited supplies available to researchers at the beginning of the pandemic.

Contents

Introduction: 00:00-02:00Why PCR tests are so valuable: 02:00-03:10Changes in clinical detection rate and infectivity: 03:10-8:00Infectivity and exceptions to the rule: 08:00-09:00Sample collection methods, sensitivity and encouraging testing uptake 09:00-17:00The Broad Institute's mass testing regimen: 17:00-21:00Developments during the pandemic and no RNA extraction PCR: 21:00-27:00Dreams for improving COVID-19 testing: 27:00- 30:00

This episode was supported by Roche sequencing and life science. Follow these links to find out more about the LightCycler 480 System and LightCycler 96 System. 

Returning to the contentious topic of the Reproducibility crisis – the inability of many study results to be replicated by different research groups or labs – this episode, supported by Zymo Research, zeros in on the topic within the field of microbiomics.

Speaking to me about the topic is Raul Cano, Chief Scientific Officer at the BioCollective. Raul discusses the crisis and explains why it is prevalent in the emerging field of microbiomics before taking a look at the key role that microbiomics is beginning to play in the field of diagnostics, and how – if we make changes now – lasting improvements can be made in the field.

Raul also lays out the three key areas that are holding back reproducibility in microbiomics and explains the actions that can be taken to improve the situation.

Contents:

Introduction: 00:00-02:00Explaining the reproducibility crisis: 02:00-02:55How microbiomics compare to other fields in terms of reproducibility: 02:55-04:05Challenges in reproducibility specific to microbiomics: 04:05-05:45The importance of reproducibility in microbiomics: 05:45-07:00Microbiomics in diagnostics: 07:00-10:00 Three key causes of poor reproducibility in microbiomics: 10:00-11:30Is detailed documentation improving in the life sciences? 11:30- 13:00Actions that can improve reproducibility: 13:00-14:15Fecal references: 14:15-16:05The realities of preparing fecal references: 16:05-18:1 5The reception to the new fecal references: 18:15-20:35References vs Standards: 20:35-22:15Standardizing microbiomics data: 22:15-23:20Assessing reproducibility in previous studies: 23:20-25:15Dreams for reproducibility in microbiomics: 25:15-26:55

This episode is supported by Zymo Research. If you would like more information about the fecal reference mentioned in the podcast, you can visit the product page here.

Spotlight: precision medicine and companion diagnostics by Taylor & Francis Group

Virtual audits: limitations and future trends by Taylor & Francis Group

This International Women’s Day takeover episode, with special guest host BioTechniques’ Senior Digital Editor Abi Sawyer, takes a look at the results of Future Science Group’s (London, UK) survey for the scientific community on gender equality and parity in STEM.

Abi’s guests on this episode are the Vice President of Epidemiology and Clinical Evidence at IQVIA (NC, USA), Dr Christina Mack; the Executive Director for the Pharmaceutical Research Computing Center at the University of Maryland School of Pharmacy (MD, USA), Dr Ebere Onukwugha; a Lecturer, Science Communicator and Author based in Cardiff (UK), Dr Emma Yhnell; and the Director of the Neuroscience Center Microscopy Core at the University of North Carolina–Chapel Hill (NC, USA), Dr Michelle Itano.

They discuss the results of Future Science Group’s survey, share their own experiences of gender inequality as well as situations where they’ve felt supported, and outline how the STEM community can push further towards gender equality and parity.

Contents:

Introduction: 00:00 – 1:47

Gender inequality, experiences and impact on STEM careers: 1:48 – 10:41

Underlying reasons for gender disparity in STEM: 10:42 – 17:51

Promoting gender equality in the STEM work environment: 17:52 – 30:34

Looking forward: representation and mentoring: 30:35 – 39:32

Conclusions: 39:33 – 40:10

3DMedNet International Women's Day: an interview with Lee-Bath Nelson by Taylor & Francis Group

This episode takes a look at the role the COVID-19 Genomics UK Consortium (COG-UK) has played sequencing SARS-CoV-2 and surveying for COVID-19. To do this I speak to two key members of the consortium; Steve Paterson, Professor of genetics at the University of Liverpool and lead for the wastewater working group of COG-UK; and Josh Quick, Future Leaders Fellow at the University of Birmingham and lead at the COG-UK Sequencing working group.

Steve discusses some of the techniques required to detect SARS-CoV-2 in wastewater, the challenges that such a vibrant sample can present, and gives his account of the part that wastewater surveillance played in the management of the new variant B.1.1.7.

Josh provides us with further insight into the technologies used to sequence SARS-CoV-2 and explains how he designed the ARTIC protocol for sequencing the virus and why it came to be so widely used. Josh also explains the bizarre act of serendipity that aided in the discovery of the B.1.1.7 variant.

In the Zone: how do we decide a vaccine is effective? by Taylor & Francis Group

RT-PCR, antigen and antibody testing; each has its niche and each has a flaw. But what are the key differences between each of these tests and when what are the key things to consider when selecting the appropriate COVID-19 diagnostic for you?

In this podcast, supported by Zymo Research, I speak to Senior Scientist in assay development Paolo Piati in order to answer this question. Whether you are a concerned citizen looking for the best test to take to inform your behavior, or a researcher aiming to understand which testing systems you need to set up in your lab – this episode should have the answers for you.

In addition to these key points, Paolo addresses the importance of testing during the rollout of vaccine programs and issues of false negatives in diagnostics, examining what, if anything, can be done to improve the accuracy of testing programs.

In this podcast, Juandem Agendia and Sarah Alexander (NCTC, UK) discuss bacteriophages, the function of the NCTC and the importance of depositing bacteriophages in the NCTC collection to improve accessibility and reproducibility in science.