Epidemiological and Evolutionary Dynamics of Influenza B Viruses in Malaysia, 2012-2014

Abstract

Epidemiological and evolutionary dynamics of influenza B Victoria and Yamagata lineages remained poorly understood in the tropical Southeast Asia region, despite causing seasonal outbreaks worldwide. From 2012–2014, nasopharyngeal swab samples collected from outpatients experiencing acute upper respiratory tract infection symptoms in Kuala Lumpur, Malaysia, were screened for influenza viruses using a multiplex RT-PCR assay. Among 2,010/3,935 (51.1%) patients infected with at least one respiratory virus, 287 (14.3%) and 183 (9.1%) samples were tested positive for influenza A and B viruses, respectively. Influenza-positive cases correlate significantly with meteorological factors—total amount of rainfall, relative humidity, number of rain days, ground temperature and particulate matter (PM10). Phylogenetic reconstruction of haemagglutinin (HA) gene from 168 influenza B viruses grouped them into Yamagata Clade 3 (65, 38.7%), Yamagata Clade 2 (48, 28.6%) and Victoria Clade 1 (55, 32.7%). With neuraminidase (NA) phylogeny, 30 intra-clade (29 within Yamagata Clade 3, 1 within Victoria Clade 1) and 1 inter-clade (Yamagata Clade 2-HA/Yamagata Clade 3-NA) reassortants were identified. Study of virus temporal dynamics revealed a lineage shift from Victoria to Yamagata (2012–2013), and a clade shift from Yamagata Clade 2 to Clade 3 (2013–2014). Yamagata Clade 3 predominating in 2014 consisted of intra-clade reassortants that were closely related to a recent WHO vaccine candidate strain (B/Phuket/3073/2013), with the reassortment event occurred approximately 2 years ago based on Bayesian molecular clock estimation. Malaysian Victoria Clade 1 viruses carried H274Y substitution in the active site of neuraminidase, which confers resistance to oseltamivir. Statistical analyses on clinical and demographic data showed Yamagata-infected patients were older and more likely to experience headache while Victoria-infected patients were more likely to experience nasal congestion and sore throat. This study describes the evolution of influenza B viruses in Malaysia and highlights the importance of continuous surveillance for better vaccination policy in this region.

Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015

“…In North America, studies have reported rates of (3.11–12.50) x 10 −3 [52] and 5.41 x 10 −3 [53]. For influenza B viruses, the nucleotide substitution rate of the NA gene in the present study is comparable to those reported in Australia and New Zealand (mean nucleotide substitution rate of 2.04 × 10 −3 substitutions/site/year for the Victoria lineage and 2.25 × 10 −3 substitutions/site/year for the Yamagata lineage) [54] and Malaysia (2.5–3.4 x 10 −3 ) [55]. In contrast, the mean nucleotide substitution rate of the NA gene of A(H1N1)pdm09 in the present study was slightly lower than a previous study of 5.21 × 10 −3 substitutions/site/year [3] and 5.27 x 10 −3 [56], which may be attributed to the study sample size and sequence diversity of the strains.…”

Influenza B viruses in pigs, Taiwan

“…All sIBVs carry V124A substitution in the 120‐loop, which has been also found in one of Italian IBVs (B/Milano/35CA/2016) . I146V substitution in the 150‐loop of all sIBVs has been also observed in 89.6% of B/Victoria clade 1 strains isolated in Italy during the period 2010‐15, several influenza B‐Victoria lineage viruses isolated in Cambodia in 2010‐11 as well as 67 Victoria‐1 viruses isolated in Malaysia, 2012‐14 . None of Amino acid substitutions in the 160‐loop were found in all sIBVs.…”

Time series analysis of weekly influenza-like illness rate using a one-year period of factors in random forest regression

“…In the analysis of variable importance, we also checked weather conditions, which could influence influenza virus transmission (15)(16)(17). The weather conditions, including the weekly average temperature, humidity, wind speed, and maximum temperature, seemed insignificant for predication because their influence could be implied by the history observations.…”