GHSA-x3vf-39hj-gxr4 is a medium-severity (CVSS 4.9) XML External Entity (XXE) vulnerability in biopython. O3 Security confirms whether GHSA-x3vf-39hj-gxr4 is actually reachable in your code before you act, and blocks exploitation at runtime until you patch.
Biopython is vulnerable to doctype XML external entity (XXE) injection through Bio.Entrez
Real-World Exposure
biopythonReal-time download stats are indexed for npm and PyPI packages. This vulnerability affects PyPI packages — download data is not available via public APIs for these ecosystems.
Description
Bio.Entrez in Biopython through 1.86 allows doctype XXE.
Affected Packages
| Ecosystem | Package | Vulnerable range | Fix |
|---|---|---|---|
| 🐍PyPI | biopython | all versions | No fix |
Detection & mitigation playbook
Open-source dependencyDetect
Scan your dependency tree (package-lock.json, pnpm-lock.yaml, requirements.txt, go.sum, etc.) for biopython. O3's reachability analysis confirms whether the vulnerable code path is actually invoked in your application, so you act on real exposure instead of every transitive match.
Remediation status
No patched version of biopython has shipped for GHSA-x3vf-39hj-gxr4 yet. Where your build allows, override or pin the dependency away from the vulnerable range, and apply any maintainer-recommended mitigation.
Mitigate without a patch
If you can't upgrade right away: gate or disable the affected feature, validate untrusted input at the boundary, and avoid passing attacker-controlled data into the vulnerable path. O3's runtime protection blocks exploitation in production as an interim safeguard until the upgrade lands.
How O3 protects you
O3 pinpoints whether GHSA-x3vf-39hj-gxr4 is reachable in your code and exactly where to fix it, then blocks exploitation in production at runtime until the patched version is deployed.
Tailored to GHSA-x3vf-39hj-gxr4. Runtime protection reduces exposure until a permanent patch is applied and verified — it complements patching, it doesn't replace it.
Frequently Asked Questions
Is GHSA-x3vf-39hj-gxr4 in your dependencies?
O3 detects GHSA-x3vf-39hj-gxr4 across PyPI dependencies and uses function-level reachability to confirm whether the vulnerable code path is actually reachable — not just present. No false positives.