Coinfections in COVID-19

Research Projects

Are you involved in research projects or collaborations around secondary infections? Has your existing project changed focus or expanded to include COVID-19?

Link to project websites and any public data or protocols that you’d like to share here.


We’re currently gathering data for a meta-analysis of reported coinfections in COVID-19 - something we have the statistical expertise for and can usefully do from home while the lab is shut.


I have just submitted a project to the UKRI open call on co-infections and SARS-CoV-2, probing the bacterial pathogens normally found in ICU.


Sounds great Freya, if other’s drop by and have data that they would be happy to contribute to the meta-analysis are they OK to get in touch? Do you want to start a separate topic for that purpose?

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Good luck Jose! Anecdotally are you seeing the usual secondary infection suspects?

Enterobacteriaceae and fungi (aspergillus) seem to be the important ones. But this may change from hospital setting to the other. There is very limited evidence, and I am not sure the data is being collected or even whether samples are being processed unless there is a positive blood culture. In any case, at least for ICU patients I will be extremely surprised if co-infection/superinfection is not an issue.

Thanks Mike, very happy for others to get in touch. I think the three of us need to get our heads down on the initial manuscripts and data requests so we will likely go quiet for a few days, then set up a new topic thread when we’ve got a clearer idea of what data are available/missing. At the mo it might be information overload and I think this way it’ll be easier for people to contribute and see where there’s a gap their expertise can fill.

Hi all, anecdotally seeing quite a few Staph aureus secondaries in Edinburgh. We’re planning to do some WGS soon and examine in context of clinical data. Interested to compare notes between localities.


Are you looking at Candida? Two of the manuscripts from China mention C. albicans in severe/critical patients. Good luck with the funding!

We are planing Candida albicans and Aspergillus.


We’ve re-purposed the inhale project (, Twitter @HAP_Diagnostics) to study secondary lung infections in covid patients.

We are recruiting iCU patients and testing them at the point of care with the Biofire Pneumonia panel which detects a range of bacteria, viruses and resistance genes, with results used to guide antimicrobial treatment. It early days but results so far suggest a lot of co-infections, with aetiology similar to that seen in HAP/VAP


Hello all, Nick asked me to post. We have been using SISPA based metagenomics (RNA) on patients with COVID-19 (under ISARIC-4C) compared to patients with MERS. Patients with severe MERS seem to have proper co-infections (that require treatment). These include influenza virus and also patients with Klebsiella (sorry if spelt wrong - I’m a virologist!). For the small sample set we have looked at so far there is nothing that jumps out from patients with COVID-19. May have remembered this wrong but clinical friends say most if not all patients in ICU on antibiotics anyhow. Of course this might also be due to sampling and we are doing RNA rather than DNA but animal models also get severe infections too - these tend towards being specific pathogen free (SPF).

So there is a background microbiome but maybe not co-infections in all patients in
the clinical sense.


I saw the tweet about this, very exciting.

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Sounds great Julian!

Defining a secondary infection here (or a co-infection) is going to be interesting. I would say if a known potential pathogen is detected that is not normally part of the respiratory microbiome then you have a strong case. Especially as this is RNA and indicates activity.

Couple this with clinical evidence and measures like procalcitonin too?

With antibiotics is the argument that if they’re on antibiotics anyway, it doesn’t matter whether a secondary pathogen is detected?

Hi Jose and anyone interested on fungi detection, we developed a protocol for amplicon nanopore identification that might be of help. Here the link to the preprint

Rapid and real-time identification of fungi up to the species level with long amplicon Nanopore sequencing from clinical samples


Hi all!
I’m Pablo Acera, PhD student at Australian National University. I and other colleges have been working on a deep learning algorithm that can classify FASTQ reads into different classes related to SARS-CoV-2 and other co-infection viruses. So far it classify reads into ‘Cornidovirineae’, ‘Human’, ‘Influenza’, ‘Metapneumovirus’, ‘Rhinovirus’ and ‘Sars_cov_2’.
Please we want this to be as useful as possible, any comment/question/collaboration will be appreciated.


Hi Pablo, sounds great! Do you have a link to the project or GitHub you’re able to share?

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Hi Julian,
sounds really interesting.
In this case, I’m not a virologist, but we intend to develop the protocol for DNA and RNA metagenomics. Would be great to have any input from your side

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Hi Mike, thank you very much for your interest! We are doing last validations and sanity checks. As soon as it is ready to use in the field I will send you the link!


As of today (25/4) we have collected material from 27 endotracheal tubes recovered from SARS-nCoV-2 positive patients. Will continue collecting ETs but managed to obtain most of the stuff required to start culture-based analysis next week. Will look for usual and unusual suspects - bacteria and fungi- and plan on determine susceptibility as well. Hopefully we will soon be able to collect ETs from SARS-nCoV-2 negative patients that are being cared for in the same hospital (obviously different ward) to see whether there is something that sets these two groups apart. Will do 16S-based metagenomics as well. As we do this with leftover budgets (haven’t been able to secure funding…) we won’t be able to do massive numbers but hope to have approx 40 pos and 10-20 neg patients.