Genetic and antigenic characterisation of influenza A(H3N2) viruses isolated in Yokohama during the 2016/17 and 2017/18 influenza seasons.

BACKGROUND: Influenza A(H3N2) virus rapidly evolves to evade human immune responses, resulting in changes in the antigenicity of haemagglutinin (HA). Therefore, continuous genetic and antigenic analyses of A(H3N2) virus are necessary to detect antigenic mutants as quickly as possible. AIM: We attempted to phylogenetically and antigenically capture the epidemic trend of A(H3N2) virus infection in Yokohama, Japan during the 2016/17 and 2017/18 influenza seasons. METHODS: We determined the HA sequences of A(H3N2) viruses detected in Yokohama, Japan during the 2016/17 and 2017/18 influenza seasons to identify amino acid substitutions and the loss or gain of potential N-glycosylation sites in HA, both of which potentially affect the antigenicity of HA. We also examined the antigenicity of isolates using ferret antisera obtained from experimentally infected ferrets. RESULTS: Influenza A(H3N2) viruses belonging to six clades (clades 3C.2A1, 3C.2A1a, 3C.2A1b, 3C.2A2, 3C.2A3 and 3C.2A4) were detected during the 2016/17 influenza season, whereas viruses belonging to two clades (clades 3C.2A1b and 3C.2A2) dominated during the 2017/18 influenza season. The isolates in clades 3C.2A1a and 3C.2A3 lost one N-linked glycosylation site in HA relative to other clades. Antigenic analysis revealed antigenic differences among clades, especially clade 3C.2A2 and 3C.2A4 viruses, which showed distinct antigenic differences from each other and from other clades in the antigenic map. CONCLUSION: Multiple clades, some of which differed antigenically from others, co-circulated in Yokohama, Japan during the 2016/17 and 2017/18 influenza seasons.

Monitoring Influenza C and D Viruses in Patients With Respiratory Diseases in Japan, January 2018 to March 2023.

BACKGROUND: Influenza viruses can cause zoonotic infections that pose public health risks. Surveillance of influenza A and B viruses is conducted globally; however, information on influenza C and D viruses is limited. Longitudinal monitoring of influenza C virus in humans has been conducted in several countries, but there has been no long-term monitoring of influenza D virus in humans. The public health risks associated with the influenza D virus therefore remain unknown. METHODS: We established a duplex real-time RT-PCR to detect influenza C and D viruses and analyzed respiratory specimens collected from 2144 patients in Japan with respiratory diseases between January 2018 and March 2023. We isolated viruses and conducted hemagglutination inhibition tests to examine antigenicity and focus reduction assays to determine susceptibility to the cap-dependent endonuclease inhibitor baloxavir marboxil. RESULTS: We detected three influenza C viruses belonging to the C/Kanagawa- or C/Sao Paulo-lineages, which recently circulated globally. None of the specimens was positive for the influenza D virus. The C/Yokohama/1/2022 strain, isolated from the specimen with the highest viral RNA load and belonging to the C/Kanagawa-lineage, showed similar antigenicity to the reference C/Kanagawa-lineage strain and was susceptible to baloxavir. CONCLUSIONS: Our duplex real-time RT-PCR is useful for the simultaneous detection of influenza C and D viruses from the same specimen. Adding the influenza D virus to the monitoring of the influenza C virus would help in assessing the public health risks posed by this virus.

Increased risk of rhinovirus infection in children during the coronavirus disease-19 pandemic.

BACKGROUND: Coronavirus disease (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first detected in Japan in January 2020 and has spread throughout the country. Previous studies have reported that viral interference among influenza virus, rhinovirus, and other respiratory viruses can affect viral infections at the host and population level. METHODS: To investigate the impact of COVID-19 on influenza and other respiratory virus infections, we analyzed clinical specimens collected from 2244 patients in Japan with respiratory diseases between January 2018 and September 2020. RESULTS: The frequency of influenza and other respiratory viruses (coxsackievirus A and B; echovirus; enterovirus; human coronavirus 229E, HKU1, NL63, and OC43; human metapneumovirus; human parainfluenza virus 1, 2, 3, and 4; human parechovirus; human respiratory syncytial virus; human adenovirus; human bocavirus; human parvovirus B19; herpes simplex virus type 1; and varicella-zoster virus) was appreciably reduced among all patients during the COVID-19 pandemic except for that of rhinovirus in children younger than 10 years, which was appreciably increased. COVID-19 has not spread among this age group, suggesting an increased risk of rhinovirus infection in children. CONCLUSIONS: Rhinovirus infections should be continuously monitored to understand their increased risk during the COVID-19 pandemic and viral interference with SARS-CoV-2.

Analysis of Human Parechovirus Genotypes in Yokohama District from 2000 to 2016.

Human parechovirus (HPeV) infections in Yokohama City, Japan, were surveyed from 2000 to 2016. The sequence of the VP1 region of HPeVs was used to construct a phylogenetic tree and to reveal the putative amino acid (aa) sequences. Phylogenetic analysis showed the presence of 3 genotypes in Yokohama City: HPeV1 (25 specimens), HPeV3 (86 specimens), and HPeV4 (2 specimens). HPeV1 was detected nearly every year, with the highest number detected in 2014. HPeV3 was not detected until 2005, but was detected over a 1- or 3-yr period thereafter. HPeV1 was most prevalent from July to November, whereas HPeV3 peaked in July and August each year. HPeV1 was mainly detected in patients with infectious gastroenteritis or respiratory tract infections. In contrast, 87% of HPeV3-positive cases were in patients less than 2 months of age with a viral-induced fever. An analysis of the aa sequence of VP1 revealed a divergence within the same HPeV genotype, which was useful in analyzing the emergence and re-emergence of HPeV infections during the survey period. These findings suggest that molecular analysis of HPeVs may contribute to a better understanding of its epidemiology.

Genotyping of mumps virus detected in Yokohama City from 1999 to 2010.

A survey of mumps infections from 1999 to 2010 was conducted in Yokohama City, Japan, and 17 cases--including 4 cases of aseptic meningitis--were positive for mumps virus (MuV). Based on the phylogenetic analysis of the small hydrophobic gene of the MuV genome, 3, 2, and 12 of the isolates were classified into genotypes B, L, and G, respectively. The results were supported by phylogenetic analysis of hemagglutinin-neuraminidase genes. The 3 isolates of genotype B, obtained in 2000, 2004, and 2007, were closely related to indigenous lineages and vaccine strains in Japan. Two isolates obtained from 1999 to 2000 were assigned to genotype L. Twelve isolates obtained from 2000 to 2010 were classified into genotype G, in which 8 isolates obtained from 2000 to 2006 and 4 isolates obtained in 2010 were closely related to MuVi/Gloucester.GBR/32.96 and MuVi/London.GBR/0.03, respectively. Precise analyses of nucleotide sequences suggested that the 4 viruses isolated in 2010 were not directly derived from the evolution of MuV existing before 2006 in the Yokohama area.