Genetic Analysis of Human Norovirus Strains in Japan in 2016–2017

Abstract

In the 2016/2017 winter season in Japan, HuNoV GII.P16-GII.2 strains (2016 strains) emerged and caused large outbreaks of acute gastroenteritis. To better understand the outbreaks, we examined the molecular evolution of the VP1 gene and RdRp region in 2016 strains from patients by studying their time-scale evolutionary phylogeny, positive/negative selection, conformational epitopes, and phylodynamics. The time-scale phylogeny suggested that the common ancestors of the 2016 strains VP1 gene and RdRp region diverged in 2006 and 1999, respectively, and that the 2016 strain was the progeny of a pre-2016 GII.2. The evolutionary rates of the VP1 gene and RdRp region were around 10-3 substitutions/site/year. Amino acid substitutions (position 341) in an epitope in the P2 domain of 2016 strains were not found in pre-2016 GII.2 strains. Bayesian skyline plot analyses showed that the effective population size of the VP1 gene in GII.2 strains was almost constant for those 50 years, although the number of patients with NoV GII.2 increased in 2016. The 2016 strain may be involved in future outbreaks in Japan and elsewhere.

Linking ecology and systematics of acidobacteria: Distinct habitat preferences of the Acidobacteriia and Blastocatellia in tundra soils

“…All previously available knowledge of Acidobacteria diversity in the tundra zone refers to the ecosystems with developed plant communities, i.e. tundra heaths with a mosaic vegetation of dwarf shrubs and alpine grasses [19,34], wetlands with mixed cover of lichens and mosses [20] or forested tundra with lichen cover [35]. All of these studies report SDs 1, 2 and 3 (belonging to the class Acidobacteriia) as the major groups of tundra-inhabiting Acidobacteria.…”

“…Good tolerance of low temperatures, wide repertoires of carbohydrate-active enzymes encoded in their genomes and pronounced hydrolytic capabilities explain wide distribution of Granulicella species in tundra habitats [42][43][44][45]. The OTU31, which was shared between SF and MS plots in site I and was highly abundant in MS plots of site II, is represented by 'Acidisarcina'-like bacteria, which were also isolated from lichendominated tundra soils and displayed chitinolytic and xylanolytic capabilities [35].…”

Detection of novel coronaviruses in bats in Myanmar

“…Land use change will likely continue bringing people into closer proximity with bats, raising encounter rates and opportunities for spillover, facilitating the emergence of zoonotic viruses, and supporting the need for surveillance [12,43]. Historically, human activities have arguably played a significant role in interspecies transmission events.…”

Norovirus GII.P16/GII.2 Strain in Shenzhen, China: A Retrospective Study

“…However, the reemergence GII.P16/GII.2 caused rapidly increasing AGE outbreaks in China in winter 2016 [20]. And during a short time, GII.P16/GII.2 recombination strain swept Japan, Italy, Germany and other countries [21][22][23].…”

“…A study in United States reported 3,960 NoV outbreaks between 2009 and 2013 and found that long-term care homes were the most frequent sites of NoV outbreaks [37]. Another study from Qin [38] shown that middle schools were the most important setting of NoV outbreaks in China, followed by primary schools between 2006 and 2016. In this study, we classi ed the outbreak settings into 12 categories, and the results shown that most outbreaks were occurred in child care centers, followed by primary school.…”