Longitudinal Epidemiology of Viral Infectious Diseases Combining Virus Isolation, Antigenic Analysis, and Phylogenetic Analysis as Well as Seroepidemiology in Yamagata, Japan, between 1999 and 2018

Establishment and evaluation of qPCR and real-time recombinase-aided amplification assays for detection of largemouth bass ranavirus

Largemouth bass ranavirus disease (LMBVD) caused by largemouth bass ranavirus (LMBV) has resulted in severe economic losses in the largemouth bass (Micropterus salmoides) farming industry in China. Early and accurate diagnosis is the key measure for the prevention and control of LMBVD. In this study, a quantitative polymerase chain reaction (qPCR) and a real-time recombinase-aided amplification (real-time RAA) assay were established for the detection of LMBV. The sensitivity and specificity of these two methods, and the efficacy for detection of LMBV from clinical samples were also evaluated. Results showed that the real-time RAA reaction was completed in <30 min at 39℃ with a detection limit of 58.3 copies, while qPCR reaction required 60 min with a detection limit of 5.8 copies. Both methods were specific for LMBV, where no cross-reactions observed with the other tested fish pathogens. Comparing the amplification results of both assays to the results obtained by virus isolation using 53 clinical tissue samples, results showed that the clinical sensitivity of real-time RAA and qPCR were 93.75% and 100% respectively, and the clinical specificity of both were 100%. Our results showed that qPCR is more suitable for quantitative analysis and accurate detection of LMBV in the laboratory, while real-time RAA is more suitable as a point-of-care diagnostic tool for on-site detection and screening of LMBV under farm conditions and in poorly equipped laboratories.

Recombinant parechovirus A3 possibly causes various clinical manifestations, including myalgia; findings in Yamagata, Japan in 2019

BACKGROUND

Parechovirus A3 was first reported in 2004 and has been recognized as a causative agent of mild and severe infections in children. Since we first reported an outbreak of adult parechovirus A3-associated myalgia in Yamagata, Japan in 2008, this disease has since been recognized across Japan, but has not yet been reported from other countries.

AIM

We analysed 19 cases of parechovirus A3 infections identified in Yamagata in 2019 to further clarify the epidemiology of this disease.

METHODS

We performed phylogenetic analyses of parechovirus A3 isolates and analysed the clinical manifestations and the genomic clusters.

RESULTS

There were two clusters, with cluster 2019B replacing 2019 A around October/November. Phylogenetic analysis revealed that 2019B cluster strains and Australian recombinant strains, which appeared between 2012 and 2013, were grouped in one cluster at non-structural protein regions, suggesting that the ancestor to these regions of 2019B cluster strains were Australian recombinant lineage strains. The strains from both clusters caused various infections in children including myalgia. These findings strongly support that parechovirus A3 strains cause myalgia and other paediatric infections irrespective of the virus strains involved, including recombinant strains.　　.

CONCLUSIONS

We have reported repeatedly sporadic cases of myalgia and here showed that recombinant strains also cause myalgia. We hope our experiences will help better understand these infections and possibly result in detection of more cases in the world.

Seroprevalence of coxsackievirus A21 neutralizing antibodies in Yamagata, Japan, between 1976 and 2019; coxsackievirus A21 has rarely affected young children

Although coxsackievirus A21 (CV-A21) has been associated with an acute respiratory infection (ARI) as well as poliomyelitis-like paralysis, reports of CV-A21 detection have been quite limited both globally and in Japan. CV-A21 strains were isolated from five sporadic pediatric cases with ARI in 2019 in Yamagata, Japan. Neutralizing antibodies (NT Abs) were then measured against CV-A21 using sera collected in 1976, 1985, 1999, 2009, and 2019 in Yamagata, to clarify the longitudinal epidemiology of CV-A21. The total Ab-positive rate in each year was 15.2% (35/233), 10.7% (30/281), 14.3% (28/196), 3.1% (7/236), and 1.3% (3/226), respectively. Ab-positive rates generally increased with age, especially between 1976 and 1999. Among the total Ab-positive cases, the Ab titers were relatively low; 50 cases belonged to the 1:8-1:16, 40 to 1:32-1:64, 12 to 1:128-1:256, and 1 to 1:1024< groups, respectively. No Ab-positive cases under the age of 10 were observed in any of the years analyzed. In conclusion, this study and previous works suggested that CV-A21 is a unique enterovirus, which is not transmitted readily among young children but causes sporadic ARI cases mainly among those ≥15 years of age in the community.

Proposal for the Recognition of a New Disease Concept from Japan: Parechovirus A3-Associated Myalgia

Parechovirus A3 (PeVA3) was first reported in 2004 and has been recognized as a causative agent of mild and severe infectious diseases in children. We first reported an outbreak of PeVA3-associated myalgia (PeVA3-M) in Yamagata, Japan, in 2008. We have repeatedly observed PeVA3-M cases in 2011, 2014, and 2016, and identified the first child case in 2014. Reports of PeVA3-M have increased since 2014, indicating that the recognition of PeVA3-M has spread across Japan. The findings showed that PeVA3-M commonly occurs among adults aged 30-40 years, particularly in males. Elevation of creatinine phosphokinase, C-reactive protein, and myoglobin, as well as magnetic resonance imaging findings, suggest inflammation of the muscles and/or fascia of the four limbs. Patients recover within 1-2 weeks without any sequelae. A longitudinal molecular epidemiological study in Yamagata revealed that PeVA3 strains cause a variety of diseases, ranging from mild to severe, including PeVA3-M, in subjects ranging from neonates to adults, irrespective of their genetic cluster. As PeVA3-M has not yet been reported abroad, more widespread recognition of PeVA3-M as an emerging disease is important. We hope this review will help clinicians and researchers in understanding PeVA3-M and therefore advance related research in Japan as well as around the world.

Isolation of Human Coronaviruses OC43, HKU1, NL63, and 229E in Yamagata, Japan, Using Primary Human Airway Epithelium Cells Cultured by Employing an Air-Liquid Interface Culture

Isolation of seasonal coronaviruses, which include human coronavirus (HCoV) OC43, HCoV-HKU1, and HCoV-NL63, from primary cultures is difficult because it requires experienced handling, an exception being HCoV-229E, which can be isolated using cell lines such as RD-18S and HeLa-ACE2-TMPRSS2. We aimed to isolate seasonal CoVs in Yamagata, Japan to obtain infective virions useful for further research and to accelerate fundamental studies on HCoVs and SARS-CoV-2. Using modified air-liquid interface (ALI) culture of the normal human airway epithelium from earlier studies, we isolated 29 HCoVs (80.6%: 16, 6, 6, and 1 isolates of HCoV-OC43, HCoV-HKU1, HCoV-NL63, and HCoV-229E, respectively) from 36 cryopreserved nasopharyngeal specimens. In ALI cultures of HCoV-OC43 and HCoV-NL63, the harvested medium contained more than 1 × 10⁴ genome copies/µL at every tested time point during the more than 100 days of culture. Four isolates of HCoV-NL63 were further subcultured and successfully propagated in an LLC-MK2 cell line. Our results suggest that ALI culture is useful for isolating seasonal CoVs and sustainably obtaining HCoV-OC43 and HCoV-NL63 virions. Furthermore, the LLC-MK2 cell line in combination with ALI cultures can be used for the large-scale culturing of HCoV-NL63. Further investigations are necessary to develop methods for culturing difficult-to-culture seasonal CoVs in cell lines.

Seroprevalence of parechovirus A1, A3 and A4 antibodies in Yamagata, Japan, between 1976 and 2017

Introduction. Although new parechovirus A (PeVA) types, including parechovirus A3 (PeVA3) and PeVA4, have been reported in this century, there have not yet been any seroepidemiological studies on PeVA over a period of several decades.Hypothesis/Gap Statement. The authors hypothesize that PeVA3 and PeVA4 emerged recently.Aims. The aim was to clarify changes in the seroprevalence of PeVA1, PeVA3 and PeVA4.Methodology. Neutralizing antibodies (NT Abs) were measured among residents in Yamagata, Japan in 1976, 1983, 1985, 1990, 1999 and 2017.Results. The total NT Ab-positive rate for PeVA1 was between 90.7 and 100 % for all years analysed, with that for PeVA3 increasing from 39.6 % in 1976 to 69.6 % in 2017, and that for PeVA4 decreasing from 93.9 % in 1976 to 49.1 % in 2017. The distribution of NT Ab titres for PeVA1, PeVA3 and PeVA4 among those aged less than 20 years old was as follows: those ≥1 : 32 for PeVA1 were between 68.0-89.2 % for all years analysed; those ≥1 : 32 for PeVA3 was 15.4 % in 1976, 44.3-54.9 % in 1983-1990 and 64.8-68.0 % in 1999-2017; and those ≥1 : 32 for PeVA4 were between 49.1-67.2 % in 1976-1990, 41.3 % in 1999 and 23.8 % in 2017.Conclusions. Our findings in this seroepidemiological study over four decades suggested that PeVA1 has been stably endemic, while PeVA3 appeared around 1970s and has spread since then as an emerging disease, and occasional PeVA4 infections were common in 1970s and 1980s but have been decreasing for several decades in our community.

Longitudinal epidemiology of human coronavirus OC43 in Yamagata, Japan, 2010-2017: Two groups based on spike gene appear one after another

Human coronavirus OC43 (HCoV-OC43) is divided into genotypes A to H based on genetic recombination including the spike (S) gene. To investigate the longitudinal transition of the phylogenetic feature of the HCoV-OC43 S gene in a community, phylogenetic analysis of the S1 region of the S gene was conducted using 208 strains detected in Yamagata during 2010 to 2017 with reference strains of the genotype. The S1 sequences were divisible into four groups: A to D. All Yamagata strains belonged to either group B or group D. In group B, 46 (90.2%) out of 51 Yamagata strains were clustered with those of genotype E reference strains (cluster E). In group D, 28 (17.8%) and 122 (77.7%) out of 157 Yamagata strains were clustered, respectively, with genotype F and genotype G reference strains. In cluster G, 28 strains formed a distinct cluster. Monthly distributions of HCoV-OC43 in Yamagata in 2010 to 2017 revealed that group B and group D appeared one after another. In group B, the cluster E strains were prevalent recurrently. In conclusion, epidemics of HCoV-OC43 in Yamagata, Japan might be attributable to two genetically different groups: group B showed a recurrent epidemic of strains belonging to a single phylogenetic cluster and group D showed epidemic strains belonging to multiple clusters.

Comparison of suspension MDCK cells, adherent MDCK cells, and LLC-MK2 cells for selective isolation of influenza viruses to be used as vaccine seeds

BACKGROUND

Cell-based influenza vaccines can solve the problem of the frequent occurrence of egg adaptation-associated antigenic changes observed in egg-based vaccines. Seed viruses for cell-based vaccines can be prepared from clinical specimens by cell culture; however, clinical samples risk harboring respiratory viruses other than influenza virus. Therefore, it is necessary to investigate the patterns of co-infection in clinical samples and explore whether cell culture technology can selectively propagate influenza viruses from samples containing other respiratory viruses.

METHODS

A total of 341 clinical specimens were collected from patients with influenza or influenza-like illness and analyzed by ResPlex II assay to detect 18 respiratory viruses. The patterns of co-infection were statistically analyzed with Fisher's exact test. The samples with double or triple infections were passaged in suspension MDCK cells (MDCK-S), adherent MDCK cells (MDCK-A), and LLC-MK2D cells. Cell-passaged samples were analyzed by ResPlex II assay again to investigate whether each cell line could amplify influenza viruses and eliminate other respiratory viruses.

RESULTS

Double infections were detected in 8.5% and triple infections in 0.9% of the collected clinical specimens. We identified four pairs of viruses with significant correlation. For all samples with double and triple infection, MDCK-S and MDCK-A could selectively propagate influenza viruses, while eliminating all contaminating viruses. In contrast, LLC-MK2D showed lower isolation efficiency for influenza virus and higher isolation efficiency for coxsackievirus/echovirus than MDCK-S and MDCK-A.

CONCLUSIONS

Both MDCK-S and MDCK-A are considered suitable for the preparation of influenza vaccine seed viruses without adventitious agents or egg-adaptation mutations.