An outbreak of adenovirus has been surveyed in Taiwan in 2011. To better understand the evolution and epidemiology of adenovirus in Taiwan, full-length sequence of hexon and fiber coapsid protein was analyzed using series of phylogenetic and dynamic evolution tools. Six different serotypes were identified in this outbreak and the species B was predominant (HAdV-3, 71.50%; HAdV-7, 15.46%). The most frequent diagnosis was acute tonsillitis (54.59%) and bronchitis (47.83%). Phylogenetic analysis revealed that hexon protein gene sequences were highly conserved for HAdV-3 and HAdV-7 circulation in Taiwan. However, comparison of restriction fragment length polymorphism (RFLP) analysis and phylogenetic trees of fiber gene in HAdV-7 clearly indicated that the predominant genotype in Taiwan has shifted from 7b to 7d. Several positive selection sites were observed in hexon protein. The estimated nucleotide substitution rates of hexon protein of HAdV-3 and HAdV-7 were 0.234×10^-3 substitutions/site/year (95% HPD: 0.387~0.095×10^-3) and 1.107×10^-3 (95% HPD: 0. 541~1.604) respectively; those of the fiber protein of HAdV-3 and HAdV-7 were 1.085×10^-3 (95% HPD: 1.767~0.486) and 0.132×10^-3 (95% HPD: 0.283~0.014) respectively. Phylodynamic analysis by Bayesian skyline plot (BSP) suggested that using individual gene to evaluate the effective population size might possibly cause miscalculation. In summary, the virus evolution is ongoing, and continuous surveillance of this virus evolution will contribute to the control of the epidemic.

Canine parvovirus type 2c (CPV-2c) emerged in 2000 and is known for causing a more severe disease than other CPV-2 variants in puppies. In 2015, the emerging CPV-2c variant was isolated in Taiwan and it subsequently became the predominant variant. To trace the evolution of Taiwanese CPV-2c, we compared complete VP2 genes of CPV-2c from Taiwan and sequences obtained from GenBank. The evolutionary rate of CPV-2c was estimated to be 4.586 × 10⁻⁴ substitutions per site per year (95% highest posterior density (HPD) was 3.284–6.076 × 10⁻⁴). The time to the most recent common ancestor (TMRCA) dated to 1990 (95% HPD: 1984–1996) and 2011 (95% HPD: 2010–2013) for the CPV-2c variant and Taiwanese isolates, respectively. The CPV-2c variant isolated from Taiwan was clustered with CPV-2c from China. This phylogenetic clade began to branch off in approximately 2010 (95% HPD was 3.823–6.497). Notably, two unique mutations of Taiwanese CPV-2c were found, Q383R and P410L. In summary, this is the first report on the genome evolution of CPV-2c in Taiwan, revealing that this CPV-2c variant shares a common evolutionary origin with strains from China. The demographic history inferred by the Bayesian skyline plot showed that the effective population of CPV-2c increased until 2006 and then slowly declined until 2011.

The activity of norovirus varies from season to season, and the effect of climate change on the incidence of norovirus outbreaks is a widely recognized yet poorly understood phenomenon. Investigation of the possible association between climatic factors and the incidence of norovirus is key to a better understanding of the epidemiology of norovirus and early prediction of norovirus outbreaks. In this study, clinical stool samples from acute gastroenteritis outbreaks were collected from January 2015 to June 2019 in Taiwan. Data analysis from our study indicated that more than half of the cases were reported in the winter and spring seasons, including those caused by norovirus of genotypes GII (genogroup II).2, GII.3, GII.6, and GII.17, and 45.1% of the patients who tested positive for norovirus were infected by the GII.4 norovirus in autumn. However, GII.6 norovirus accounted for a higher proportion of the cases reported in summer than any other strain. Temperature is a crucial factor influencing patterns of epidemic outbreaks caused by distinct genotypes of norovirus. The results of this study may help experts predict and issue early public warnings of norovirus transmission and understand the effect of climate change on norovirus outbreaks caused by different genotypes and occurring in different locations.

Norovirus is the leading cause of food‐borne disease outbreaks. We conducted this study to examine the incidence and molecular characteristics of norovirus genogroup I infections from acute gastroenteritis outbreaks in Taiwan. Between January 2015 and June 2019, 2121 acute gastroenteritis clusters were reported to Taiwan CDC, of which 351 (16.5%) clusters were positive for NoV GI, and GI.3 was the most prevalent (36.8%) during the study period. The GI.3 infections were significantly higher than non‐GI.3 infections in the age groups of 0–5 and 6–18 years. The phylogenetic analysis of the MCC tree revealed that VP1 genes were divided into 3 groups: the GI.P3‐GI.3 strains in Taiwan were genetically close to Japan and the GI.Pd‐GI.3 strains were segregated into 2 other groups which were genetically closely related to China. In addition, 7 GI.Pd‐GI.3 recombinants were identified circulating in Taiwan between 2018 and 2019, and the prevalence of GI.Pd‐GI.3 should be monitored to assess whether this could become the new predominant strains in neighboring Asian countries or other parts of the world. Both GI.P3‐GI.3 and GI.Pd‐GI.3 strains cocirculate, the recombination among these two lineages occurs frequently, contributing to the genetic diversity and multiple occurrences of different norovirus lineages, and their rapid evolution makes future control more difficult. Continued surveillance and timely interventions are critical to understand the complexity of norovirus gene variation and to monitor the new emerging norovirus strains.

Taiwan has been recognized by the World Organization for Animal Health as rabies-free since 1961. Surprisingly, rabies virus (RABV) was identified in a dead Formosan ferret badger in July 2013. Later, more infected ferret badgers were reported from different geographic regions of Taiwan. In order to know its evolutionary history and spatial temporal dynamics of this virus, phylogeny was reconstructed by maximum likelihood and Bayesian methods based on the full-length of glycoprotein (G), matrix protein (M), and nucleoprotein (N) genes. The evolutionary rates and phylogeographic were determined using Beast and SPREAD software. Phylogenetic trees showed a monophyletic group containing all of RABV isolates from Taiwan and it further separated into three sub-groups. The estimated nucleotide substitution rates of G, M, and N genes were between 2.49 × 10⁻⁴–4.75 × 10⁻⁴ substitutions/site/year, and the mean ratio of dN/dS was significantly low. The time of the most recent common ancestor was estimated around 75, 89, and 170 years, respectively. Phylogeographic analysis suggested the origin of the epidemic could be in Eastern Taiwan, then the Formosan ferret badger moved across the Central Range of Taiwan to western regions and separated into two branches. In this study, we illustrated the evolution history and phylogeographic of RABV in Formosan ferret badgers.