Virological characteristics of the SARS-CoV-2 Omicron BA.2 spike

Soon after the emergence and global spread of the SARS-CoV-2 Omicron lineage BA.1, another Omicron lineage, BA.2, began outcompeting BA.1. The results of statistical analysis showed that the effective reproduction number of BA.2 is 1.4-fold higher than that of BA.1. Neutralization experiments revealed that immunity induced by COVID vaccines widely administered to human populations is not effective against BA.2, similar to BA.1, and that the antigenicity of BA.2 is notably different from that of BA.1. Cell culture experiments showed that the BA.2 spike confers higher replication efficacy in human nasal epithelial cells and is more efficient in mediating syncytia formation than the BA.1 spike. Furthermore, infection experiments using hamsters indicated that the BA.2 spike-bearing virus is more pathogenic than the BA.1 spike-bearing virus. Altogether, the results of our multiscale investigations suggest that the risk of BA.2 to global health is potentially higher than that of BA.1.

Molecular-Epidemiological Features of SARS-CoV-2 in Japan, 2020-2021

There were five epidemic waves of coronavirus disease 2019 in Japan between 2020 and 2021. It remains unclear how the domestic waves arose and abated. To better understand this, we analyzed the pangenomic sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and characterized the molecular epidemiological features of the five epidemic waves in Japan. In this study, we performed deep sequencing to determine the pangenomic SARS-CoV-2 sequences of 1,286 samples collected in two cities far from each other, Tokyo Metropolis and Nagoya. Then, the spatiotemporal genetic changes of the obtained sequences were compared with the sequences available in the Global Initiative on Sharing All Influenza Data (GISAID) database. A total of 873 genotypes carrying different sets of mutations were identified in the five epidemic waves. Phylogenetic analysis demonstrated that sharp displacements of lineages and genotypes occurred between consecutive waves over the 2 years. In addition, a wide variety of genotypes were observed in the early half of each wave, whereas a few genotypes were detected across Japan during an entire wave. Phylogenetically, putative descendant genotypes observed late in each wave displayed regional clustering and evolution in Japan. The genetic diversity of SARS-CoV-2 displayed uneven dynamics during each epidemic wave in Japan. Our findings provide an important molecular epidemiological basis to aid in controlling future SARS-CoV-2 epidemics.

Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant

The emergence of the Omicron variant of SARS-CoV-2 is an urgent global health concern¹. In this study, our statistical modelling suggests that Omicron has spread more rapidly than the Delta variant in several countries including South Africa. Cell culture experiments showed Omicron to be less fusogenic than Delta and than an ancestral strain of SARS-CoV-2. Although the spike (S) protein of Delta is efficiently cleaved into two subunits, which facilitates cell-cell fusion^2,3, the Omicron S protein was less efficiently cleaved compared to the S proteins of Delta and ancestral SARS-CoV-2. Furthermore, in a hamster model, Omicron showed decreased lung infectivity and was less pathogenic compared to Delta and ancestral SARS-CoV-2. Our multiscale investigations reveal the virological characteristics of Omicron, including rapid growth in the human population, lower fusogenicity and attenuated pathogenicity.

Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation

During the current coronavirus disease 2019 (COVID-19) pandemic, a variety of mutations have accumulated in the viral genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and, at the time of writing, four variants of concern are considered to be potentially hazardous to human society¹. The recently emerged B.1.617.2/Delta variant of concern is closely associated with the COVID-19 surge that occurred in India in the spring of 2021 (ref. ²). However, the virological properties of B.1.617.2/Delta remain unclear. Here we show that the B.1.617.2/Delta variant is highly fusogenic and notably more pathogenic than prototypic SARS-CoV-2 in infected hamsters. The P681R mutation in the spike protein, which is highly conserved in this lineage, facilitates cleavage of the spike protein and enhances viral fusogenicity. Moreover, we demonstrate that the P681R-bearing virus exhibits higher pathogenicity compared with its parental virus. Our data suggest that the P681R mutation is a hallmark of the virological phenotype of the B.1.617.2/Delta variant and is associated with enhanced pathogenicity.

A study of quality assessment in SARS-CoV-2 pathogen nucleic acid amplification tests performance; from the results of external quality assessment survey of clinical laboratories in the Tokyo Metropolitan Government external quality assessment program in 2020

Introduction

The Tokyo Metropolitan Government (TMG) conducted an external quality assessment (EQA) survey of pathogen nucleic acid amplification tests (NAATs) as a TMG EQA program for SARS-CoV-2 for clinical laboratories in Tokyo.

Methods

We diluted and prepared a standard product manufactured by Company A to about 2,500 copies/mL to make a positive control and distribute it with a negative control. The participants reported the use of the NAATs methods for SARS-CoV-2, the name of the real-time RT-PCR kit, the name of the detection device, the target gene(s), nucleic acid extraction kit, Threshold Cycle value in the case of RT-PCR and the Threshold time value and Differential calculation value in the case of Loop-Mediated Isothermal Amplification (LAMP) method.

Results

As a result, 17 laboratories using fully automated equipment and 34 laboratories using the RT-PCR method reported generally appropriate results in this EQA survey. On the other hand, among the laboratories that adopted the LAMP method, there were a plurality of laboratories that judged positive samples to be negative.

Conclusion

The false negative result is considered to be due to the fact that the amount of virus genome contained in the quality control reagent used this time was below the detection limit of the LAMP method combined with the rapid extraction reagent for influenza virus. On the other hand, false positive results are considered to be due to the non-specific reaction of the NAATs. The EQA program must be continued for the proper implementation of the pathogen NAATs.

A pilot study of viral load in stools of patients with COVID-19 and diarrhea

It is known that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be detected in the stools of patients with the coronavirus disease 2019 (COVID-19) and that the virus can be transmitted by oral-fecal route. However, there are few reports on the viral load in stools. This pilot study aimed to evaluate the clinical characteristics and viral load of SARS-CoV-2 in the stools of 13 patients with confirmed COVID-19 using as control the pepper mild mottle virus, which was proposed as a potential indicator of human fecal contamination of environmental water. SARS-CoV-2 RNA was detected in stool samples from four patients (31%), among whom three presented diarrhea symptoms. One patient experiencing long-term diarrhea (22 days) had high levels of viral RNA in the stools (8.28 log10 copies/g). However, we could not isolate the SARS-CoV-2 in the stool of any patients, using VeroE6/TMPRESS2 cells for four weeks. Our results suggest that SARS-CoV-2 RNA may be detected in the stools of patients with the diarrhea symptoms. Further studies evaluating the relationship between SARS-CoV-2 viral load in stools and diarrhea symptoms in larger patient cohorts and upon adjusting for other causative factors and virus infectivity are still needed.

Does the SARS-CoV-2 rapid antigen test result correlate with the viral culture result?

Rapid antigen tests (RATs) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have advantages over viral culture in terms of cost and rapidity of testing, but they have low sensitivity. In addition, RATs tend to be negative from approximately 11 days after symptom onset. To determine whether the antigen-negative state indicates a lack of infectiousness, we assessed the association between viral culture and RAT results. Viral culture, reverse transcription-quantitative polymerase chain reaction (RT-qPCR), and rapid antigen testing were performed on stored nasopharyngeal samples with threshold cycle values < 30, based on previous RT-qPCR testing. SARS-CoV-2 was isolated by viral culture from nine samples (45%) and one sample (17%) with positive and negative RAT results, respectively. The RAT and viral culture results were both associated with the viral load level and their cutoffs were similar, but the associations were not statistically significant. RAT might be a useful indicator of infectiousness, which can be helpful to control infection. However, further studies with larger sample size are warranted to confirm this observation.

Male-Dominant Hepatitis A Outbreak Observed among Non-HIV-Infected Persons in the Northern Part of Tokyo, Japan

Recently, we experienced an outbreak of acute hepatitis A virus (HAV) infection between 2018 and 2020. Herein, we describe this male-dominant HAV infection outbreak observed among non-human immunodeficiency virus (HIV)-infected persons in the northern part of Tokyo, Japan. Clinical information was collected from patient interviews and from medical record descriptions. In the present study, 21 patients were retrospectively analyzed. A total of 90.4 and 33.3% of patients were males, and men who have sex with men (MSM), respectively. The total bilirubin levels and platelet counts tended to be lower in the MSM group than in the non-MSM group. C-reactive protein (CRP) levels tended to be higher in acute liver failure (ALF) patients than in non-ALF patients. Prolonged cholestasis was observed in one patient (4.8%). We also found that 18 HAV isolates belonged to HAV subgenotype IA/subgroup 13 (S13), which clustered with the HAV isolate (KX151459) that was derived from an outbreak of HAV infection among MSM in Taiwan in 2015. Our results suggest that the application of antivirals against HAV, as well as HAV vaccines, would be useful for the treatment and prevention of severe HAV infection.

Seroprevalence of Entamoeba histolytica at a voluntary counselling and testing centre in Tokyo: a cross-sectional study

BACKGROUND

Amebiasis, which is caused by Entamoeba histolytica, is a re-emerging public health issue owing to sexually transmitted infection (STI) in Japan. However, epidemiological data are quite limited.

METHODS

To reveal the relative prevalence of sexually transmitted E. histolytica infection to other STIs, we conducted a cross-sectional study at a voluntary counselling and testing (VCT) centre in Tokyo. Seroprevalence of E. histolytica was assessed according to positivity with an ELISA for E. histolytica-specific IgG in serum samples collected from anonymous VCT clients.

RESULTS

Among 2083 samples, seropositive rate for E. histolytica was 2.64%, which was higher than that for HIV-1 (0.34%, p<0.001) and comparable to that for syphilis (rapid plasma reagin (RPR) 2.11%, p=0.31). Positivity for Chlamydia trachomatis in urine by transcription-mediated amplification (TMA) was 4.59%. Seropositivity for E. histolytica was high among RPR/Treponema pallidum hemagglutination (TPHA)-positive individuals and it was not different between clients with and without other STIs. Both seropositivity of E. histolytica and RPR were high among male clients. The seropositive rate for anti-E. histolytica antibody was positively correlated with age. TMA positivity for urine C. trachomatis was high among female clients and negatively correlated with age. Regression analysis identified that male sex, older age and TPHA-positive results are independent risk factors of E. histolytica seropositivity.

CONCLUSIONS

Seroprevalence of E. histolytica was 7.9 times higher than that of HIV-1 at a VCT centre in Tokyo, with a tendency to be higher among people at risk for syphilis infection. There is a need for education and specific interventions against this parasite, as a potentially re-emerging pathogen.

Estimating HIV-1 incidence in Japan from the proportion of recent infections

The first step of the UNAIDS/WHO 90-90-90 targets to encourage early diagnosis with treatment for the control of HIV-1 epidemic is to achieve 90% HIV-1 diagnosis in infected individuals. In Japan, approximately 30% of newly reported cases have been annually identified by AIDS onset, implying that substantial numbers of HIV-1-infected individuals remain undiagnosed. However, the proportion of undiagnosed cases has not yet been determined. In the present study, the proportion of recent HIV-1 infections to newly-diagnosed cases was determined from 2006 to 2015 using a recent infection assay for three metropolitan areas in Japan: Tokyo, Osaka, and Fukuoka. Estimated median periods between infection and diagnosis were 1.0, 1.8, and 2.9 years for Tokyo, Osaka, and Fukuoka, respectively. Estimation of annual HIV-1 incidence by a back-calculation method using these data as well as HIV/AIDS national surveillance data indicated proportions of undiagnosed to new HIV-1 infections from 2006 to 2015 to be 18% in Tokyo, 22% in Osaka, 38% in Fukuoka, and 28% in Japan. This is the first report estimating HIV-1 incidence in Japan using a serological biomarker in combination with national HIV/AIDS surveillance data.

P3468Tentative criteria of a combined RV3+SV3 voltage for early diagnosis of pediatric patients with hypertrophic cardiomyopathy

Background

A high voltage in midprecordial leads, termed the Katz-Wachtel sign, is a surrogate marker of left- or bi-ventricular hypertrophy. Asymmetrical interventricular hypertrophy is a characteristic feature of hypertrophic cardiomyopathy (HCM). In Japan, a school-based electrocardiographic (ECG) screening program was developed for all 1st, 7th, and 10th graders. Our hypothesis is that a combined voltage of RV3+SV3 {V3(R+S)} is a marker to screen pediatric HCM.

Purpose

[1] To develop V3(R+S) voltage criteria in 1st, 7th, and 10th graders at the screening program and [2] to determine whether the criteria are useful for the early diagnosis of HCM.

Methods

[1] Overall, 48,401 digitally stored ECGs from 16,773 1st graders (6-year-olds), 18,126 7th graders (12-year-olds), and 13,502 10th graders (15-year-olds) were obtained after excluding ECGs of subjects with underlying diseases, arrhythmias, and ST/T changes. The prevalence of HCM in children is estimated at 2.9 per 100,000 (1/34,000). The screening points were assumed to be between 1/2,000 and 1/5,000 to exclude the possibility of false negatives. [2] In 12 HCM patients (males/females=10/2) who were diagnosed after 12 years of age (one case was diagnosed at 9 years of age), the ECGs at the screening program of their first grade (at 6 years of age) were retrospectively examined.

Results

[1] The V3(R+S) criteria were 6.0 mV, 6.0 mV, and 5.5 mV for 1st, 7th, and 10th grader males, and 5.0 mV, 4.5 mV, and 4.0 mV for 1st, 7th, and 10th grade females, respectively. The number of subjects (and prevalence in parentheses) selected by the criteria were 2 (1/4175), 3 (1/2981), and 1 (1/6477) for 1st, 7th, and 10th grade males, and 2 (1/4212), 3 (1/3061), and 1 (1/3513) for 1st, 7th, and 10th grade females, respectively. [2] Four of 12 cases fulfilled the criteria. Of these, one suddenly died at 18 years of age, one experienced out-of-hospital cardiac arrest at 16 years of age, and one already had an interventricular thickness of 19 mm at 12 years of age.

Conclusions

These tentative V3(R+S) voltage criteria may be useful for the early diagnosis of pediatric HCM patients, particularly severe patients. The children and adolescents who were screened can be followed at 2–3-year intervals with ECGs and echocardiography. Early diagnosis and intervention including lifestyle modification and medication may prevent them expiring from out-of-hospital cardiac arrest or sudden death. Finally, the criteria should be validated in clinical settings.

Acknowledgement/Funding

A Health and Labour Sciences Grant from the Ministry of Health, Labour and Welfare of Japan (H27-019)

P4654Clinical and electrocardiographic features of restrictive cardiomyopathy in children

Introduction

Restrictive cardiomyopathy (RCM) is a rare myocardial disease with an impaired diastolic function and poor prognosis. The mean survival duration after a diagnosis of RCM is reported to be around 2 years in children and most need heart transplantations.

Purpose

This study aimed to determine the 12-lead electrocardiogram (ECG) diagnostic criteria of RCM based on the initial diagnostic electrocardiogram.

Methods

ECGs in pediatric cardiomyopathy patients were collected from 15 institutes in Japan between 1979 and 2013. We compared the ECG findings, especially of the P wave, in RCM patients between the cardiomyopathy group and healthy children group separately for each gender and the age. The ECGs in the healthy group were obtained from school heart screening in Japan of first-graders, and seventh-graders. Statistical significance was determined as p<0.001.

Results

Among 376 registered cardiomyopathy patients, 63 had hypertrophic cardiomyopathy (HCM) (36%), 91 (24%) dilated cardiomyopathy (DCM), 106 (28%) a left ventricular myocardial noncompaction (LVNCs), 25 (7%) restrictive cardiomyopathy (RCM), 14 (4%) arrhythmogenic right ventricular cardiomyopathy (ARVC), and 5 (1%) other cardiomyopathies. Of the 25 RCM patients (9.9±3.4 years old, F:M=11:14), 36% were discovered during school heart screening. The first onset was an abnormal ECG in 9, symptoms of heart failure in 6, respiratory tract infections in 3, syncope in 1, and 6 with other. Of those patients, 2 (8%) had a family history of RCM, 24 (92%) no family history. A genetic diagnosis was performed in 5 of the 25 cases, and 3 had genetic abnormalities related to RCM. The mean follow-up period was 65±95 months (mean±standard deviation). During follow up, 19 patients (76%) survived, 6 (24%) died, 7 (28%) had heart transplantations, and 3 (12%) were waiting for heart transplantations with a left ventricular assist device.

The P wave was bimodal in lead I or biphasic in lead V1 in 15 patients (93%), and 13 (81%) patients had both variations. We evaluated the duration and amplitude of the first and second component of the P wave as P1 and P2. The number of control and RCM patients (control/RCM), duration of P1+P2, and sum total absolute value of the amplitude of P1+P2 in lead V1 were 8350/5, 90±9/116±10ms, and 72±28/528±278μV in first grade boys, 8423/3, 91±10/120±22ms, and 66±28/326±229μV in first grade girls, 8943/1, 97±1/100ms, and 71±31/328μV in seventh grade boys, and 9183/5, 98±11/112±10ms, and 55±27/315±56μV in seventh grade girls. Although the number of patients in the RCM group was small, sum total absolute value of the amplitude of P1+P2 in lead V1 showed a significant difference in any group.

Conclusion

The ECG in children with RCM exhibits P wave abnormalities in almost all patients. In particular, not the P wave interval but P wave shape in I and V1 and the sum total absolute value of the amplitude of P1+P2 in lead V1 were observed differences.

P6544A real world study of high frequency atrial anti-tachycardia pacing in new algorithm for atrial arrhythmia

Background

Advanced pacemakers feature atrial antitachycardia pacing (aATP) therapies for terminating atrial arrhythmia. Previous studies showed the efficacy of combined atrial preventive pacing and aATP in patients with pacemakers. The independent effect of aATP and the impact for patients outside the clinical trials has not been well elucidated.

Methods

In a single center, prospective, all-comers trial, we enrolled 567 patients implanted cardiac devices with Reactive ATP function. History of permanent atrial fibrillation (AF) was not included. After device interrogation of the AF burden and the longest AF duration in the last 6 months, aATP was programmed as a bit more aggressive setting than MINERVA trial (time interval was set as every 2 hours). As for newly implanted devices, aATP was activated after at least 3 months run-in period. Primary and secondary outcomes were the longest AF duration and cumulative percentage of progression into permanent AF, respectively.

Results

Of 541 eligible patients, aged 75.3±10.7 years, 356 pacemaker, 82 ICD and 103 CRT patients, the longest single episode of AF lasted ≤6 min in 439 patients (81.1%), >6 min to 6 h in 43 (8.0%), >6–24 h in 33 (6.1%), and >24 h in 26 (4.8%) at the enrollment. During mean follow-up of 1.9 years, the longest AF episode lasted >24 h in 49 patients (9.1%) and 14 patients (2.6%) progressed into permanent AF. According with baseline longest single episode of AF, patients with AF ≤6 min developed an episode >24 h in 0.8% at 1 year and 3.2% at 2 years follow up; patients with AF >6 min to 6 h developed an episode >24 h in none at 1 year and 7% at 2 years follow up; and patients with AF >6–24 h developed an episode >24 h in 19% at 1 year and 42% at 2 years follow up, respectively. In a subgroup analysis of in 192 patients with at least 1 aATP, 46 patients with high efficacy (>44%) did not developed an episode >24 h. Only one patient developed into permanent AF without aATP therapy. On multivariate analysis, neither ICD nor CRT was independent risk factor for developing the longest AF episode >24 h.

Conclusions

The independent use of aATP without atrial preventive pacing was effective for preventing AF progression in a real world cohort. Even without the previous AF episodes, aATP could prevent AF development, especially in patients showing high aATP efficacy. Future research is required to enhance the aATP success rate.