Whole genome sequencing of human metapneumoviruses from clinical specimens using MinION nanopore technology

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Human metapneumovirus (HMPV), a member of the Pneumoviridae family, is a causative agent of respiratory illness in young children, the elderly, and immunocompromised individuals. Globally, viruses belonging to two main genetic lineages circulate, A and B, which are further divided into four genetic sublineages (A1, A2, B1, B2). Classical genotyping of HMPV is based on the sequence of the fusion (F) and attachment (G) glycoprotein genes, which are under direct antibody-mediated immune pressure. Whole genome sequencing provides more information than sequencing of subgenomic fragments and is therefore a powerful tool for studying virus evolution and disease epidemiology and for identifying transmission events and nosocomial outbreaks. Here, we report a robust method to obtain whole genome sequences for HMPV using MinION Nanopore technology. This assay is able to generate HMPV whole genome sequences from clinical specimens with good coverage of the highly variable G gene and is equally sensitive for strains of all four genetic HMPV sublineages. This method can be used for studying HMPV genetics, epidemiology, and evolutionary dynamics.

Original languageEnglish
Article number198490
JournalVirus Research
Publication statusPublished - Sept 2021

Bibliographical note

Funding Information:
The authors would like to thank Dr. B. B. Oude Munnink for helping with troubleshooting during the optimization process of the assay and the ErasmusMC virology diagnostic department for carrying out the qRT-PCR on clinical specimens.

Publisher Copyright:
© 2021

Research programs

  • EMC MM-04-54-08-A


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