Whole Blood PCR Preferred for Timely Diagnosis of Neuroinvasive West Nile Virus Infections: Lessons from the 2021 Arizona Outbreak

In 2021, the state of Arizona experienced the largest focal outbreak of West Nile Virus (WNV) in US history. Timely and accurate diagnostic testing remains a challenge for WNV due to transient viremia and limited immunoassay specificity. Recent studies have identified whole blood (WB) and urine as more sensitive specimen types for the detection of WNV RNA. We evaluated ordering practices, test performance and patient characteristics of probable and confirmed cases. In total we identified 190 probable and proven cases, including 127 patients (66.8%) with neuroinvasive disease. Among all cases, only 29.5% had WNV polymerase chain reaction (PCR) testing ordered on WB, of which 80.3% resulted as positive, including 7 cases in which WNV serologic testing was negative and 5 cases for which serologic testing was not ordered. In comparison, only 23.7% of cases that had cerebrospinal fluid (CSF) PCR ordered had a positive result, which included 3 cases that were negative by PCR on WB. In contrast, WNV PCR on WB detected 12 neuroinvasive cases that were CSF PCR negative. WNV PCR testing in urine was only ordered on 2 patients, both of which were positive. Crossing cycle threshold (Ct) values were not significantly different between WB and CSF specimen types, nor was there a correlation between Ct value and days from symptom onset at the time of sample collection; all specimen types and timepoints had Ct values, with 98% above 30. WB was positive by WNV PCR in several patients for more than 7 days (range: 7 to 25 days) after symptom onset, as was the CSF PCR. Taken together these findings indicate that WNV PCR testing on WB may be the best initial test for timely diagnosis of WNV infection, irrespective of clinical manifestation, however if negative in patients with suspected neuroinvasive disease, WNV PCR testing on CSF should be ordered.