A SARS-CoV-2 Delta variant containing mutation in the probe binding region used for RT-qPCR test in Japan exhibited atypical PCR amplification and might induce false negative result.

INTRODUCTION: A recent pandemic of SARS-CoV-2 infection has caused severe health problems and substantially restricted social and economic activities. RT-qPCR plays a vital role in the diagnosis of SARS-CoV-2 infection. The N protein-coding region is widely analyzed in RT-qPCR to diagnose SARS-CoV-2 infection in Japan. We recently encountered two cases of SARS-CoV-2-positive specimens showing atypical amplification curves in the RT-qPCR. METHODS: We performed whole-genome sequencing of 63 samples (2 showing aberrant RT-qPCR curve and 61 samples infected with SARS-CoV-2 simultaneously in the same area) followed by Phylogenetic tree analysis. RESULTS: We found that the viruses showing abnormal RT-qPCR curves were Delta-type variants of SARS-CoV-2 with a single nucleotide mutation in the probe-binding site. There were no other cases with the same mutation, indicating that the variant had not spread in the area. After searching the database, hundreds of variants were reported globally, and one in Japan contained the same mutation. Phylogenetic analysis showed that the variant was very close to other Delta variants endemic in Japan but quite far from the variants containing the same mutation reported from outside Japan, suggesting sporadic generation of mutant in some domestic areas. CONCLUSIONS: These findings propose two key points: i) mutations in the region used for SARS-CoV-2 RT-qPCR can cause abnormal amplification curves, and ii) various mutations can be generated sporadically and unpredictably; therefore, efficient and robust screening systems are needed to promptly monitor the emergence of de novo variants.

Amyloid deposits derived from transthyretin in the ligamentum flavum as related to lumbar spinal canal stenosis.

Amyloidosis is a protein conformational disorder with the distinctive feature of extracellular accumulation of amyloid fibrils that come from different proteins. In the ligamentum flavum of the lumbar spine, amyloid deposits were frequently found in elderly patients with lumbar spinal canal stenosis and were at least partially formed by wild-type transthyretin. However, how amyloid deposits in the ligamentum flavum affect lumbar spinal canal stenosis has remained unclear. In this study, we analyzed clinical, pathologic, and radiologic findings of patients with lumbar spinal canal stenosis who had amyloid deposits in the ligamentum flavum. We studied 95 ligamentum flavum specimens obtained from 56 patients with lumbar spinal canal stenosis and 21 ligamentum flavum specimens obtained from 19 patients with lumbar disk herniation. We evaluated histopathologic findings and clinicoradiologic manifestations, such as thickness of the ligamentum flavum and lumbar spinal segmental instability. We found that all 95 ligamentum flavum specimens resected from patients with lumbar spinal canal stenosis had amyloid deposits, which we classified into two types, transthyretin-positive and transthyretin-negative, and that transthyretin amyloid formation in the ligamentum flavum of patients with lumbar spinal canal stenosis was an age-associated phenomenon. The amount of amyloid in the ligamentum flavum was related to clinical manifestations of lumbar spinal canal stenosis, such as thickness of the ligamentum flavum and lumbar spinal segmental instability, in the patients with lumbar spinal canal stenosis with transthyretin-positive amyloid deposits. To our knowledge, this report is the first to show clinicopathologic correlations in transthyretin amyloid deposits of the ligamentum flavum. In conclusion, transthyretin amyloid deposits in the ligamentum flavum may be related to the pathogenesis of lumbar spinal canal stenosis in elderly patients.

A micro-disc-based multiplex method for monitoring emerging SARS-CoV-2 variants using the molecular diagnostic tool Intelli-OVI.

BACKGROUND: Highly transmissible viruses including SARS-CoV-2 frequently accumulate novel mutations that are detected via high-throughput sequencing. However, there is a need to develop an alternative rapid and non-expensive approach. Here we developed a novel multiplex DNA detection method Intelli-OVI for analysing existing and novel mutations of SARS-CoV-2. METHODS: We have developed Intelli-OVI that includes the micro-disc-based method IntelliPlex and computational algorithms of objective variant identification (OVI). More than 250 SARS-CoV-2 positive samples including wastewater ones were analysed to verify the efficiency of the method. RESULTS: IntelliPlex uses micro-discs printed with a unique pictorial pattern as a labelling conjugate for DNA probes, and OVI allows simultaneous identification of several variants using multidimensional data obtained by the IntelliPlex method. Importantly, de novo mutations can be identified by decreased signals, which indicates that there is an emergence of de novo variant virus as well as prompts the need to design additional primers and probes. We have upgraded probe panel according to the emergence of new variants and demonstrated that Intelli-OVI efficiently identified more than 20 different SARS-CoV-2 variants by using 35 different probes simultaneously. CONCLUSIONS: Intelli-OVI can be upgraded to keep up with rapidly evolving viruses as we showed in this study using SARS-CoV-2 as an example and may be suitable for other viruses but would need to be validated.

As the COVID-19 pandemic progresses, it is increasingly becoming important to be able to detect emerging new variants of concerns of SARS-CoV-2, the virus that causes COVID-19, for accurate surveillance and timely interventions. We developed a rapid diagnostic method for detecting multiple SARS-CoV-2 variants and tested it using various starting materials such as sputum, nasopharyngeal swabs and wastewater. The method could accurately detect multiple subvariants of Omicron and showed potential for rapid adaptability to detect the virus as it evolves. This technology could enable continuous monitoring of emerging SARS-CoV-2 variants and the opportunity to intercept transmission with timely interventions to prevent viral spread.

Degradation of amyloid beta by human induced pluripotent stem cell-derived macrophages expressing Neprilysin-2.

The purpose of this study was to evaluate the therapeutic potential of human induced pluripotent stem (iPS) cell-derived macrophage-like cells for Alzheimer's disease (AD). In previous studies, we established the technology to generate macrophage-like myeloid lineage cells with proliferating capacity from human iPS cells, and we designated the cells iPS-ML. iPS-ML reduced the level of Aß added into the culture medium, and the culture supernatant of iPS-ML alleviated the neurotoxicity of Aß. We generated iPS-ML expressing the Fc-receptor-fused form of a single chain antibody specific to Aß. In addition, we made iPS-ML expressing Neprilysin-2 (NEP2), which is a protease with Aß-degrading activity. In vitro, expression of NEP2 but not anti-Aß scFv enhanced the effect to reduce the level of soluble Aß oligomer in the culture medium and to alleviate the neurotoxicity of Aß. To analyze the effect of iPS-ML expressing NEP2 (iPS-ML/NEP2) in vivo, we intracerebrally administered the iPS-ML/NEP2 to 5XFAD mice, which is a mouse model of AD. We observed significant reduction in the level of Aß in the brain interstitial fluid following administration of iPS-ML/NEP2. These results suggested that iPS-ML/NEP2 may be a potential therapeutic agent in the treatment of AD.

Effect of age and sex differences on wild-type transthyretin amyloid formation in familial amyloidotic polyneuropathy: a proteomic approach.

BACKGROUND: Age and sex differences are closely related to the onset of senile systemic amyloidosis (SSA) caused by wild-type (WT) transthyretin (TTR). However, the effects of these differences on the amyloid formation mechanism in familial amyloid polyneuropathy (FAP) caused by variant TTR, have remained unclear. To elucidate age and sex differences in FAP, we investigated biochemical characteristics of amyloid deposits in different tissue sites of FAP by proteomic analysis. METHODS: We used shotgun liquid chromatography/tandem mass spectrometry to analyze the proportions of variant and WT TTR in amyloid deposits in different tissues, such as cardiac, kidney, peripheral nerves, and gastrointestinal tissues, from 23 autopsied FAP cases. RESULTS AND CONCLUSIONS: The analysis revealed a highly significant correlation between the proportion of WT TTR and age at autopsy in cardiac tissues, whereas the analysis indicated no correlation in kidney, peripheral nerves, and gastrointestinal tissues. In addition, we demonstrated age-related significantly increased WT TTR deposits, but not variant TTR deposits, in cardiac tissues of male patients. Taken together, these data suggest that both age and sex differences affect cardiac amyloid formation, mainly derived from WT TTR, in FAP.