Collection of clinical samples for molecular testing from all suspected cases is recommended not only for genetic characterization (Chapter 7. Molecular epidemiology of measles and rubella), but also case confirmation by detection of virus-specific RNA by RT-PCR (chapter 6). This is especially important if a positive IgM result is obtained from a sporadic case with an unknown source. Unless there is an epidemiologic link or a high index of suspicion (e.g., recent travel), a positive IgM result may be questioned due to the low PPV in elimination settings. When appropriate precautions are in place to reduce the risk of cross-contamination, and adequate controls are included to detect cross-contamination, a positive RT-PCR result for virus-specific RNA confirms the case.
In addition to providing support for a positive IgM result, detection of virus-specific RNA by RT-PCR is particularly useful for case confirmation when a negative IgM result is obtained from serum collected in the first few days after rash onset. Among suspected cases that have not been recently vaccinated, a positive RT-PCR result can provide confirmation of acute infection even if the IgM result is negative. Occasionally, the reliability of a positive RT-PCR result may be questioned if a high Ct value (near the cut-off) is obtained and/or a repeat test produces an indeterminate or negative result (Chapter 6. Detection of viral RNA by RT-PCR for the confirmation of measles and rubella infection). When RT-PCR results are considered inconclusive, an attempt may be made to re-extract the RNA and repeat the test if there is any clinical specimen remaining.
However, because negative RT-PCR results may be obtained due to poor sample quality, failure to detect virus-specific RNA should not be used to rule out a case. Timeliness of collection, while a primary determinant of the sample quality, is not the only variable that can compromise the ability to detect virus-specific RNA (Chapter 6. Detection of viral RNA by RT-PCR for the confirmation of measles and rubella infection). In addition, negative RT-PCR results may be obtained from measles reinfection cases, even when clinical specimens are promptly collected (see 8.5 Measles reinfections: characteristics and case confirmation). If RT-PCR results are inconclusive or adequate samples were not collected, the case must be classified based upon the results of IgM testing. Depending on the epidemiologic context, additional specimen collection and/or laboratory testing may be pursued to resolve a challenging case with conflicting or inconclusive results (see 8.3 Difficult cases and situations that may require additional testing and 8.4 Additional testing to aid case classification).