Background Public health breakdown from the Syrian government's targeting of healthcare systems in politically unsympathetic areas has yielded a resurgence of infectious diseases. Suspected cholera recently reappeared but conflict-related constraints impede laboratory confirmation. Given the government's previous under-reporting of infectious outbreaks and the reliance of the WHO on government reporting, we sought to assess the reliability of current surveillance systems.

Methods We compared weekly surveillance reports of waterborne diseases from the Syrian government's (WHO-associated) Early Warning and Response System (EWARS), based in Damascus, and the independent, non-governmental Early Warning and Response Network (EWARN) headquartered in Gaziantep, Turkey. We compared raw case rates by EWARS and EWARN and assessed the quality of reporting against the WHO benchmarks.

Results We identified significant under-reporting and delays in the government's surveillance. On average, EWARS reports were published 24 days (range 12–61) after the reference week compared with 11 days (5–21) for EWARN. Average completeness for EWARS was 75% (55–84%), compared with 92% for EWARN (85–99%). Average timeliness for EWARS was 79% (51–100%), compared with 88% for EWARN (70–97%). EWARS made limited use of rapid diagnostic tests, and rates of collection of stool samples for laboratory cholera testing were well below reference levels.

Conclusions In the context of the current Syrian war, the government's surveillance is inadequate due to lack of access to non-government held territory, an incentive to under-report the consequence of government attacks on health infrastructure, and an impractical insistence on laboratory confirmation. These findings should guide the WHO reform for surveillance in conflict zones.