Generation of recombinant viruses directly from clinical specimens of COVID-19 patients.

Rapid characterization of the causative agent(s) during a disease outbreak can aid in the implementation of effective control measures. However, isolation of the agent(s) from crude clinical samples can be challenging and time-consuming, hindering the establishment of countermeasures. In the present study, we used saliva specimens collected for the diagnosis of SARS-CoV-2-a good example of a practical target-and attempted to characterize the virus within the specimens without virus isolation. Thirty-four saliva samples from coronavirus disease 2019 patients were used to extract RNA and synthesize DNA amplicons by PCR. New primer sets were designed to generate DNA amplicons of the full-length spike (S) gene for subsequent use in a circular polymerase extension reaction (CPER), a simple method for deriving recombinant viral genomes. According to the S sequence, four clinical specimens were classified as BA. 1, BA.2, BA.5, and XBB.1 and were used for the de novo generation of recombinant viruses carrying the entire S gene. Additionally, chimeric viruses carrying the gene encoding GFP were generated to evaluate viral propagation using a plate reader. We successfully used the RNA purified directly from clinical saliva samples to generate chimeric viruses carrying the entire S gene by our updated CPER method. The chimeric viruses exhibited robust replication in cell cultures with similar properties. Using the recombinant GFP viruses, we also successfully characterized the efficacy of the licensed antiviral AZD7442. Our proof-of-concept demonstrates the novel utility of CPER to allow rapid characterization of viruses from clinical specimens. IMPORTANCE: Characterization of the causative agent(s) for infectious diseases helps in implementing effective control measurements, especially in outbreaks. However, the isolation of the agent(s) from clinical specimens is often challenging and time-consuming. In this study, saliva samples from coronavirus disease 2019 patients were directly subjected to purifying viral RNA, synthesizing DNA amplicons for sequencing, and generating recombinant viruses. Utilizing an updated circular polymerase extension reaction method, we successfully generated chimeric SARS-CoV-2 viruses with sufficient in vitro replication capacity and antigenicity. Thus, the recombinant viruses generated in this study were applicable for evaluating the antivirals. Collectively, our developed method facilitates rapid characterization of specimens circulating in hosts, aiding in the establishment of control measurements. Additionally, this approach offers an advanced strategy for controlling other (re-)emerging viral infectious diseases.

Primary lymphoplasmacytic lymphoma of the larynx mimicking extramedullary plasmacytoma: A case report.

Primary haematological neoplasms of the larynx are uncommon; therefore, information regarding their epidemiology is limited and the diagnosis of histological types requires careful consideration. The current study describes the case of a 72-year-old male patient with primary laryngeal lymphoplasmacytic lymphoma (LPL) that was difficult to distinguish from plasmacytoma. Imaging examinations of the neck revealed a mass in the right laryngeal folds, 25×12×25 mm in size, which was surgically resected by direct laryngoscopy. Histopathologically, the mass showed diffuse proliferation of plasma cells with CD138 (+) and IgG (+) in the submucosal stroma. Flow cytometry revealed the tumour was positive for CD19 and negative for CD56. Based on these findings, the final diagnosis was confirmed as LPL, albeit similar to plasmacytoma regarding phenotypic features. There was no evidence of local or systemic recurrence following surgery, and the patient has been followed up without additional treatment. This case highlights the unique presentation of laryngeal lymphoma mimicking solitary plasmacytoma. The key factor in the diagnosis was the expression pattern of surface antigen markers.

Prolonged shedding of viable SARS-CoV-2 in immunocompromised patients with haematological malignancies: A prospective study.

Prolonged SARS-CoV-2 infection in immunocompromised individuals has been scattered, but the details remain unclear. We conducted a prospective study with 26 COVID-19 patients with haematological malignancies to determine viral shedding kinetics and characteristics. We obtained nasopharyngeal swabs from the patients 21-28 days post-onset for a PCR test and performed virus isolation from the PCR-positive samples. A viable virus was detected in five patients (19.2%), all of whom had malignant lymphoma. Those patients had significantly lower CD4+ T-cell counts than the PCR-negative patients. A comparison of previous chemotherapy showed that anti-CD20 antibodies and bendamustine may be risk factors for prolonged viral shedding.

Possible Chronic Graft-versus-host Disease in the Central Nervous System Manifesting as Cerebellar Ataxia after Allogeneic Hematopoietic Stem Cell Transplantation for Acute Myeloid Leukemia.

A 44-year-old woman was admitted to our hospital with a fever, dizziness, and gait disturbance after undergoing allogeneic hematopoietic stem cell transplantation for acute myeloid leukemia followed by graft-versus-host disease. She presented with cerebellar ataxia, nystagmus, and numbness of the lower extremities. Brain magnetic resonance imaging and perfusion scintigraphy showed progressive cerebellar involvement. Cerebrospinal fluid tests showed mildly elevated protein and IgG levels without pleocytosis. Anti-ganglioside antibodies were detected, but their levels did not follow the patient's clinical course. The patient did not respond sufficiently to steroids or other immunotherapies. We herein report the clinical characteristics of this case and a literature review.

Clinical characteristics of the severe acute respiratory syndrome coronavirus 2 omicron variant compared with the delta variant: a retrospective case-control study of 318 outpatients from a single sight institute in Japan.

Background: Clinical characteristics, including laboratory parameters, of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant have been limited. Methods: This retrospective case-control study was conducted in a single hospital. Patients with coronavirus disease 2019 (COVID-19) who visited the Asahikawa City Hospital outpatient department as new patients and underwent blood tests were included in this study. We analyzed the data from January 2022 to April 2022 during the Omicron phase and from April 2021 to October 2021 during the Delta phase. Patients who were treated at other hospitals after visiting our hospital were excluded. All blood tests were performed before treatment for COVID-19 was initiated. Demographic information, laboratory data, and clinical courses were extracted from electronic medical records. We matched the two groups by age and comorbidities and compared their characteristics. We also analyzed factors associated with pneumonia in the Omicron phase. Results: A total of 151 Omicron patients and 167 delta patients were analyzed in this study. The mean age, rate of comorbidities, and vaccination were significantly higher in the Omicron group. The number of patients with pneumonia or those requiring oxygen, admissions, or both was significantly lower in the Omicron group. Lactate dehydrogenase (LDH), C-reactive protein (CRP), ferritin, aspartate aminotransferase (AST), and neutrophil-to-lymphocyte ratio (NLR) levels were significantly lower in the Omicron group. Compared with the mild symptom and pneumonia groups in the Omicron group, older age, higher body mass index (BMI), higher non-vaccination, higher LDH, and higher CRP levels were associated with the pneumonia group. Conclusion: The Omicron variant is associated with a reduction in hospitalization and the risk of pneumonia compared to the delta variant in a real-life clinical setting. In the Omicron variant, the risk of pneumonia is related to high-risk factors, laboratory data such as LDH and CRP levels, and no vaccination.

Acute exacerbation of idiopathic hypereosinophilic syndrome following asymptomatic coronavirus disease 2019: a case report.

BACKGROUND: Previous research has suggested that some autoimmune diseases develop after the occurrence of coronavirus disease 2019. Hypereosinophilic syndrome is a rare disease presenting with idiopathic eosinophilia and multiple organ involvement, including the skin, lungs, gastrointestinal tract, heart, and nervous system. The diagnosis of idiopathic hypereosinophilic syndrome poses a dilemma because clinical manifestation and serum biomarkers are similar to those of eosinophilic granulomatosis with polyangiitis. Only a few cases have been reported where coronavirus disease 2019 may have caused the new onset or exacerbation of eosinophilic granulomatosis with polyangiitis or idiopathic hypereosinophilic syndrome. CASE PRESENTATION: We present the case of a 48-year-old Japanese woman with history of asthma who developed deteriorating symptoms of insidiously developed idiopathic hypereosinophilic syndrome following asymptomatic coronavirus disease 2019. She developed acute-onset back pain, tachycardia, abdominal discomfort, loss of appetite, weight loss, skin rash on the back, and numbness of the extremities 3 days after the quarantine period. Extreme hypereosinophilia with multiple abnormal findings including pulmonary ground-glass opacity lesions and mononeuritis multiplex was consistent with hypereosinophilic syndrome. Normal cellularity with eosinophilic proliferation in the bone marrow and negative FIP1L1-PDGFRA raised the diagnosis of idiopathic hypereosinophilic syndrome. Although the patient tested negative for anti-neutrophilic cytoplasmic antibodies and skin biopsy was negative for vasculitis, eosinophilic granulomatosis with polyangiitis could not be excluded. Since glucocorticoids are a standard therapy for both idiopathic hypereosinophilic syndrome and eosinophilic granulomatosis with polyangiitis, we initiated glucocorticoids following a multidisciplinary discussion. CONCLUSION: Although the relationship between asymptomatic coronavirus disease 2019 and acute idiopathic hypereosinophilic syndrome exacerbation was uncertain, the chronological order of the symptomatic development suggested a possible link. More clinical cases and population-based studies are needed to determine the potential effect of coronavirus disease 2019 on autoimmune diseases.

Mutations in the nonstructural proteins of SARS-CoV-2 may contribute to adverse clinical outcome in patients with COVID-19.

BACKGROUND: From late March through April 2021, we experienced a cluster of patients with COVID-19, named "Cluster K", with rapid severe illness compared with those who were infected before. METHODS: Patients with COVID-19 who were enrolled in this study were divided into two groups: 66 patients from November 2020 to March 2021 (group A) and 37 patients whose infection links were traced from Cluster K (group B). The primary outcome was mortality rate, and the secondary outcome was maximal oxygen flow rate as the severity of the disease. Viral genome sequences were compared between the two groups. RESULTS: Mortality rates were 6.1% in group A and 16.2% in group B (odds ratio: 2.97, 95% confidence interval: 0.65-15.38). The patients in group B required high oxygen flow rate (O2 ≥10 l/min) in the earlier clinical course (P = 0.029). Viral genome sequences revealed five amino acid mutations; of these, four were found on three nonstructural proteins (NSPs): one in nsp3 and nsp15, two in nsp6 (one of them is near the potential sites under positive selective pressure). Another one was on the S protein. CONCLUSION: This study suggests that mutations in NSPs, especially nsp6, are associated with adverse clinical outcome in patients with COVID-19.

Impact of Antibody Cocktail Therapy Combined with Casirivimab and Imdevimab on Clinical Outcome for patients with COVID-19 in A Real-Life Setting: A Single Institute Analysis.

BACKGROUND: Recent data from clinical trials suggest that antibody cocktail therapy, which combined casirivimab and imdevimab, is linked to the reduction of the risk of hospitalization or death among high-risk patients with COVID-19. However, it remains unclear how effective the therapy is in a real-life clinical practice. METHODS: We retrospectively analyzed patients with COVID-19 with high-risk factors who underwent the antibody cocktail therapy, compared with those who were not given the cocktail therapy while being isolated in nonmedical facilities during the same period. RESULTS: Data from 55 patients who received the antibody cocktail therapy and 53 patients with initial isolation in nonmedical facilities were analyzed. A total of 22 (41.5 %) of 53 patients staying in isolation facilities were eventually hospitalized and received medical interventions. By contrast, 13 (23.6 %) of 55 patients who received the antibody cocktail therapy subsequently underwent further medical interventions. In multivariate analysis, the antibody cocktail therapy significantly reduced the need for further medical interventions by 70 % compared with isolation (odds ratio=0.30, 95%CI [0.10-0.87], p=0.027). Patients with percutaneous oxygen saturation 96% or higher were significantly favoured for the therapy and had an advantage. CONCLUSION: The results of this study indicate that the antibody cocktail therapy is associated with reducing burden on hospitals during the COVID-19 pandemic.

Regulation of Epstein-Barr Virus Life Cycle and Cell Proliferation by Histone H3K27 Methyltransferase EZH2 in Akata Cells.

Epigenetic modifications play a pivotal role in the expression of the genes of Epstein-Barr virus (EBV). We found that de novo EBV infection of primary B cells caused moderate induction of enhancer of zeste homolog 2 (EZH2), the major histone H3 lysine 27 (K27) methyltransferase. To investigate the role of EZH2, we knocked out the EZH2 gene in EBV-negative Akata cells by the CRISPR/Cas9 system and infected the cells with EBV, followed by selection of EBV-positive cells. During the latent state, growth of EZH2-knockout (KO) cells was significantly slower after infection compared to wild-type controls, despite similar levels of viral gene expression between cell lines. After induction of the lytic cycle by anti-IgG, KO of EZH2 caused notable induction of expression of both latent and lytic viral genes, as well as increases in both viral DNA replication and progeny production. These results demonstrate that EZH2 is crucial for the intricate epigenetic regulation of not only lytic but also latent gene expression in Akata cells.IMPORTANCE The life cycle of EBV is regulated by epigenetic modifications, such as CpG methylation and histone modifications. Here, we found that the expression of EZH2, which encodes a histone H3K27 methyltransferase, was induced by EBV infection; therefore, we generated EZH2-KO cells to investigate the role of EZH2 in EBV-infected Akata B cells. Disruption of EZH2 resulted in increased expression of EBV genes during the lytic phase and, therefore, efficient viral replication and progeny production. Our results shed light on the mechanisms underlying reactivation from an epigenetic point of view and further suggest a role for EZH2 as a form of innate immunity that restricts viral replication in infected cells.

Experimental infection of highly and low pathogenic avian influenza viruses to chickens, ducks, tree sparrows, jungle crows, and black rats for the evaluation of their roles in virus transmission.

Highly pathogenic avian influenza viruses (HPAIVs) have spread in both poultry and wild birds. Determining transmission routes of these viruses during an outbreak is essential for the control of avian influenza. It has been widely postulated that migratory ducks play crucial roles in the widespread dissemination of HPAIVs in poultry by carrying viruses along with their migrations; however close contacts between wild migratory ducks and poultry are less likely in modern industrial poultry farming settings. Therefore, we conducted experimental infections of HPAIVs and low pathogenic avian influenza viruses (LPAIVs) to chickens, domestic ducks, tree sparrows, jungle crows, and black rats to evaluate their roles in virus transmission. The results showed that chickens, ducks, sparrows, and crows were highly susceptible to HPAIV infection. Significant titers of virus were recovered from the sparrows and crows infected with HPAIVs, which suggests that they potentially play roles of transmission of HPAIVs to poultry. In contrast, the growth of LPAIVs was limited in each of the animals tested compared with that of HPAIVs. The present results indicate that these common synanthropes play some roles in influenza virus transmission from wild birds to poultry.

Protection against H5N1 highly pathogenic avian and pandemic (H1N1) 2009 influenza virus infection in cynomolgus monkeys by an inactivated H5N1 whole particle vaccine.

H5N1 highly pathogenic avian influenza virus (HPAIV) infection has been reported in poultry and humans with expanding clade designations. Therefore, a vaccine that induces immunity against a broad spectrum of H5N1 viruses is preferable for pandemic preparedness. We established a second H5N1 vaccine candidate, A/duck/Hokkaido/Vac-3/2007 (Vac-3), in our virus library and examined the efficacy of inactivated whole particles of this strain against two clades of H5N1 HPAIV strains that caused severe morbidity in cynomolgus macaques. Virus propagation in vaccinated macaques infected with either of the H5N1 HPAIV strains was prevented compared with that in unvaccinated macaques. This vaccine also prevented propagation of a pandemic (H1N1) 2009 virus in macaques. In the vaccinated macaques, neutralization activity, which was mainly shown by anti-hemagglutinin antibody, against H5N1 HPAIVs in plasma was detected, but that against H1N1 virus was not detected. However, neuraminidase inhibition activity in plasma and T-lymphocyte responses in lymph nodes against H1N1 virus were detected. Therefore, cross-clade and heterosubtypic protective immunity in macaques consisted of humoral and cellular immunity induced by vaccination with Vac-3.