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Behind the paper: human collaboration to study virus interactions

In this ‘behind the paper’ post, Anna Sims discusses her experience working in a virology lab during the height of the COVID-19 pandemic while not working in SARS-CoV-2, and the importance of collaboration and discussion with peers in science.

My name is Anna Sims and I’m a final year PhD student at the MRC-University of Glasgow Centre for Virus Research (CVR). Our new paper focuses on virus interactions within individual hosts, which is a typically understudied area of infection biology.  We used influenza viruses encoding a fluorescent marker in conjunction with some of the CVR’s excellent microscopy capabilities to try to understand this process. By firstly modelling spreading infections in 2D cell culture, and eventually moving onto mouse lungs, we showed that the dynamics of infection and a mechanism known as superinfection exclusion cause virus populations to split out into regions – causing a patchwork effect inside the airway.

Fluorescently tagged influenza virus infection leads to a patchwork effect in 2D cell culture. This is due to a mechanism known as superinfection exclusion which blocks secondary infection of a cell a few hours after primary infection.
Image credit

Anna Sims, CC BY 4.0

I’ve always been particularly interested in the interface between viruses and the host, and my research so far has been focused on influenza viruses. It is fascinating to me to understand the kind of challenges viruses face as they attempt to establish an infection, and the barriers the host puts up to try and block this from happening.

For me, this was a pandemic project. I began the project in February 2020, a month or so before the first COVID-19 lockdowns in the UK, and had only just worked out where my new research group kept the tissue culture flasks before we were all booted from the lab. The next 5 months were spent in my parents’ garden, reading papers and learning how to code with my dog Tilly by my side. When I was allowed to return to work on the project in July 2020, we were only allowed to have one person in our lab at a time. Therefore, a typical day for me during this project involved pulling a nightshift in the tissue culture lab, as my group members needed it during the day, and doing the data analysis in my bedroom on my underpowered laptop. (I didn’t have a desk set up, so my bed was my office).

Learning to code with Tilly “the menace” Sims in my childhood bedroom. Photo taken June 2020.
Image credit

Anna Sims, CC BY 4.0

For a long time, it felt like we were working on this project in a tight bubble, as physical separation made it harder to introduce myself to people in my institute, let alone the wider virology field. In the wider community, the pandemic led to an increase in global collaborations, as people realised that many experts in many disciplines were required to tackle a problem as huge as SARS-CoV-2. In my personal experience though, collaboration and feedback became a lot more challenging in the pandemic. For the record, the lockdowns were necessary and important to control the virus, but I don’t think it’s a controversial take to say they were hard on all of us. It is hard to spark inspiration over zoom, and for what felt like eternity, people had bigger things to worry about. So, my supervisory meetings and my lab meeting moved online (side note: it is extremely hard to explain mathematical formulae over zoom), tacit knowledge and casual problem-solving chats became impossible. It felt like each person was alone with their science, even if everyone around wanted to help.

It was only after the majority of the strict restrictions were lifted in the UK that I was able to attend my first in-person conference, in March 2022. It was a small conference, around 50 people, on the topic of ‘The Social Lives of Viruses.’ The irony of the theme was not lost on any in attendance I believe, as all of us had put our own social lives on hold for over a year to prevent viral spread. We were still testing and wearing masks, but I could now meet my fellow academics face to face and discuss science – without anyone accidentally ending up on mute or their cat standing in the way of the camera! There I met many wonderful, intelligent, and interesting people, not least the editor in chief of PLOS Biology, Nonia Pariente, who gave me some incredibly useful advice including “have you considered submitting to PLOS Biology?” (I had not).

It feels weird to study the social lives of viruses during viral pandemic lockdowns. At least influenza viruses have the choice to actively exclude each other, as shown in this image.
Image credit

Anna Sims, CC BY 4.0

Following this, the data I had gathered began to form properly into a short report. We set up a collaboration with a group at the Beatson Institute for Cancer Research in Glasgow to look in mice at the phenomenon we had been studying ourselves in tissue culture. We contacted PLOS Biology again to ask for advice on how to shape the paper into something of interest to their readers. As seeking advice became easier, we found ourselves discussing the paper more and gathering more perspectives from incredibly intelligent people.

Therefore, this paper to me is a testament to the power of open science discussion, collaboration, and conferences. Although it is important to have good solid data, and an interesting observation, open communication in the scientific community is invaluable.

The pandemic had a huge impact on scientific research, with 58% of researchers reporting to the UKRI, the body that directs public research funding in the UK, that “COVID-19 had made it impossible to do the research they planned”. As I only had a handful of months in academic research prior to the pandemic, I can’t say whether the way science is done has fundamentally changed from pre-pandemic, but the difference the lockdowns had on my own work when carrying out this project is undeniable. This project, and I’m sure many others, benefited from open scientific collaboration and communication despite all the challenges. As we move towards a more collaborative scientific community post-pandemic, looking back on this project reminds me how important it is that we talk to each other.

About the author

This is an image of the author

I am a PhD student in the group of Ed Hutchinson at the MRC-University of Glasgow Centre for Virus Research (CVR). I mostly work on interactions between influenza viruses within an infected host. Before starting my PhD in 2019 I studied influenza entry in the lab of Yohei Yamauchi at the University of Bristol, and autoimmune disease pathogenesis in the scientific R&D department of GlaxoSmithKline (GSK). 0000-0002-5531-1100 @annasimsbiol

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