Genetic Characteristics of Measles Viruses Isolated in Taiwan between 2015 and 2020

Abstract

A genetic analysis of circulating measles virus (MeV) provides strong evidence of an interruption in endemic measles and supports the elimination status of this disease. This study investigated 219 MeVs isolated between 2015 and 2020. Based on the 450 nucleotide sequences of the nucleoprotein gene (N-450), three genotypes of the H1, D8 and B3 with 8, 18 and 6 different N-450 sequences, respectively, were identified. The H1 genotype virus has not circulated in Taiwan since 2017, and the D8 and B3 genotype MeVs became dominant between 2018 and 2019. Different D8 genotype variants were imported from neighboring countries, and the majority of MeV variants were detected only for a short period. However, MVs/Gir Somnath.IND/42.16[D8], a named strain designated by the World Health Organization (WHO), was detected over 2 years. To explore whether the endemic transmission of measles has been underestimated, another sequence window of the hypervariable, noncoding regions between the matrix (M) and fusion (F) genes (MF-NCR) was introduced to clarify the transmission chain. From the chronological sequence analysis of MeVs with N-450 and MF-NCR sequence windows, no endemic MeV variants lasted over 4 weeks, providing strong evidence to support the contention that Taiwan has reached the status for measles elimination.

Keywords: elimination; genotype; measles.

Figure 1

Phylogenetic tree of the genotype B3 and H1 MeV strains. The phylogenetic tree was constructed using the neighbor-joining method based on the N-450 nucleotide sequences. Circles colored in blue indicate strains detected in Taiwan between 2015 and 2020. Circles colored in red indicate the N-450 sequences of WHO-named strains identical to MeV variants in Taiwan. The square colored in red indicates WHO reference MV strains. Diamonds colored in black indicate the N-450 sequences of variants in GenBank identical to MeV variants in Taiwan. Sequences without additional labels were other WHO-named strain viruses with genotypes B3 and H1. The number (n) of each MeV strain with an identical N-450 sequence is shown. Genotype B3 sublineage B3-N1 tentatively proposed in this study is indicated.

Figure 2

Phylogenetic tree of the genotype D8 MeV strains. The analysis and labeling methods of the MeV strains are described in the legend of Figure 1. Genotype D8 sublineage D8-N1 and D8-N2 as tentatively proposed in this study are indicated.

Figure 3

Phylogenetic tree of the genotype B3 and D8 MeV strains. The phylogenetic tree was constructed using the neighbor-joining method based on the MF-NCR sequences. Circles colored in blue indicate strains detected in Taiwan that had MF-MCR sequences identical to those of the MeV strain found in GenBank. The circle colored in red indicates that strains detected in Taiwan had identical MF-MCRs but deviated from N-450 sequences. Diamonds colored in black indicate the overseas MeV strains with an MF-NCR sequence identical to one or another of the MeV strains detected in Taiwan. The number (n) of each MeV strain with an identical MF-NCR sequence is shown. The other sequences without additional labels were other B3 and D8 MF-NCR variants. Genotype D8 sub-lineage D8-1, D8-2 and genotype B3-1 as tentatively proposed in this study are indicated.