Direct comparison of Xpert Xpress, FilmArray Respiratory Panel, Lumipulse antigen test, and RT-qPCR in 165 nasopharyngeal swabs.

BACKGROUND: The nucleic acid amplification test (NAAT) and antigen test are approved diagnostic tests for COVID-19. In this study, we aimed to investigate the assay performance of two NAATs (Xpert Xpress SARS-CoV-2 and FilmArray Respiratory Panel) and a quantitative antigen test (Lumipulse). METHODS: One hundred and sixty-five nasopharyngeal swabs were subjected to Xpert, FilmArray, Lumipulse, and RT-qPCR assays. RESULTS: Of 165 samples, RT-qPCR showed 100 positives and 65 negatives. The Xpert had an overall agreement of 99.4% (95% confidence interval [CI]: 96.7-99.4%), sensitivity of 99% (95% CI: 96.8-99%), and specificity of 100% (95% CI: 96.6-100%). FilmArray had an overall agreement of 98.8% (95% CI: 95.9-98.8%), sensitivity of 98% (95% CI: 95.6-98%), and specificity of 100% (95% CI: 96.3-100%). Lumipulse had an overall agreement of 95.5% (95% CI: 91.8-95.5%), sensitivity of 92.3% (95% CI: 89.2-92.3%), and specificity of 100% (95% CI: 95.5-100%). The κ coefficient showed excellent agreement between each test and RT-qPCR. There was a high correlation between Xpert Ct values, RT-qPCR Ct values, viral loads and antigen level. CONCLUSIONS: Xpert Xpress and FilmArray Respiratory Panel exhibited an equivalent performance. The Lumipulse antigen test was slightly less sensitive than the NAATs, but showed high assay performance except for samples with low viral load. The Xpert Xpress, FilmArray Respiratory Panel and Lumipulse antigen tests offer rapid sample-to-answer data, allowing random access detection on automated devices.

Cystoisospora belli associated persistent diarrhea in an AIDS patient.

Cystoisospora belli infection is regarded as an indicator disease of AIDS in Japan; however, only a few case reports showing this association are present. Our case study involved a 49-year-old Thai woman living in Japan since her marriage to a Japanese man. She was repeatedly hospitalized owing to persistent diarrhea. Considering her native country, she was suggested of having AIDS. Serological examination for HIV-1 tested positive, and C. belli infection was diagnosed on detection of oocysts in her stool samples. She was treated successfully for the parasitic infection with oral trimethoprim-sulphamethoxazole therapy for 10 days. No AIDS-associated opportunistic infections other than cystoisosporiasis were detected. Thus, this study suggests that an immunocompromised individual with persistent and recurrent diarrhea should be examined to confirm for C. belli infection. Moreover, it is possible that a person in a high-latitude region will develop a parasitic infection common in tropical areas because of globalization.

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.

Food allergy in nursery children of Kawasaki city, Japan.

BACKGROUND: Food allergies are often life threatening. In order to establish appropriate food allergy measures in nursery children, it is important to analyze local epidemiological data on the food allergy prevalence in nursery children. However, no such data are currently available for the city of Kawasaki, Japan. OBJECTIVE: The present study retrospectively evaluated food allergy prevalence among nursery children in Kawasaki city. METHODS: Data from children with food allergies requiring food avoidance in the nurseries of Kawasaki city between 2007 and 2016 were evaluated. RESULTS: From 2007 to 2016, the prevalence of food allergies among nursery children in Kawasaki city increased from 2.7% to 5.3%. The increase of food allergy prevalence was higher in 2-5 year-old children than in 0-1 year-old children (2.0% to 4.7% vs. 5.3% to 7.0%, respectively). The top five most common food allergies were hen's egg (73.0%), cow's milk (29.3%), nuts (9.7%), soy (8.9%), and wheat (6.5%). Hen's egg was consistently identified as a causative food of food allergy in more than 70% (73.0-89.1%) of food avoidance cases over the 10 year period. The increase of egg allergy prevalence was higher in 2-5 year-old children than in 0-1 year-old children (1.7% to 3.2% vs. 5.2% to 6.0%, respectively). CONCLUSIONS: Food allergies, to hen's egg in particular, have increased considerably among nursery children in the city of Kawasaki, Japan, and that increase was higher among older children.

The utility of ground-glass attenuation score for anticancer treatment-related acute exacerbation of interstitial lung disease among lung cancer patients with interstitial lung disease.

BACKGROUND: Acute exacerbation (AE) of interstitial lung disease (ILD) is a fatal adverse event in the treatment of lung cancer patients with ILD. The value of pre-treatment radiological findings obtained by high-resolution computed tomography for the detection of anticancer treatment-related AE of ILD has not been established. METHODS: Two medical record-based retrospective studies were performed. The chemotherapy cohort included 105 lung cancer patients with ILD who received chemotherapy at Tokyo Medical and Dental University between October 2008 and December 2017. The immune checkpoint inhibitor (ICI) cohort included 48 advanced non-small cell lung cancer patients with ILD treated with ICIs at nine institutions between January 2016 and September 2018. Variables were compared between AE-positive and -negative groups. Candidate variables were analyzed by multivariate logistic regression. A P value < 0.05 was considered statistically significant. RESULTS: Anticancer treatment-related AE of ILD occurred in 12 patients (11.4%) in the chemotherapy cohort and seven patients (14.5%) in the ICI cohort. In the multivariate logistic regression analysis, ground-glass attenuation (GGA) score was the only factor significantly associated with the development of AE of ILD in both cohorts (P = 0.037 and 0.01 in the chemotherapy and ICI cohorts, respectively). CONCLUSION: Evaluation of GGA may help predict anticancer treatment-related AE of ILD.

[A child case of surfer's myelopathy].

We report a case of so-called "surfer's myelopathy" involving a 15-year-old girl. Preceding episodes of vaccination and infection were absent. She experienced back pain during a surfing class for beginners, followed by weakness in both legs, which progressed to paraperesis. Then, 2 days later, sensory disturbance and bladder/rectal disturbance also developed. Spinal MRI revealed a ischemic lesion compatible with anterior spinal cord syndrome. A combination of methylprednisolone pulse therapy and high-dose intravenous immunoglobulin therapy was effective leaving no residual dysfunction. The acute onset during the surfing class and characteristic MRI findings led to the diagnosis of surfer's myelopathy. Although rarely reported, warnings are warranted to prevent surfer's myelopathy and avoid the progressive deterioration of neurological dysfunction.

Brief Report: Tepotinib as a Treatment Option in MET Exon 14 Skipping-Positive Lung Cancers-Investigating Discordance Between ArcherMET and the Oncomine Dx Target Test.

Introduction: NSCLC is a leading cause of cancer-related mortality worldwide. Specific genetic alterations, such as MET exon 14 (METex14) skipping, have been identified in NSCLC, allowing targeted therapy. Tepotinib, a highly selective MET inhibitor, has displayed promise in patients with advanced NSCLC. Nevertheless, challenges arise when identifying treatment strategies for patients with discordant results regarding METex14 skipping detection between diagnostic tests. Methods: We investigated patients with NSCLC and discordant results for METex14 skipping between the Oncomine Dx Target Test (ODxTT) and ArcherMET. Clinical response, adverse events, and the duration of tepotinib treatment were assessed, and statistical analysis was performed. Results: Among the 19 patients deemed METex14 skipping positive by ODxTT, only 10 had concordant results with ArcherMET. The number of METex14 skipping reads detected by ODxTT was significantly lower in discordant cases. Of the 19 patients, 14 received tepotinib, and comparable response and disease control rates were observed in both concordant and discordant cases. The duration of treatment did not significantly differ between the two groups. Conclusions: Our findings suggest that tepotinib has comparable therapeutic effects in patients with METex14 skipping-positive NSCLC irrespective of the concordance of results between ODxTT and ArcherMET. Tepotinib is a possible treatment option for patients with METex14 skipping, even in patients with discordant test results.

Comparison of diagnostic performance between Oncomine Dx target test and AmoyDx panel for detecting actionable mutations in lung cancer.

Companion diagnostic (CDx) tests play important roles in identifying oncogenic driver genes and tailoring effective molecularly targeted therapies for lung cancer patients. In Japan, the Oncomine Dx target test (ODxTT) and the AmoyDx pan lung cancer PCR panel (AmoyDx) are prominent CDx tests and only one of these tests is covered by the domestic insurance system. However, these CDx tests cover different target regions and apply different technologies (ODxTT is amplicon-based next-generation sequencing and AmoyDx is multiplex PCR-based assay), which may lead to missing of actionable mutations affecting patient prognosis. Here, we performed a direct comparison analysis of 1059 genetic alterations of eight driver genes from 131 samples and evaluated the concordance between two CDx tests for detecting actionable variants and fusions. When excluding the eight uncovered variants (ODxTT: two variants, AmoyDx: six variants), the overall percent agreement was 97.6% (1026/1051) with 89.0% of overall positive percent agreement (89/100) and 98.5% of overall negative percent agreement (937/951). Of the 25 discordant genetic alterations, two were undetected despite being covered in the AmoyDx (one EGFR variant and one ROS1 fusion). Furthermore, there were potential false positives in the ODxTT (nine MET exon 14 skippings) and in the AmoyDx (five variants, six ROS1 and three RET fusions). These potential false positives in the AmoyDx likely due to non-specific amplification, which was validated by the unique molecular barcoding sequencing. The ODxTT missed two uncovered EGFR rare variants, which was visually confirmed in the raw sequencing data. Our study provides insights into real-world performance of CDx tests for lung cancer and ensures reliability to advance precision medicine.

[Drunkenness caused by isoniazid in a tuberculosis patient with extrapulmonary lesions on hemodialysis: a case report].

The patient was a 55-year-old man who had been on hemodialysis for 6 years for diabetic nephropathy. He was clinically diagnosed with pulmonary tuberculosis with extrapulmonary lesion after 3 years of chronic fever. His fever subsided immediately after the beginning of antituberculosis drug therapy and the antituberculosis drugs were discontinued 3 days after the initiation of the therapy. He experienced a sense of drunkenness when he received isoniazid, apparently not in association with any of the other antituberculosis drugs given. His blood trough concentration of isoniazid was nearly equal to the usual peak levels measured in patients with normal renal function. Isoniazid is often prescribed for patients with chronic renal failure without dose-reduction, because of its hepatic metabolism. But blood level of INH was found to accumulate at high levels in this patient. The high blood concentration of isoniazid in this patient with chronic renal failure may have elicited his neurological side effect.

Cytokine release syndrome complicated with severe rashes induced by nivolumab plus ipilimumab therapy in a patient with non-small cell lung cancer: A case report.

Cytokine release syndrome (CRS) is a severe and life-threatening toxicity typically reported in chimeric antigen receptor T cell therapy and is rarely reported in immune checkpoint inhibitor (ICI) therapy. This study reports the case of a 75-year-old Japanese woman who received nivolumab plus ipilimumab therapy for the postoperative recurrence of non-small cell lung cancer. She was admitted to our hospital with fever, hypotension, hepatic disorder, and thrombocytopenia. We observed slight skin rashes on her neck on admission, which spread rapidly across her body within a few days. We diagnosed CRS complicated by severe rashes. CRS symptoms were resolved with corticosteroid therapy, and did not recur thereafter. CRS is a rare, but important, immune-related adverse event associated with ICI therapy.

Lung tropism in hospitalized patients following infection with SARS-CoV-2 variants from D614G to Omicron BA.2.

BACKGROUND: The genetic and pathogenic characteristics of SARS-CoV-2 have evolved from the original isolated strains; however, the changes in viral virulence have not been fully defined. In this study, we analyzed the association between the severity of the pathogenesis of pneumonia in humans and SARS-CoV-2 variants that have been prevalent to date. METHODS: We examined changes in the variants and tropism of SARS-CoV-2. A total of 514 patients admitted between February 2020 and August 2022 were included and evaluated for pneumonia by computed tomography (CT) as a surrogate of viral tropism. RESULTS: The prevalence of pneumonia for each variant was as follows: D614G (57%, 65/114), Alpha (67%, 41/61), Delta (49%, 41/84), Omicron BA.1.1 (26%, 43/163), and Omicron BA.2 (11%, 10/92). The pneumonia prevalence in unvaccinated patients progressively declined from 70% to 11% as the variants changed: D614G (56%, 61/108), Alpha (70%, 26/37), Delta (60%, 38/63), BA.1.1 (52%, 15/29), and BA.2 (11%, 2/19). The presence of pneumonia in vaccinated patients was as follows: Delta (16%, 3/19), BA.1.1 (21%, 27/129), and BA.2 (11%, 8/73). Compared with D614G, the areas of lung involvement were also significantly reduced in BA.1.1 and BA.2 variants. CONCLUSIONS: Compared with previous variants, there was a marked decrease in pneumonia prevalence and lung involvement in patients infected with Omicron owing to decreased tropism in the lungs that hindered viral proliferation in the alveolar epithelial tissue. Nevertheless, older, high-risk patients with comorbidities who are infected with an Omicron variant can still develop pneumonia and require early treatment.

The SARS-CoV-2 virus changes over time with the differing viruses described as variants. The different variants of SARS-CoV-2 have an impact on how easily they infect people and the effects they have on infected individuals. Here, we examined images of the lungs of patients hospitalized with COVID-19 to investigate whether they had pneumonia, a type of swelling in the lung. Compared with the variant found early in the pandemic, the more recent Omicron variant led to a decreased rate of pneumonia in infected individuals. Our findings emphasize the need for early treatment, as pneumonia may progress in older patients or those with other illnesses.

Nucleic Acid Quality Assessment is Critical to the Success of the Oncomine Dx Target Test for Lung Cancer.

BACKGROUND AND OBJECTIVE: The Oncomine Dx Target Test (ODxTT) has been used as a companion diagnostic test for lung cancer. Here, we evaluated whether the amount of nucleic acid and the degree of RNA degradation are related to the success of the ODxTT. METHODS: This study included 223 samples from 218 patients with lung cancer. For all samples, DNA and RNA concentrations were quantified using Qubit, and the degree of RNA degradation was evaluated using the Bioanalyzer. RESULTS: Of the 223 samples, 219 samples were successfully analyzed in the ODxTT and four were not. DNA analysis failed in two samples, which were attributed to low DNA concentrations and both were cytology specimens. Meanwhile, RNA analysis failed in the other two samples. These samples had sufficient amounts of RNA, but it was highly degraded with DV200 (the percentage of RNA fragments > 200 base pairs) less than 30. Compared with RNA samples with DV200 ≥ 30, analysis of RNA with DV200 < 30 yielded significantly fewer reads for the internal control genes. This test showed actionable mutations were identified in 38% (83/218) of all patients and in 46.6% (76/163) of patients with lung adenocarcinoma. CONCLUSIONS: DNA concentration and degree of RNA degradation are key factors determining the success of diagnostic testing by the ODxTT.

Multidrug-resistant mutations to antiviral and antibody therapy in an immunocompromised patient infected with SARS-CoV-2.

BACKGROUND: Antiviral and antibody therapies for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are being recommended for high-risk patients, but the potential for the development of multidrug-resistant mutations in immunocompromised patients is unclear. METHODS: To investigate the treatment course in cases of prolonged viral shedding in an immunocompromised patient with SARS-CoV-2 infection, we conducted longitudinal measurements of laboratory tests, chest computed tomography (CT) image evaluations, antibody titers, and antigen levels in nasopharyngeal swabs. Furthermore, we performed whole-genome sequencing and digital PCR analysis to examine the mechanisms of drug resistance. FINDINGS: We present a case of a 65-year-old man with a history of malignant lymphoma who was treated with multiple antiviral and antibody therapies, including sotrovimab, remdesivir, paxlovid (nirmatrelvir/ritonavir), and molnupiravir. Initially, viral antigen levels decreased after treatments. However, after the virus rebounded, the patient showed no virologic response. The viral genome analysis revealed a single Omicron subvariant (BA.1.1), which evolved within the host during the disease progression. The viruses had acquired multiple resistance mutations to nirmatrelvir (3 chymotrypsin-like protease [3CLpro] E166 A/V), sotrovimab (spike P337L and E340K), and remdesivir (RNA-dependent RNA polymerase [RdRp] V166L). CONCLUSIONS: Our results indicate that viruses with multidrug-resistant mutations and survival fitness persist in the infected subpopulation after drug selection pressure. FUNDING: This study was supported by the JSPS KAKENHI Early-Career Scientists 18K16292 (Y.H.), Grant-in-Aid for Scientific Research (B) 20H03668 and 23H02955 (Y.H.), the YASUDA Medical Foundation (Y.H.), the Uehara Memorial Foundation (Y.H.), the Takeda Science Foundation (Y.H.), and Kato Memorial Bioscience Foundation (Y.H.).

Urinary L-Type Fatty Acid-Binding Protein Predicts Oxygen Demand of COVID-19 in Initially Mild Cases.

Early detection of illness trajectory in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected patients is crucial for patients and healthcare workers. An effective, noninvasive approach, with simple measurement for decision-making, is necessary in a pandemic to discriminate between high- and low-risk patients, even though both groups may exhibit mild symptoms in the beginning. OBJECTIVES: To predict COVID-19 disease severity within 10 days, distinguishing cases that will progress to moderate or severe versus mild, patient urinary L-type fatty acid-binding protein (L-FABP) was assayed within 4 days of receiving a diagnosis. The study also examined whether L-FABP point of care (POC) test is helpful in risk screening. DESIGN: Symptomatic subjects who tested positive for SARS-CoV-2 and were hospitalized were prospectively enrolled at the National Center for Global Health and Medicine (NCGM), Yamanashi Prefectural Central Hospital (YPCH), and Sinai Hospital in Maryland. The outcome of each case was evaluated 7 days after admission and the diagnostic performance of L-FABP was assessed. SETTING AND PARTICIPANTS: Subjects were treated for COVID-19 at public healthcare centers in Japan from January 31, 2020, to January 31, 2021, to NCGM, YPCH, and at Sinai Hospital in Baltimore, MD, during the same period. MAIN OUTCOMES AND MEASURES: The primary outcome was to determine whether urinary L-FABP within 48 hours of admission can predict the patient's severity of COVID-19 1 week later. We obtained demographic data, information on clinical symptoms, radiographic images, and laboratory data. RESULTS: Diagnostic performance was assessed using receiver operating characteristic analysis. Of the 224 participants in the study, 173 initially had a mild form of COVID-19. The area under the curve (AUC) for a severe outcome was 93.5%. L-FABP POC risk prediction of a severe outcome had an AUC of 88.9%. CONCLUSIONS AND RELEVANCE: Urinary L-FABP can predict patient risk of COVID-19 illness severity. L-FABP POC is implementable for patient management. (ClinicalTrials.gov number, NCT04681040).

Impairment of Social-Related Quality of Life in COVID-19 Pneumonia Survivors: A Prospective Longitudinal Study.

The post-acute sequelae of SARS-CoV-2 (PASC) pose a threat to patients' health-related quality of life (HRQOL). Here, the impact of COVID-19 on HRQOL and the clinical factors associated with impaired HRQOL were examined. Discharged COVID-19 patients were assessed at 3 and 6 months after disease onset. The patients completed a medical examination and the SF-36 questionnaire at these two time points and underwent pulmonary function testing at 6 months after disease onset. All had undergone computed tomography (CT) imaging upon hospital admission. Of the 74 included patients, 38% reported respiratory symptoms at 3 months, and 26% reported respiratory symptoms at 6 months after disease onset. The aggregated SF-36 scores declined in the role/social component summary (RCS), a category related to social activity. Patients with lower RCS tended to have respiratory sequelae or a relatively lower forced vital capacity. The CT score that reflected the extent of COVID-19 pneumonia was inversely correlated with the RCS score (3 months, p = 0.0024; 6 months, p = 0.0464). A high CT score (≥10 points) predicted a low RCS score at 6 months (p = 0.013). This study highlights the impairment of RCS and its associations with respiratory sequelae. The study also emphasizes the importance of radiological findings in predicting long-term HRQOL outcomes after COVID-19.

[Two cases of pulmonary tuberculosis with an intra-familial transmission route].

Two patients with smear-positive adult-type pulmonary tuberculosis (TB) were admitted to our hospital. The patients in case 1 and case 2 were a 33-year-old woman and a 33-year-old man, respectively. None of the patients' family members had any apparent symptom indicating TB. However, the father of patient 1 was found to have recurrent TB with a positive smear in the contact investigation. The mother of patient 2 was then admitted to a hospital with acute respiratory failure caused by recurrence of TB. Her sputum sample also turned out to be smear-positive. Restriction fragment length polymorphism (RFLP) analysis of the isolates revealed identical DNA patterns in each pair of family members. These cases were typical examples of intra-familial infections involving young adults and their parents. This route of transmission is still important in areas with low prevalence of the disease.

Measures for food allergy emergency in nurseries.

Background: As food allergy potentially can induce life-threatening anaphylaxis, measures for food allergy are required at nurseries caring for food allergy children, but a large-scale factual investigation has not been carried out. Objective: We evaluated measures for food allergy emergency in nurseries. Methods: A questionnaire survey regarding emergency measures in all authorized nurseries (411 facilities including 20,586 children) was conducted in Kawasaki city, Japan. Results: The recovery rate of the questionnaire was 46.5%, which include 14,343 children of 191 facilities in total. A total of 637 children (4.4%) in 157 facilities (82.2%) requires elimination diets that were suggested by physicians. Among them, 22 children had been suggested to undergo the use of epinephrine auto-injection kit for emergency. 161 facilities (84.3%) had set a specific manual for emergency of food allergy. Emergency cases over the past one year were 4 cases and there was no case that had been suggested to use epinephrine auto-injection kit. All were anaphylaxis and the causes of these included 2 accidental digestion of culprit foods and the causes of other 2 cases were unknown. A case who required no elimination diet showed first episode of anaphylaxis. All cases were recovered. Conclusion: High percentage of nurseries in Kawasaki city has cared for food allergy children. While many children with food allergy have been in nurseries, only several cases of anaphylaxis have been reported for a 1 year. Among 4 cases of anaphylaxis, no specific cause has been recognized in 2 cases and 1 case has been the first episode of anaphylaxis. While most of nurseries have set specific measures for emergency of food allergy, there is certain possibility that nursery staffs can encounter the first episode of anaphylaxis even if there is no food allergy child. For all nurseries, emergency measures for food allergy are vital.

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.

A phase II feasibility study of carboplatin and nab-paclitaxel for advanced non-small cell lung cancer patients with interstitial lung disease (YLOG0114).

BACKGROUND: A standard treatment regimen for advanced non-small cell lung cancer (NSCLC) patients with interstitial lung disease (ILD) has not been established since most clinical trials exclude such patients because of the high risk of acute exacerbation of ILD. This study aimed to prospectively investigate the efficacy and safety of carboplatin and nab-paclitaxel as a first-line regimen for NSCLC patients with ILD. METHODS: The enrolled patients had treatment-naïve advanced NSCLC with ILD. The patients received 4-6 cycles of carboplatin (area under the curve = 5) on day 1 and nab-paclitaxel 100 mg/m2 on days 1, 8, and 15 every 4 weeks. The primary endpoint was the completion rate of four or more cycles. Secondary endpoints included toxicity, overall response rate (ORR), disease control rate (DCR), progression-free survival (PFS), and overall survival (OS). RESULTS: Twenty-five patients were enrolled in this study. Nine patients had adenocarcinoma, 11 had squamous cell carcinoma, one had large cell carcinoma, and four had NSCLC, not otherwise specified. The completion rate of ≥4 cycles was 76% (95% confidence interval: 56.2%-88.8%), which met the primary endpoint. The ORR and DCR were 44% and 88%, respectively. The median PFS and OS were 5.8 months and 15.8 months, respectively. Three patients experienced grade ≥2 pneumonitis, and one patient met the acute exacerbation criteria. CONCLUSION: The 4-week modified regimen of carboplatin and nab-paclitaxel showed tolerable toxicity with favorable efficacy in NSCLC patients with ILD. This regimen may be an effective treatment option for patients in real clinical settings.