Whole-genome analysis of human group A rotaviruses in 1980s Japan and evolutionary assessment of global Wa-like strains across half a century.

Historically, the Wa-like strains of human group A rotavirus (RVA) have been major causes of gastroenteritis. However, since the 2010s, the circulation of non-Wa-like strains has been increasingly reported, indicating a shift in the molecular epidemiology of RVA. Although understanding RVA evolution requires the analysis of both current and historical strains, comprehensive pre-1980's sequencing data are scarce globally. We determined the whole-genome sequences of representative strains from six RVA gastroenteritis outbreaks observed at an infant home in Sapporo, Japan, between 1981 and 1989. These outbreaks were mainly caused by G1 or G3 Wa-like strains, resembling strains from the United States in the 1970s-1980s and from Malawi in the 1990s. Phylogenetic analysis of these infant home strains, together with Wa-like strains collected worldwide from the 1970s to 2020, revealed a notable trend: pre-2010 strains diverged into multiple lineages in many genomic segments, whereas post-2010 strains tended to converge into a single lineage. However, Bayesian skyline plot indicated near-constant effective population sizes from the 1970s to 2020, and selection pressure analysis identified positive selection only at amino acid 75 of NSP2. These results suggest that evidence supporting the influence of rotavirus vaccines, introduced globally since 2006, on Wa-like RVA molecular evolution is lacking at present, and phylogenetic analysis may simply reflect natural fluctuations in RVA molecular evolution. Evaluating the long-term impact of RV vaccines on the molecular evolution of RVA requires sustained surveillance.

Sequence analysis of a feline- and porcine-origin G3P[9] rotavirus A strain in a child with acute gastroenteritis in Japan.

We isolated the rare G3P[9] rotavirus strain RVA/Human-wt/JPN/R11-035/2015/G3P[9] from a 2-year-old girl presenting with vomiting and diarrhea who had daily contact with cats in Japan, 2015. Full-genome analysis revealed that the R11-035 strain had an AU-1-like genetic constellation, except for the NSP3 (T) gene: G3-P[9]-I3-R3-C3-M3-A3-N3-T1-E3-H6. Phylogenetic analysis showed that strain R11-035 is closely related to human/feline-like human strains, and only the NSP3 (T1) gene was clustered together with Taiwanese porcine strains. We postulate that the R11-035 strain was directly transmitted from a cat to the patient and acquired its NSP3 gene through intergenotype reassortment with porcine strains before being transmitted to humans.

Molecular evolutionary analysis of novel NSP4 mono-reassortant G1P[8]-E2 rotavirus strains that caused a discontinuous epidemic in Japan in 2015 and 2018.

In the 2010s, several unusual rotavirus strains emerged, causing epidemics worldwide. This study reports a comprehensive molecular epidemiological study of rotaviruses in Japan based on full-genome analysis. From 2014 to 2019, a total of 489 rotavirus-positive stool specimens were identified, and the associated viral genomes were analyzed by next-generation sequencing. The genotype constellations of those strains were classified into nine patterns (G1P[8] (Wa), G1P[8]-E2, G1P[8] (DS-1), G2P[4] (DS-1), G3P[8] (Wa), G3P[8] (DS-1), G8P[8] (DS-1), G9P[8] (Wa), and G9P[8]-E2). The major prevalent genotype differed by year, comprising G8P[8] (DS-1) (37% of that year's isolates) in 2014, G1P[8] (DS-1) (65%) in 2015, G9P[8] (Wa) (72%) in 2016, G3P[8] (DS-1) (66%) in 2017, G1P[8]-E2 (53%) in 2018, and G9P[8] (Wa) (26%) in 2019. The G1P[8]-E2 strains (G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1) isolated from a total of 42 specimens in discontinuous years (2015 and 2018), which were the newly-emerged NSP4 mono-reassortant strains. Based on the results of the Bayesian evolutionary analyses, G1P[8]-E2 and G9P[8]-E2 were hypothesized to have been generated from distinct independent inter-genogroup reassortment events. The G1 strains detected in this study were classified into multiple clusters, depending on the year of detection. A comparison of the predicted amino acid sequences of the VP7 epitopes revealed that the G1 strains detected in different years encoded VP7 epitopes harboring distinct mutations. These mutations may be responsible for immune escape and annual changes in the prevalent strains.

A rare pathogen Raoultella planticola caused urinary tract infection in child with congenital anomalies of kidney and urinary tract: case report.

Raoultella planticola was previously considered an environmental organism in soil, water, and plants. However, several cases of human infection have recently been reported in association with R. planticola, some of which have been life-threatening. Most cases were in adults with reduced immunity, with few cases in children. To our knowledge, there have only been two reported cases of urinary tract infection (UTI) caused by R. planticola in children, including one case of cystitis. Here, we present the first case of UTI caused by R. planticola with congenital anomalies of kidney and urinary tract (CAKUT) in a 4-month-old male infant. The patient presented to the emergency department with fever and was diagnosed with UTI. We started third-generation cephalosporins empirically for gram-negative bacteria in the urine, presuming infection with Escherichia coli. On day 1, the patient's fever resolved immediately. On day 2, urine culture was positive for a rare pathogen, R. planticola, and we narrowed antibiotics to first-generation cephalosporins. The patient's fever did not return and he was discharged on day 7. The patient was seen in the clinic 1 week after discharge, with complete resolution of symptoms. Magnetic resonance urography and dynamic renal scintigraphy performed 2 months after discharge revealed severe bilateral hydronephroureter and obstruction of urine flow in the right kidney. As of 6 months after UTI onset, we have continued low-dose cephalexin (10 mg/kg) to prevent the recurrence of UTI and there has been no recurrence. As in this case, children with UTI caused by R. planticola may be associated with CAKUT; therefore, we should actively screen to detect CAKUT. Patients with CAKUT are at high risk of UTI recurrence, so long-term use of unnecessary broad-spectrum antibiotics should be avoided to prevent antimicrobial resistance. However, R. planticola infection is sometimes life-threatening. Hence, it is also important to use sufficiently strong antibiotics for an appropriate period. Although the optimal management of R. planticola infection in children has not been clearly established, we suggest that we can treat UTI caused by R. planticola mainly using first-generation cephalosporins.

Effects of infection by Turnip mosaic virus on the population growth of generalist and specialist aphid vectors on turnip plants.

Recent studies have revealed that relationships between plant pathogens and their vectors differ depending on species, strains and associated host plants. Turnip mosaic virus (TuMV) is one of the most important plant viruses worldwide and is transmitted by at least 89 aphid species in a non-persistent manner. TuMV is fundamentally divided into six phylogenetic groups; among which Asian-BR, basal-BR and world-B groups are known to occur in Japan. In Kyushu Japan, basal-BR has invaded approximately 2000 and immediately replaced the predominant world-B virus group. To clarify the relationships between TuMV and vector aphids, we examined the effects of the TuMV phylogenetic group on the population growth of aphid vectors in turnip plants. The population growth of a generalist aphid, Myzus persicae, was not significantly different between non-infected and TuMV-infected treatments. The population growth of a specialist aphid, Lipaphis erysimi, was higher in TuMV-infected plants than non-infected ones. Similar results were obtained in experiments using world-B and basal-BR groups of TuMV. Therefore, we conclude that L. erysimi is more mutualistic with TuMV than M. persicae, and differences in TuMV phylogenetic groups do not affect the growth of aphid vectors on turnip plants.

Seasonal Occurrence of Uroleucon nigrotuberculatum (Hemiptera: Aphididae) in Northern Kyushu and Mechanisms of Its Summer Disappearance.

Regulation mechanisms of insect population dynamics are important for conservation biology and insect pest management. The aphid Uroleucon nigrotuberculatum (Olive), native to North America, was introduced into Japan in the late 1980s. A previous study revealed that, in Japan, the aphid population densities increased in spring, but they suddenly disappeared from low-elevation areas in midsummer (called "summer disappearance"). However, the aphids were found continuously in a mountainous area throughout the season. Field investigations and field and laboratory experiments were conducted to clarify the mechanism of such population dynamics. Although the number of aphids increased in spring, they rapidly decreased in lowland and mountainous areas in early summer. Both top-down and bottom-up effects seemed to contribute to the rapid decline because the density of predators peaked in the growing season and the host plant height reached 60­80 cm, which suppressed the reproduction of aphids in our laboratory experiment. Then the aphids disappeared from lowland areas in midsummer when the maximum air temperature reached 35°C there. The laboratory experiment revealed that the aphid does not survive at 35°C. In addition, our field experiment in summer showed that U. nigrotuberculatum disappeared regardless of the presence or absence of an aphidophagous coccinellid, and the aphids did not disappear even on the tall plant treatment in the laboratory experiment. These results strongly suggest that high temperature in lowland areas causes the summer disappearance of U. nigrotuberculatum. Therefore, the population density of U. nigrotuberculatum is regulated by different factors between seasons and altitudes.