Changes in Viral Dynamics Following the Legal Relaxation of COVID-19 Mitigation Measures in Japan From Children to Adults: A Single Center Study, 2020-2023

INTRODUCTION

Respiratory infections are an ongoing global health challenge. The COVID-19 pandemic triggered global nonpharmacological measures that reshaped public health. In Japan, the shift from legal to individual discretion in pandemic management started on May 8, 2023. However, it still unknown how the relaxation of measures affects respiratory pathogens across age groups.

METHODS

We collected 16,946 samples from 13,526 patients between February 2020 and September 2023, analyzing the circulating respiratory pathogen dynamics using FilmArray respiratory panel.

RESULTS

Our analysis revealed significant increases in the positivity rates of respiratory pathogens across multiple age groups after relaxation. The pathogens including adenovirus, Bordetella pertussis, parainfluenza 2 and parainfluenza 4 showed increased positivity predominantly in children aged under 10 years. Conversely, some pathogens including human metapneumovirus, rhinovirus/enterovirus, and respiratory virus (RSV) increased in broad range of age groups. SARS-CoV-2 positivity rates decreased in children under 10 years but increased in those aged over 60 years.

DISCUSSION

Age-stratified analysis reveals a dynamic pattern of circulating pathogen in each age group after relaxation measures. This study provides essential epidemiologic data that can guide strategies to protect different age groups and effectively respond to respiratory infections in post-COVID-19 era.

Impact of the FilmArray Rapid Multiplex PCR Assay on Clinical Outcomes of Patients with Bacteremia

Bacteremia is a serious disease with a reported mortality of 30%. Appropriate antibiotic use with a prompt blood culture can improve patient survival. However, when bacterial identification tests based on conventional biochemical properties are used, it takes 2 to 3 days from positive blood culture conversion to reporting the results, which makes early intervention difficult. Recently, FilmArray (FA) multiplex PCR panel for blood culture identification was introduced to the clinical setting. In this study, we investigated the clinical impact of the FA system on decision making for treating septic diseases and its association with patients' survival. Our hospital introduced the FA multiplex PCR panel in July 2018. In this study, blood-culture-positive cases submitted between January and October 2018 were unbiasedly included, and clinical outcomes before and after the introduction of FA were compared. The outcomes included (i) the duration of use of broad-spectrum antibiotics, (ii) the time until the start of anti-MRSA therapy to MRSA bacteremia, and (iii) sixty-day overall survival. In addition, multivariate analysis was used to identify prognostic factors. In the FA group, overall, 122 (87.8%) microorganisms were concordantly retrieved with the FA identification panel. The duration of ABPC/SBT use and the start-up time of anti-MRSA therapy to MRSA bacteremia were significantly shorter in the FA group. Sixty-day overall survival was significantly improved by utilizing FA compared with the control group. In addition, multivariate analysis identified Pitt score, Charlson score, and utilization of FA as prognostic factors. In conclusion, FA can lead to the prompt bacterial identification of bacteremia and its effective treatment, thus significantly improving survival in patients with bacteremia.

Classification of Omicron BA.1, BA.1.1, and BA.2 sublineages by TaqMan assay consistent with whole genome analysis data

OBJECTIVES

Recently, the Omicron strain of SARS-CoV-2 has spread and replaced the previously dominant Delta strain. Several Omicron sublineages (BA.1, BA.1.1, and BA.2) have been identified, with in vitro and preclinical reports showing that the pathogenicity and therapeutic efficacy differs between BA.1 and BA.2. We sought to develop a TaqMan assay to identify these subvariants.

METHODS

A TaqMan assay was constructed for rapid identification and genotyping of Omicron sublineages with 171 samples. We analyzed three characteristic mutations of the spike gene, Δ69-70, G339D, and Q493R, by TaqMan assay. The accuracy of the TaqMan assay was examined by comparing its results with the results of whole genome sequencing (WGS) analysis.

RESULTS

A total of 171 SARS-CoV-2 positive samples were analyzed by WGS and TaqMan assay. The 127 samples determined as BA.1/BA.1.1 by WGS were all positive for Δ69-70, G339D and Q493R by TaqMan assay. A total of 42 samples, determined as BA.2 by WGS, were negative for Δ69-70 but positive for G339D and Q493R by TaqMan. Two samples with G339N were determined to be inconclusive by the TaqMan method. Except for these two samples, the concordance rate between WGS and the TaqMan assay was 100% (169/169).

CONCLUSION

TaqMan assays targeting characteristic mutations are useful for identification and discrimination of Omicron sublineages.

Non-pharmaceutical interventions during the COVID-19 epidemic changed detection rates of other circulating respiratory pathogens in Japan

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has circulated worldwide and causes coronavirus disease 2019 (COVID-19). At the onset of the COVID-19 pandemic, infection control measures were taken, such as hand washing, mask wearing, and behavioral restrictions. However, it is not fully clear how the effects of these non-pharmaceutical interventions changed the prevalence of other pathogens associated with respiratory infections. In this study, we collected 3,508 nasopharyngeal swab samples from 3,249 patients who visited the Yamanashi Central Hospital in Japan from March 1, 2020 to February 28, 2021. We performed multiplex polymerase chain reaction (PCR) using the FilmArray Respiratory Panel and singleplex quantitative reverse transcription PCR targeting SARS-CoV-2 to detect respiratory disease-associated pathogens. At least one pathogen was detected in 246 (7.0%) of the 3,508 samples. Eleven types of pathogens were detected in the samples collected from March-May 2020, during which non-pharmaceutical interventions were not well implemented. In contrast, after non-pharmaceutical interventions were thoroughly implemented, only five types of pathogens were detected, and the majority were SARS-CoV-2, adenoviruses, or human rhinoviruses / enteroviruses. The 0-9 year age group had a higher prevalence of infection with adenoviruses and human rhinoviruses / enteroviruses compared with those 10 years and older, while those 10 years and older had a higher prevalence of infection with SARS-CoV-2 and other pathogens. These results indicated that non-pharmaceutical interventions likely reduced the diversity of circulating pathogens. Moreover, differences in the prevalence of pathogens were observed among the different age groups.

The dynamic change of antibody index against Covid-19 is a powerful diagnostic tool for the early phase of the infection and salvage PCR assay errors

BACKGROUND

Currently, PCR assay is a golden standard for diagnosis of Covid-19. However, it needs nasopharyngeal swabs, expensive instruments and expertise. It even causes PCR errors.

METHODS

We validated the antibody assay (Roche) in 36 followed patients and 1879 controls (medical staffs).

RESULTS

Of 1879 medical staffs, only two (0.11%) were positive by Cut off Index (COI; 1.0) (mean ± SD, 0.094 ± 0.047). Thirty six patients were composed of three groups; Group A,4 from Diamond Princess cruise ship, Group B, 2 infected in Africa, and Group C, 30 infected in Japan. PCR assays were conducted at outside laboratories before and repeated in house after hospitalized. Of 36 at admission, positive antibody was seen in 4/4 from the ship, 0/2 from Africa, and 5/30 from Japan. Two from Africa showed the increase of COI and became positive on days 8 and 13. Thirty Japanese was divided in two groups, e.g., 23 showed dynamic increase of COI up to 84.4 within 3 days while active virus replication present (Group C). In remaining 7 (7/30, 23%) (Group C'), no rise of antibody nor positive in house PCR assays, indicative of false positive results of PCR at the beginning.

CONCLUSION

This antibody testing has a wide dynamic ranges of COI and, thus, could be utilized in the early infection phase. This may also compliment and even help to avoid possible PCR errors. Therefore, this can serve as a powerful diagnostic tool, needed in the frontline of the clinic and hospitals.

Comparison of Roche and Lumipulse quantitative SARS-CoV-2 antigen test performance using automated systems for the diagnosis of COVID-19

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread worldwide. Here, we evaluated the performance of two quantitative antigen (Ag) tests, the Roche and Lumipulse Ag tests, using automated platforms.

Methods

We collected 637 nasopharyngeal swab samples from 274 individuals. Samples were subjected to quantitative reverse transcription PCR (RT-qPCR), the Roche Ag test and Lumipulse Ag test.

Results

When RT-qPCR was used as a reference, the overall concordance rate of the Roche Ag test was 77.1% (491/637) with 70.0% (341/487) sensitivity and 100% specificity (150/150). When inconclusive results of the Lumipulse Ag test were excluded, the overall concordance rate of the Lumipulse Ag test was 88.3% (467/529) with 84.8% (330/389) sensitivity and 97.9% (137/140) specificity. The overall concordance rate between the Roche and Lumipulse Ag tests was 97.9% (518/529) with 96.7% (322/333) sensitivity and 100% (196/196) specificity. Quantitative Ag levels determined using the Roche and Lumipulse Ag tests were highly correlated (R² = 0.922). The Roche and Lumipulse Ag tests showed high concordance up to nine days after symptom onset, with progressively lower concordance after that.

Conclusions

The Roche and Lumipulse Ag tests showed equivalent assay performance and represent promising approaches for diagnosing coronavirus disease 2019.

Pooling RT-qPCR testing for SARS-CoV-2 in 1000 individuals of healthy and infection-suspected patients

Severe acute respiratory coronavirus 2 (SARS-CoV-2) testing reagents are expected to become scarce worldwide. However, little is known regarding whether pooling of samples accurately detects SARS-CoV-2. To validate the feasibility of pooling samples, serial dilution analysis and spike-in experiments were conducted using synthetic DNA and nucleic acids extracted from SARS-CoV-2-positive and -negative patients. Furthermore, we studied 1000 individuals, 667 of whom were “healthy” individuals (195 healthcare workers and 472 hospitalized patients with disorders other than COVID-19 infection), and 333 infection-suspected patients with cough and fever. Serial dilution analysis showed a limit of detection of around 10–100 viral genome copies according to the protocol of the National Institute of Infectious Diseases, Japan. Spike-in experiments demonstrated that RT-qPCR detected positive signals in pooled samples with SARS-CoV-2-negative and -positive patients at 5-, 10-, 20-fold dilutions. By screening with this pooling strategy, by the end of April 2020 there were 12 SARS-CoV-2-positive patients in 333 infection-suspected patients (3.6%) and zero in 667 “healthy” controls. We obtained these results with a total of 538 runs using the pooling strategy, compared with 1000 standard runs. In a prospective study, we successfully detected SARS-CoV-2 using 10- to 20-fold diluted samples of nasopharyngeal swabs from eighteen COVID-19 patients with wide ranges of viral load. Pooling sample is feasible for conserving test reagents and detecting SARS-CoV-2 in clinical settings. This strategy will help us to research the prevalence infected individuals and provide infected-status information to prevent the spread of the virus and nosocomial transmission.

Analysis of a persistent viral shedding patient infected with SARS-CoV-2 by RT-qPCR, FilmArray Respiratory Panel v2.1, and antigen detection

Various diagnostic tests utilizing different principles are currently under development for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, these tests can occasionally produce discrepant results, causing confusion in their interpretation. Here, we evaluated the performance and features of three diagnostic assays: quantitative reverse transcription polymerase chain reaction (RT-qPCR), FilmArray Respiratory Panel (RP) v2.1, and the LUMIPULSE antigen test. Twenty-seven serial nasopharyngeal swabs were collected from a prolonged viral shedding patient who had been hospitalized for 51 days. We examined the SARS-CoV-2 detection rates of the three tests. The overall agreement rate was 81% between RT-qPCR and FilmArray RP v2.1, 63% between the antigen test and FilmArray RP v2.1, and 59% between the antigen test and RT-qPCR. We obtained concordant results in samples with high viral loads (low threshold cycle values) by all three tests. RT-qPCR and FilmArray RP v2.1 accurately detected SARS-CoV-2 at the early to intermediate phases of infection, but the results varied at the late phase. The antigen test also produced a positive result at the early phase but varied at the intermediate phase and consistently produced negative results at late phase of infection. These results demonstrated FilmArray RP v2.1 could detect SARS-CoV-2 with accuracy comparable to RT-qPCR. Further, there were discrepant results using different types of diagnostic tests during the clinical course of prolonged viral shedding patient. We provided insights into how to utilize different types of kits to assess and manage SARS-CoV-2 infections.

Comparison of automated SARS-CoV-2 antigen test for COVID-19 infection with quantitative RT-PCR using 313 nasopharyngeal swabs, including from seven serially followed patients

In routine clinical practice, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is determined by reverse-transcription PCR (RT-PCR). In the current pandemic, a more rapid and high-throughput method is in growing demand. Here, we validated the performance of a new antigen test (LUMIPULSE) based on chemiluminescence enzyme immunoassay. A total of 313 nasopharyngeal swabs (82 serial samples from 7 infected patients and 231 individual samples from 4 infected patients and 215 uninfected individuals) were analyzed for SARS-CoV-2 with quantitative RT-PCR (RT-qPCR) and then subjected to LUMIPULSE. We determined the cutoff value for antigen detection using receiver operating characteristic curve analysis and compared the performance of the antigen test with that of RT-qPCR. We also compared the viral loads and antigen levels in serial samples from seven infected patients. Using RT-qPCR as the reference, the antigen test exhibited 55.2% sensitivity and 99.6% specificity, with a 91.4% overall agreement rate (286/313). In specimens with > 100 viral copies and between 10 and 100 copies, the antigen test showed 100% and 85% concordance with RT-qPCR, respectively. This concordance declined with lower viral loads. In the serially followed patients, the antigen levels showed a steady decline, along with viral clearance. This gradual decline was in contrast with the abrupt positive-to-negative and negative-to-positive status changes observed with RT-qPCR, particularly in the late phase of infection. In summary, the LUMIPULSE antigen test can rapidly identify SARS-CoV-2-infected individuals with moderate to high viral loads and may be helpful for monitoring viral clearance in hospitalized patients.

Analysis of Covid-19 and non-Covid-19 viruses, including influenza viruses, to determine the influence of intensive preventive measures in Japan

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The prevalence of infected patients with SARS-CoV-2 or other viruses is unknown.

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We analyzed SARS-CoV-2 and 17 viruses in 191 patients with cold-like symptom in Japan.

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21 % of patient (n = 40) was infected at least one virus, including SARS-CoV-2 (n = 8).

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No influenza virus was observed in this study.

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The data implies different infectivity between influenza and SARS-CoV2.

Background

Severe acute respiratory coronavirus 2 (SARS-CoV-2) has spread and caused death worldwide. Preventive measures and infection control are underway, and some areas show signs of convergence. Other viruses in addition to SARS-CoV-2 cause cold-like symptoms and spread in the winter. However, the extent to which SARS-CoV-2, influenza viruses and other causative viruses have prevailed since implementing preventive measures is unclear.

Objectives

We aim to investigate the incidence of causative viruses and pathogens in patients.

Study design

We collected 191 nasopharyngeal swabs from patients with cold-like symptoms in Japan. All samples were subjected to multiplex PCR with the FilmArray Respiratory Panel and reverse transcription PCR (RT-PCR) to detect SARS-CoV-2.

Results

FilmArray Respiratory Panel analysis detected at least one virus in 32 of 191 patients with cold-like symptoms (21 %). Of these, we frequently identified human rhinoviruses/enteroviruses (5.8 %, n=11), human metapneumovirus (3.7 %, n=7), coronavirus 229E (2.1 %, n=4) and coronavirus OC43 (1.6 %, n=3); while no influenza viruses were detected. RT-PCR analysis detected SARS-CoV-2 (4.2 %, n=8) in patients who were not infected with the aforementioned respiratory viruses.

Conclusions

Co-infection with SARS-CoV-2 and other viruses was not observed. Causative viruses remain prevalent after implementing preventive measures. SARS-CoV-2 differs from influenza viruses in its infectivity.

Approximations for compound Poisson and Pólya processes

Suppose Xi≧0 are i.i.d., i = 1, 2, ···. We derive a saddlepoint approximation for P{∑N(t)k=1Xk> y} as y→∞ and t is fixed, where N(t), t≧0, is either a Poisson or a Pólya process. These results are then compared and contrasted with the well-known Esscher approximation.

Changes in the properties of mouse tongue muscle fibres before and after weaning

The purpose of this study was to clarify any changes in muscle fibre properties in different regions of murine tongue during development, and to assess the effects of functional changes including weaning on these muscle fibres. The tongue was divided into upper and lower regions at the lateral margin, and the expression of myosin heavy chain (MHC) isoforms at different ages was investigated. Expression of genes encoding MHC proteins was quantified at the transcription level by quantitative reverse transcriptase polymerase chain reaction, and the protein expression of MHC isoforms was assessed by immunostaining. No difference was found in isoform expression between the upper and lower regions of the tongue before weaning. However, the expression of MHC-2b increased markedly in both regions after weaning, while that of MHC-2a decreased. At the age of 16 weeks, the expression of MHC-2b in the lower region was greater than that in the upper region. These findings show that during weaning, when there is a shift from sucking behaviour to mastication, the expression of MHC-2b increases along with an increase in the speed and strength of muscle contraction. Also, contraction force becomes stronger in the lower region of the tongue than the upper region at the age of 16 weeks.

Immunotherapy before and during pregnancy improves pregnancy outcome in women who suffer from recurrent abortion and did not benefit from immunotherapy before pregnancy

PROBLEM

The appropriate modality of immunotherapy with the husband's mononuclear cells in women with a history of recurrent abortion who aborted despite the immunotherapy performed before pregnancy was explored.

METHOD OF STUDY

Nineteen patients who had suffered from recurrent abortion who had received the immunotherapy only before pregnancy and had aborted were treated with further immunotherapy performed either only before pregnancy or twice: before and during pregnancy.

RESULTS

In 9 out of the 19 women who received further immunotherapy before pregnancy, 2 had healthy babies and 7 aborted again. In the remaining 10 patients who received further immunotherapy twice, before and during pregnancy, 8 had healthy babies and 2 aborted again.

CONCLUSION

Our results indicate that immunotherapy performed before and during pregnancy produces a better outcome compared with that performed only before pregnancy, especially in patients who showed no benefit from the immunotherapy performed only before pregnancy.

Heparin-binding activity of feline herpesvirus type 1 glycoproteins

Feline herpesvirus type 1 (FHV-1) possesses a very narrow host range, but the mechanism of its infection has not yet been analyzed. Heparan sulfate on the cell surface serves as a receptor for several herpesviruses. In this study, we determined that infection of FHV-1 is inhibited by addition of soluble heparin in cells cultures. Using heparin-affinity column, it was shown that FHV-1 gC is a major heparin-binding protein, and FHV-1 gB weakly binds to heparin, but FHV-1 gD does not. Furthermore, the FHV-1 gC expressed in insect cells can also bind to heparin despite of being immature glycosylation. Our results suggested that FHV-1 gC can bind to heparin as observed in other herpesviruses and that glycosylation of the gC does not affect its heparin-binding activity. In addition, mice immunized with the gC expressed in insect cells produced complement-dependent virus-neutralizing antibody.

Beta2-glycoprotein I-dependent anticardiolipin antibody in early recurrent spontaneous abortion

The objective of this study was to assess the clinical significance of autoimmune anticardiolipin antibody that can react with cardiolipin only in the presence of beta2-glycoprotein I (beta2-glycoprotein I-dependent anticardiolipin antibody) in the pathogenesis of early recurrent abortion. A total of 72 early recurrent spontaneous aborters and 175 normal healthy women were analysed for the occurrence of beta2-glycoprotein I-dependent anticardiolipin antibody in serum samples by an enzyme-linked immunosorbent assay specific for the detection of beta2-glycoprotein I-dependent anticardiolipin antibody. The incidence of beta2-glycoprotein I-dependent anticardiolipin antibody in the early recurrent spontaneous aborters was essentially the same as that of normal women. Thus, the beta2-glycoprotein I-dependent anticardiolipin antibody seemed to have little, if any, implication in the pathogenesis of early recurrent spontaneous abortion.

Presence of HLA-G-expressing cells modulates the ability of peripheral blood mononuclear cells to release cytokines

PROBLEM

Human leukocyte antigen-G (HLA-G) is thought to be at play in maternal-fetal immune interplay during pregnancy. Whether the expression of HLA-G protein on the target cells altered the release of cytokines from effector mononuclear cells was questioned.

METHOD OF STUDY

The amounts of cytokines released from peripheral blood mononuclear cells (PBMC) cocultured with or without HLA-G-expressing target cells were compared.

RESULTS

When cocultured with HLA-G-expressing target cell lines, the amounts of interleukin-3 (IL-3) and interleukin-1 beta (IL-1 beta) released from PBMC were increased, whereas the amounts of tumor necrosis factor-alpha (TNF-alpha) were decreased.

CONCLUSIONS

Mononuclear cells, if cultured with HLA-G-expressing cells, modulate their ability to release cytokines, suggesting a role of HLA-G in triggering maternal-fetal immune interplay and thereby maintaining pregnancy.

Human T-lymphotropic virus type I associated myelopathy treated effectively with lymphocytapheresis using a leukocyte removal filter

The patient, a 61-year-old woman, received a blood transfusion at the age of 33 years. Weakness of the lower extremities developed at the age of 42 and the diagnosis of human T-lymphotropic virus type I (HTLV-I) associated myelopathy was made. Somatosensory evoked potential examination showed that the latency of P27 evoked by peroneal nerve stimulation was 44 msec. Lymphocytapheresis was performed 3 times with one-week intervals using a leukocyte removal filter. The muscle weakness began to improve on the second day after the second lymphocytapheresis and the sensory impairment began to improve on the third day after the third lymphocytapheresis. The delayed latency of P27 improved after the lymphocytapheresis. The effectiveness of lymphocytapheresis in this case suggests that lymphocytes are involved in the pathogenesis of HTLV-I associated myelopathy.

Pharmacokinetics and optimum dose of disopyramide in patients with chronic renal failure

The pharmacokinetics and optimum dose for maintenance of disopyramide (DP) which is effective against arrhythmia were studied in patients with chronic renal failure (CRF, n = 10), who had a creatinine clearance (Ccr) less than 30 ml/min. The plasma concentrations (PC) of DP and mono-isopropyl-disopyramide (MDP) an active metabolite of DP, were measured by high performance liquid chromatography. Samples from patients and controls were obtained at 0, 1, 2, 3, 4, 6, 8, 12, 24, 33, and 48 hr after oral administration (OA) of 100 mg DP. The pharmacokinetic parameters were calculated using a two-compartment model. In CRF, the plasma half life (T 1/2) of DP was 5.25 to 22.42 hr (average is 12.45 hr) and that of MDP was 5.09 to 131.66 hr (average is 16.9 hr). In normal controls, the T 1/2 of DP was 6.05 hr, but that of MDP could not be determined the available sensitivity of measurement. T max was 3.11 hr at the total PC of DP and MDP, and C max was 2.48 g/ml on average. In conclusion, the present study revealed that: (1) the PC of a mixture of DP and MDP should rise following OA of DP every 8 or 12 hr in CRF; (2) it is necessary therefore to monitor the accumulation of MDP after rolling OA of DP; and (3) OA of DP every 24 hr can maintain an effective PC.

[Platelet aggregation in chronic renal failure--whole blood aggregation and effect of guanidino compounds]

Studies were performed on the platelet aggregation (PA) in patients with chronic renal failure (CRF) and normal subjects (NS). The PA was investigated in the whole blood by the electrical impedance method. The concentrations of plasma (P-) and erythrocyte (E-) guanidinosuccinic acid (GSA) and methylguanidine (MG) in uremic patients with CRF were determined by high performance liquid chromatography. GSA and MG are guanidino compounds (GC) and have been widely shown to act as uremic toxins. The effects of GSA and/or MG on the PA of NS were also investigated. The results showed that the PA of conservative therapy patients with CRF was significantly lower than that of NS, while the PA of hemodialysis (HD) patients was improved. The PA of continuous ambulatory peritoneal dialysis (CAPD) patients was rather high and the possibility of sugar and lipid metabolic disorders was suggested as the cause. The concentrations of P- and E-GSA and MG in uremic patients with CRF were increased. But there were no significant correlations between the PA and the concentrations of GSA and MG. In vitro, GSA and/or MG at a high concentration exerted a significant inhibitory effect, while at a low concentration they showed a lesser inhibitory effect on the PA. In conclusion, based on their inhibition of the PA in patients with CRF, the dialyzable materials, GSA and MG, are considered to represent active uremic toxins.