Identification of human metapneumovirus genotypes A and B from clinical specimens by reverse transcription loop-mediated isothermal amplification

•An RT-LAMP method was developed for detection of hMPV A and hMPV B.•RT-LAMP, RT-PCR and real-time SYBR PCR methods were compared.•The detection limit of the genotype-specific hMPV RT-LAMP assay was 10 percent of that of conventional RT-PCR.•It is worthy to recommend this method in clinical application, especially in resource-limited laboratories. Human metapneumovirus (hMPV) has been recognized as an important pathogen for acute respiratory infections in children worldwide and classified into genotypes A and B. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay is a rapid diagnostic method for detecting nucleic acids with a single step under isothermal conditions in less than 1h. RT-LAMP targeting the M gene of hMPV was developed for detecting and identifying hMPV genotypes A and B. The detection limit of the genotype-specific hMPV RT-LAMP assay was 10 times greater than that of conventional reverse transcription polymerase chain reaction (RT-PCR). No cross-reactivity was found with respiratory syncytial virus, parainfluenza virus 1–3, adenovirus, human bocavirus, human rhinovirus, influenza virus A and B, human coronaviruses and enteroviruses. One hundred and fifteen clinical specimens were detected for hMPV genotypes A and B with RT-LAMP, RT-PCR and real-time SYBR PCR. Kappa coefficients showed that there was a good agreement among these three methods. Compared with RT-PCR and real-time SYBR PCR, the genotype-specific RT-LAMP showed better specificity, sensitivity and is more convenient to perform with reduced turn-around time.