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.

Functional Morphologic Changes of the Heel Fat Pad and Plantar Fascia in Patients With Heel Pain During Weightbearing and Nonweightbearing.

Background: This study aimed to investigate the thickness changes of the heel fat pad and the plantar fascia associated with loading and unloading in healthy individuals and patients with heel pain and reveal the differences between them. Methods: The study included adult male participants with (n = 9) and without (n = 26) heel pain. The participants placed their right foot on an evaluation apparatus with a polymethylpentene resin board (PMP), while their left foot was positioned on a weighing scale used to adjust the loading weight. The heel fat pad was differentiated into superficial Microchamber and deep Macrochamber layers. These layers and plantar fascia thickness were measured using an ultrasonographic imaging device at loading phase ranging from 0% to 100% of their body weight and unloading phase from 100% to 0%. Additionally, the study examined the thickness change ratios of the superficial and deep heel fat pad layers when the load increased from 0% (unload) to 100% (full load). Results: In healthy individuals and patients with heel pain, no significant thickness changes were observed in the Microchamber layer of the heel fat pad or the plantar fascia during loading and unloading evaluations. However, significant thickness changes were observed in the Macrochamber layer of the heel fat pad, and the pattern of change differed between the loading and unloading phases. Additionally, patients with heel pain showed differences in the thickness change and thickness change ratios of the microchamber and macrochamber layers of the heel fat pad during both loading and unloading phases. The thickness of the plantar fascia did not show significant differences between both groups. Conclusion: Compared with healthy individuals, in our relatively small study, patients with heel pain had greater deep fat pad compression in loading and less recovery after load removal. This finding suggests that these patients have different intrinsic fat pad function and related morphology than those without heel pain. Level of Evidence: Level III, retrospective cohort study.

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.

Differences in Lumbopelvic Alignment in Adolescent Male Soccer Players With Bilateral and Unilateral Lumbar Bone Stress Injuries: An MRI Evaluation.

Background: Differences in the physical characteristics of bilateral and unilateral lumbar bone stress injuries (BSIs) are unknown. Purpose: To compare bilateral and unilateral lumbar BSIs in adolescent male soccer players, with a focus on lumbopelvic alignment. Study Design: Cross-sectional study; Level of evidence, 3. Methods: A total of 78 players (age range, 12-15 years) from a local soccer club who had magnetic resonance imaging (MRI) evaluations were included in the study. Lumbopelvic alignment and lumbar BSI were evaluated using short-tau inversion recovery and 3-dimensional LAVA on 3-T MRI; lumbar BSI was defined as the presence of bone marrow edema and/or the complete and incomplete fracture in the pars region on the MRI. Pelvic tilt (PT) and pelvic outflare angles were assessed on the kicking and pivoting sides, and asymmetry for each parameter was calculated by subtracting the kicking side from the pivoting side. In addition, the lumbar lordosis (LL), sacral slope (SS), and SS relative to LL (calculated by subtracting LL from the SS) were assessed. One-way analysis of variance was performed to compare lumbopelvic alignment in players with bilateral BSI, unilateral BSI, or no abnormal findings (controls). Results: No significant differences were found regarding lumbopelvic alignment between the players with bilateral versus unilateral lumbar BSI. PT asymmetry was significantly greater in both players with bilateral lumbar BSI and unilateral lumbar BSI compared with controls (P = .018 and P = .016, respectively). In addition, SS relative to LL was significantly greater in players with bilateral lumbar BSI compared with controls (P < .001). Conclusion: Although there were no significant lumbopelvic alignment differences between bilateral and unilateral BSI, players with bilateral BSI exhibited increased sacral anterior tilt relative to the LL, and the pelvis was more posterior on the pivoting side than on the kicking side in both players with bilateral BSI and unilateral BSI. Our results suggest that lumbopelvic alignment assessment may contribute to the management strategy for players with lumbar BSI and to the identification of players at high risk of lumbar BSI.

Longitudinal changes in youth baseball batting based on body rotation and separation.

BACKGROUND: Identifying the characteristics of batting mechanics, such as the proper angle and position of each body segment in youth baseball players, is important for proper instructions. This study aimed to identify the age-related changes in batting kinematics including rotational and separational movements of the head, upper trunk, pelvis, and arms, in youth baseball players. METHODS: Over the three seasons, we measured the batting motion of baseball players aged 6- to 12 years using three high-speed cameras. Participants were divided into six age categories according to the little league eligibility rules (players were classified according to their age as of July 31 of a given year). Toss batting was performed using an automatic tossing machine set obliquely in front of the batter. Additionally, we analyzed the rotation angles of the head, upper trunk, pelvis, and arm direction, and the separation angles-calculated using the difference of each rotational angle and the head movement distance and step width-at five points in batting phase: stance, load, foot contact, pre-swing, and ball contact. Finally, 17 players from under 8 (U8, i.e., approximately 7-8 years) to U10 and 13 from U11 to U13 were analyzed. A one-way repeated measures analysis of variance was performed to analyze age-related changes in batting kinematics. RESULTS: Several age-related changes in batting kinematics at various batting point were observed. The head-to-upper trunk separation angle increased with age from U8 to U10 during the foot contact (effect sizes [ES] = 0.658) and from U11 to U13 during the pre-swing (ES = 0.630). Additionally, the U13 showed a significantly increase in the upper and pelvis separation angles during load, foot contact, and pre-swing compared with U11 and U12 (ES = 0.131, 0.793, and 0.480). CONCLUSION: Various changes in batting kinematics occurred among each age group. Notably, U12 and U13 had the greater upper trunk-to-pelvis separation angle at foot contact and pre-swing compared to U11. Therefore, it would be important for the instruction of younger baseball players to understand the underdevelopment of trunk separation when batting and encourage the acquisition of such separation movements.

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.).

Characteristics of upper limb mass, muscle CSA and stiffness in adolescent baseball players with and without elbow injury.

Since elbow injuries are common in adolescent baseball players, this study aimed to determine the relationship between musculoskeletal status and elbow injuries in 47 baseball players aged 12-14 years. Participants answered a questionnaire and had their general body measurements taken. Magnetic resonance imaging was used to evaluate muscle cross sectional areas (CSA) of the upper arm flexor and extensor muscles, and x-ray absorptiometry was used to determine the mass of the upper arm and the total mass of the forearm and hand. Shear wave elastography was used to determine muscle stiffness of the biceps brachii, brachialis, pronator teres, and brachioradialis. An orthopedic surgeon performed a clinical assessment and elbow ultrasonography for each participant to diagnose elbow injuries. The measured values were compared between the elbow injury and control groups using two-sample t-tests. The elbow injury group had significantly higher muscle stiffness in the brachialis (p < 0.001) and brachioradialis (p = 0.004) muscles and greater elbow flexor CSA of the distal upper arm (p = 0.004) than the control group. The total mass of the forearm and hand and the mass ratio of the forearm and hand to the upper arm were significantly greater in the elbow injury group than in the control group (p = 0.002 and p < 0.001). Thus, it may be necessary to increase flexibility of the brachialis and brachioradialis flexible by stretching and massaging in addition to evaluating the mass distal to the elbow and the elbow flexor muscle size of the distal upper arm to manage elbow injury in youth baseball players. Characteristics of Upper Limb Mass, Muscle Cross-Sectional Area and Stiffness in Adolescent Baseball Players with and without Elbow Injury.

Risk factors of throwing injuries related to pitching mechanics in young baseball players: a longitudinal cohort study.

BACKGROUND: Risk factors for throwing injuries related to pitching mechanics are unknown. Insufficient pelvic rotation during pitching may be a risk factor for shoulder and elbow injury. This cohort study aimed to identify biomechanics risk factors for throwing injuries in young baseball players. We hypothesized that excessive mechanical load and motion errors would be risk factors for throwing injuries. METHODS: Young baseball pitchers (aged 8-9 years) were recruited from regional baseball leagues between December 2016 and December 2019. Pitching measurements were performed before the start of each season and after the end of the last season in December 2019. The trunk tilt angular displacement, pelvic rotation angular displacement, and forearm rotation angle were calculated using a markerless motion capture system. We also measured elbow varus torque using an accelerometer. After the initial test session, each participant was followed up for 3 years to determine the occurrence of throwing injuries. Players with throwing shoulder and elbow injuries were categorized into the throwing injury group, and those without shoulder and elbow pain for 3 years were categorized into the noninjured group. RESULTS: In this study, 97 baseball pitchers completed a 3-year follow-up. Among those participants, 66 (68.0%) had throwing injuries. A significant difference was observed between the throwing injury and noninjured groups, whereby the injured players had less pelvic rotation angular displacement. CONCLUSION: Insufficient pelvic rotation during pitching is a newly discovered risk factor related to throwing injuries.

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.

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.

Growth pattern of lumbar maturity stage at L1 to L5 during adolescent growth spurt.

PURPOSE: This study aimed to clarify the order of the lumbar maturity stage, each at L1 to L5, and the relationships between age at peak height velocity (APHV) and the lumbar maturity stage. METHODS: A total of 120 male first-grade junior high school soccer players were enrolled and followed for two years, and measurements were performed five times (T1 to T5). The lumbar maturity stage was assessed according to the degree of lesion of the epiphyseal from L1 to L5 using magnetic resonance imaging and classified into three stages: cartilaginous stage, apophyseal stage, and epiphyseal stage. The relationships between T1 and T5 temporal changes and developmental stages divided by 0.5 year increments based on APHV and the lumbar maturity stage at L1 to L5 were examined. For the apophyseal stage, developmental age calculated based on the difference between APHV and chronological age between each lumbar vertebra was compared. RESULTS: We found that part of the cartilaginous stages decreased as time progressed, while that of the apophyseal and epiphyseal stages increased at L1 to L5 (chi-square test, p < 0.01). L5 matured earlier with the apophyseal stage than L1 to L4 (p < 0.05). The lumbar maturity stage was attained toward L1 from L5, comparing different lumbar levels. CONCLUSION: The lumbar maturity stage progresses from L5 toward L1, and the apophyseal and epiphyseal stages would replace the cartilaginous stage at approximately 14 years of age or after APHV.

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.

Risk Factors for Symptomatic Bilateral Lumbar Bone Stress Injury in Adolescent Soccer Players: A Prospective Cohort Study.

BACKGROUND: Lumbar bone stress injury (BSI) is a high-risk long time-loss injury for adolescent soccer players. However, the risk factors for lumbar BSI are unclear. PURPOSE: To identify the risk factors for bilateral lumbar BSI for adolescent soccer players. STUDY DESIGN: Case-control study; Level of evidence, 3. METHODS: Adolescent soccer players underwent orthopaedic examination, whole-body dual energy x-ray scan, lumbar magnetic resonance imaging (MRI), and muscle tightness testing at baseline. Lumbar lordosis (LL), sacral slope, maturity stage of lumbar vertebral body, and bone marrow edema (BME) at the L5 were examined via MRI. In addition, bone mineral density and content; trunk lean body mass via dual energy x-ray scan; and bilateral muscle tightness including the iliopsoas, hamstrings, and quadriceps were measured. Lumbar BSI was diagnosed as positive bilateral BME and extension-based lumbar pain. All participants were examined twice, one at 6 months and one at 1 year, after the baseline examination. Multivariate logistic regression analysis was performed to identify the risk factors for bilateral lumbar BSI. RESULTS: A total of 69 (26.3%) players were diagnosed with bilateral lumbar BSI. Asymptomatic BME (odds ratio [OR], 4.260; 95% CI, 2.153-8.431), apophyseal stage of the lumbar vertebral body (OR, 3.438; 95% CI, 1.698-6.959), sacral slope relative to LL ≥5° (OR, 4.067; 95% CI, 2.021-8.181), and hamstring tightness ≥50° (OR, 3.221; 95% CI, 1.385-7.489) were significantly associated with bilateral lumbar BSI. CONCLUSION: The incidence of bilateral lumbar BSI was common at 26.2%. Asymptomatic BME, sacral anterior tilt relative to LL, immature lumbar epiphyses, and hamstring tightness were found to be risk factors for bilateral lumbar BSI. The results of this study suggest that regular MRI examination could facilitate the early detection of BME, and improvement in hamstring flexibility and lumbosacral alignment may prevent bilateral lumbar BSI in young athletes.

Effects of a 9-weeks arch support intervention on foot morphology in young soccer players: a crossover study.

BACKGROUND: A flat foot is a common cause of chronic sports injuries and therefore many opportunities for arch support interventions exist. However, young athletes change their foot morphology due to developmental influences even without intervention. Therefore, developmental influences need to be considered when examining the effects of arch support, but there have not been sufficient longitudinal studies to date. This study aimed to determine the effect of the arch support intervention by performing a 9-weeks arch support intervention on the foot morphology and cross-sectional area of the foot muscles in flat-footed young athletes. Thirty-one elementary school boys (Age 11.4 ± 0.5 years, Height 145.2 ± 7.4 cm, Weight 38.8 ± 8.3 kg, BMI 18.2 ± 2.2 kg/m2) with a decreased medial longitudinal arch in the foot posture index were selected as participants from a local soccer club and randomly divided into two groups. METHODS: In one group, in the intervention period, an existing arch supporter was used to provide arch support, while in the other group, no special intervention was provided in the observation period. To account for developmental effects, the intervention study was conducted as an 18-weeks crossover study in which the intervention and observational phases were switched at 9 weeks after the intervention. Foot morphology was assessed using a three-dimensional foot measuring machine, and the cross-sectional area (CSA) of the internal and external muscles of the foot was assessed using an ultrasound imaging device. We examined the effect of the intervention by comparing the amount of change in the measurement results between the intervention and observation periods using corresponding t-tests and Wilcoxon signed-rank sum test, analysis of covariance methods. RESULTS: After adapting the exclusion criteria, 14 patients (28 feet) were included in the final analysis. The CSA of the abductor hallucis muscle (ABH) increased 9.7% during the intervention period and 3.0% during the observation period (p = 0.01). The CSA of the flexor digitorum longus muscle (FDL) increased 7.7% during the intervention period and 4.2% during the observation period (p = 0.02). CONCLUSION: A 9-weeks arch supporter intervention may promote the development of the ABH and FDL CSA in young flat-footed soccer players.

Growth until Peak Height Velocity Occurs Rapidly in Early Maturing Adolescent Boys.

The timing and tempo of growth rate varies inter-individually during adolescence and can have an impact on athletic performance. This study aimed to determine the difference in growth rate for each maturity status. We combined data collected both retrospectively and prospectively from 78 adolescent boys aged 12 years old; growth charts were collected from their elementary school records, and the height of each participant was subsequently measured every six months over a period of two years. Take Off Age (TOA), Peak Height Velocity Age (PHVA), and Final Height Age (FHA) were estimated using the AUXAL 3.1 program. Growth Tempo 1 and 2 were calculated by dividing the height increase by the time difference between TOA and PHVA, and FHA, respectively. Our results showed three group differences based on the maturation status of PHVA: Growth Tempo 1 and 2 were both higher in the early than during middle and late maturation. Additionally, entering the height at each event as a covariate, the group differences for Growth Tempo 1 did not change; however, for Growth Tempo 2, group differences were eliminated. Therefore, we conclude that during early maturation, growth from TOA to PHVA occurs rapidly and in a shorter period.

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.

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.