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Thank you to our study funders - The Wellcome Trust, and the Medical Research Council
And finally, a huge thank you to the participants and the team at @MEIRU_Malawi for all their work in the field. Shout out to my incredible coauthors @davchaima @abenaPhD @animal_viruses @DrToniHo 🤩

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ℹ️TLDR: We studied SARS-COV-2 in urban and rural Malawi. We found that people living with HIV, and children, had low protective immunity. We recommend prioritising vaccination of people living with HIV. More testing on both groups would also be beneficial.

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With this, we recommend that children and people with HIV are the focus of future surveillance as reinfections 🤧 may be more likely due to their low immunity. Additionally, people living with HIV should be prioritised for booster vaccinations to aid in their protective immune response 📈

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Those who had been vaccinated had stronger neutralising antibody responses than those solely infected
Children 👧 had the lowest neutralising antibody responses when infected
People living with HIV had lower antibody responses than those HIV-uninfected, particularly post vaccination 💉

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📈 Our results show increasing seroprevalence over time, with higher rates in the urban (Lilongwe) site than the rural site (Karonga)
🤔 We observed that the immune landscape of SARS-CoV-2 became more complex with time as new variants emerged in the population and vaccination coverage increased

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🧫 We then characterised the protective immunity to SARS-CoV-2 variants by measuring neutralising antibodies using pseudotyped virus neutralisation assays
💉 We also tested to see if those vaccinated had also been naturally infected with the virus

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❗️With limited routine surveillance in Malawi and a high proportion of asymptomatic cases, protective immunity to SARS-CoV-2 is largely unknown.
🕰️ To study this we sampled 1,876 participants in Malawi across four time points spanning February 2021 to April 2022

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💥 Implications:
Many studies may have over-reported immunity in HIV prevalent populations
🧪 It’s time to rethink how we assess immune protection in people living with HIV.
📄 doi.org/10.1038/s415...
#HIV #Immunology #Neutralisation #COVID19 #HCV

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📢 Bottom line:
If you’re measuring immune responses (neutralising antibodies) in HIV prevalent populations – or where ART is unknown:
❌ Avoid retrovirus-based assays
✅ Use VSV-based systems

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To further test this, we added antiretroviral drugs directly to the assay 🧪
Result? Adding dolutegravir to the assays triggered false positives 🚨
Additionally, when we extracted the antibodies from the serum and tested directly, these false positives vanished

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In the UK cohort, those on integrase inhibitors (like dolutegravir) showed falsely higher immune responses when using retroviral-based PVNAs:
💊 Integrase inhibitors: 71.8%
🚫 Others: 21.3%
Unfortunately, we didn’t have ART data for the Malawi cohort 🤷

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So what was causing the interference? 🔍
We looked at participants’ antiretroviral therapy (ART) medication stats — and saw one major clue 💊

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To dig deeper, we used HIV and MLV ‘cores’ with a different outer ‘wrapper’ (VSV-G)
🎯 Result? Still high neutralisation – even though no one had known VSV exposure
✅ This confirmed the interference was from the retrovirus ‘core’ itself!

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We re-tested using vesicular stomatitis virus(VSV) core PVNAs (i.e., non-retroviral), and saw a dramatic drop in immune response:
Malawi study:
📉 >90% → 20-49%
UK study:
📉 34% → 14%
😈 Something was interfering with the retrovirus-based assays 😈

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⚠️This was unexpected: HIV lowers people’s immune responses to viruses – that’s why it’s so dangerous
❓But our results showed the opposite: people with HIV responded better to the virus!
So we asked:
Could the assay itself be causing false signals? 🤨

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In both, we saw better immune responses (% neutralisation) in people with HIV – which didn’t add up 🤔
Malawi SARS-CoV-2 study:
🧍‍♂️ HIV uninfected: 22-32%
🧍‍♂️ HIV infected: >90%
UK HCV study:
🧍‍♂️ HIV uninfected: )0%
🧍‍♂️ HIV infected: 34%

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We used these retrovirus core assays in two separate studies, both based in HIV-prevalent populations:
🇲🇼 Malawian communities looking at SARS-CoV-2 using an HIV core assay
🇬🇧 UK patients with HCV studying immune responses to HCV with an MLV core assay

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🛡️PVNAs wrap the safer ‘core’ of a modified virus with the outer ‘wrapper’ of a more dangerous one. This lets scientists experiment on dangerous viruses safely
🦠 We used retrovirus cores, with the most commonly used cores being HIV and MLV (murine leukaemia virus)

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🧪 Scientists use pseudovirus neutralisation assays (PVNAs) to safely measure neutralising antibodies – a key indicator of the immune response to viruses. This means that the virus we use in the lab is different to the real virus
⚠️ And that’s where the problems begin…