Laboratory-based surveillance and molecular epidemiology of influenza virus in Taiwan

Abstract

A laboratory-based surveillance network of 11 clinical virological laboratories for influenza viruses was established in Taiwan under the coordination of the Center for Disease Control and Prevention (CDC), Taiwan. From October 2000 to March 2004, 3,244 influenza viruses were isolated, including 1,969 influenza A and 1,275 influenza B viruses. The influenza infections usually occurred frequently in winter in the northern hemisphere. However, the influenza seasonality in Taiwan was not clear during the four seasons under investigation. For example, the influenza A viruses peaked during the winters of 2001, 2002, and 2003. However, some isolated peaks were also found in the summer and fall (June to November) of 2001 and 2002. An unusual peak of influenza B also occurred in the summer of 2002 (June to August). Phylogenetic analysis shows that influenza A isolates from the same year were often grouped together. However, influenza B isolates from the year 2002 clustered into different groups, and the data indicate that both B/Victoria/2/87-like and B/Yamagata/16/88-like lineages of influenza B viruses were cocirculating. Sequence comparison of epidemic strains versus vaccine strains shows that many vaccine-like Taiwanese strains were circulating at least 2 years before the vaccine strains were introduced. No clear seasonality of influenza reports in Taiwan occurred in contrast to other more continental regions.

FIG. 1.

Positive rate of influenza viral isolation in Taiwan and counts for different influenza A subtypes, 2000 to 2004. Positive count indicates the number of samples positive for influenza virus isolation among all respiratory-tract specimens. The positive rate indicates the percentage of the number of influenza virus positive samples, divided by the total number of respiratory tract specimens.

FIG. 2.

Sequence analysis of influenza A (H1N1) viruses in Taiwan. (A) Phylogenetic relationship of influenza A H1N1 subtype. HA nucleotide sequences used are 495-nt long, from positions 141 to 636 based on A/Puerto Rico/8/34(H1N1). (B) Percent identities of Taiwanese influenza A H1N1 isolates versus vaccine strains from 1995 to 2003. White arrows indicate that those strains were isolated at the corresponding season(s) when respective vaccine strains were selected by the WHO, and black arrows indicate the strains with high similarity with the vaccine strains before they were formally selected by the WHO.

FIG. 2.

Sequence analysis of influenza A (H1N1) viruses in Taiwan. (A) Phylogenetic relationship of influenza A H1N1 subtype. HA nucleotide sequences used are 495-nt long, from positions 141 to 636 based on A/Puerto Rico/8/34(H1N1). (B) Percent identities of Taiwanese influenza A H1N1 isolates versus vaccine strains from 1995 to 2003. White arrows indicate that those strains were isolated at the corresponding season(s) when respective vaccine strains were selected by the WHO, and black arrows indicate the strains with high similarity with the vaccine strains before they were formally selected by the WHO.

FIG. 3.

Sequence analysis of influenza A (H3N2) viruses in Taiwan. (A) Phylogenetic relationship of influenza A H3N2 subtype. HA nucleotide sequences used are 789 nt long, from positions 214 to 1002 based on A/Hong Kong/1/68(H3N2). (B) Percent identities of Taiwanese influenza A H3N2 isolates versus vaccine strains from 1996 to 2003. The 2003-2004 vaccine strain suggested by WHO was A/Moscow/10/99, although A/Panama/2007/99 (vaccine strain for 2000-2002) was widely used for vaccination.

FIG. 3.

Sequence analysis of influenza A (H3N2) viruses in Taiwan. (A) Phylogenetic relationship of influenza A H3N2 subtype. HA nucleotide sequences used are 789 nt long, from positions 214 to 1002 based on A/Hong Kong/1/68(H3N2). (B) Percent identities of Taiwanese influenza A H3N2 isolates versus vaccine strains from 1996 to 2003. The 2003-2004 vaccine strain suggested by WHO was A/Moscow/10/99, although A/Panama/2007/99 (vaccine strain for 2000-2002) was widely used for vaccination.

FIG. 4.

Sequence analysis of influenza B viruses in Taiwan. (A) Phylogenetic relationship of influenza B virus. HA nucleotide sequences used are 393 nt long, from positions 403 to 795 based on B/Lee/40. (B) Percent identities of Taiwanese influenza B isolates versus vaccine strains from 1999 to 2003.

FIG. 4.

Sequence analysis of influenza B viruses in Taiwan. (A) Phylogenetic relationship of influenza B virus. HA nucleotide sequences used are 393 nt long, from positions 403 to 795 based on B/Lee/40. (B) Percent identities of Taiwanese influenza B isolates versus vaccine strains from 1999 to 2003.