Detection of respiratory viruses in adults with respiratory tract infection using a multiplex PCR assay at a tertiary center

BackgroundRespiratory viruses (RVs) are among the most common pathogens for both upper and lower respiratory tract infections (RTIs). However, the viral epidemiology of RV-associated RTIs in adults has long been under-recognized. Through a sensitive molecular assay, it would be possible to have a better understanding of the epidemiology of RV-associated RTIs.Material and methodsRespiratory tract (RT) specimens from adults hospitalized due to RTIs were tested for RVs, using the multiplex PCR-based Luminex xTAG® Respiratory Viral Panel assay. A total of nineteen RVs, including influenza viruses and non-influenza respiratory viruses (NIRVs) were detected. Positive rates were compared using a chi-square test.ResultsA total of 2292 samples from adult patients hospitalized with RTIs were screened for RVs. The overall positive rate was 22%, with 17.8% samples positive for at least one NIRV. NIRVs had a higher positive rate in non-winter seasons. As many as 12.7% (46/363) of the samples collected through broncho-alveolar lavage and 20.5% (176/859) of the samples collected in ICUs were positive for RVs. Distribution of corona virus (CoV), human metapneumovirus (hMPV) and parainfluenza virus (PIV) demonstrated seasonal variation. Also, temperature was associated with the positive rates of specific viruses, including CoV, respiratory syncytial virus (RSV), hMPV and PIV.ConclusionRespiratory viruses, notably NIRVs, were frequently detected in adults hospitalized with RTIs. Several RVs were detected with distinctive seasonal variations. A substantial number of RVs were identified in lower RT specimens or from patients admitted to ICU, highlighting their important role in causing severe respiratory infection.     

Impact of multiplex polymerase chain reaction syndromic panel on antibiotic use among hospitalized children with respiratory tract illness during COVID-19 pandemic

Background/PurposePrecise detection of respiratory pathogens by molecular method potentially may shorten the time to diagnose and reduce unnecessary antibiotic use.MethodsMedical records of hospitalized children from January 2020 to June 2021 with acute respiratory illness who received a FilmArray RP for respiratory pathogens were reviewed and compared with data from diagnosis-matched patients without receiving the test.ResultsIn total, 283 patients and 150 diagnosis-matched controls were included. Single pathogen was detected in 84.3% (193/229) of the patients. The most common pathogen was human rhinovirus/enterovirus (31.6%, 84/266), followed by respiratory syncytial virus (18.8%, 50/266) and adenovirus (15%, 40/266). Although antimicrobial days of therapy (DOT) was significantly longer in FilmArray group than the control [7.1 ± 4.9 days vs 5.7 ± 2.7 days, P = 0.002], the former showed a higher intensive care unit (ICU) admission rate (3.9% vs 0%; P = 0.010). All ICU admissions were in FilmArray RP-positive group. There was no difference in antimicrobial DOT between FilmArray RP-positive and the negative groups, in all admissions, even after excluding ICU admissions. Antimicrobial DOT was shorter in the positive than negative group in patients with lower respiratory tract infections without admission to ICU [median (IQR): 6 (4–9) days vs 9 (4–12) days, P = 0.047].ConclusionsShorter antimicrobial DOTs were identified in children with lower respiratory tract infection admitted to general pediatric ward and with an identifiable respiratory pathogen, indicating a role of the multiplex PCR in reducing antimicrobial use for children with respiratory tract infection.     

Featuring COVID-19 cases via screening symptomatic patients with epidemiologic link during flu season in a medical center of central Taiwan

BackgroundCoronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CO-V-2), was first reported in Wuhan, Hubei province, China has now rapidly spread over 50 countries. For the prevention and control of infection, Taiwan Centers for Disease Control initiated testing of SARS-CoV-2 on January 24th 2020 for persons suspected with this disease. Until February 28th, 43 flu-like symptomatic patients were screened in China Medical University Hospital.MethodsTwo patients were confirmed positive for SARS-CoV-2 infection by rRT-PCR as COVID-19 patients A and B. Causative pathogens for included patients were detected using FilmArray™ Respiratory Panel. We retrospectively analyzed the clinical presentations, laboratory data, radiologic findings, and travel and exposure contact histories, of the COVID-19 patients in comparison to those with other respiratory infections.ResultsThrough contact with Taiwan No. 19 case patient on 27th January, COVID-19 patients A and B were infected. Both patients had no identified comorbidities and developed mild illness with temporal fever, persistent cough, and lung interstitial infiltrates. Owing to the persistence of positive SARS-CoV-2 in respiratory specimen, the two COVID-19 patients are still in the isolation rooms despite recovery until 10th of March. The results of FilmArrayTM Respiratory Panel revealed 22 of the 41 non-COVID-19 patients were infected by particular pathogens. In general, seasonal respiratory pathogens are more prevalent than SARS-CoV-2 in symptomatic patients in non- COVID-19 endemic area during the flu season. Since all patients shared similar clinical and laboratory findings, expanded surveillance of detailed exposure history for suspected patients and application of rapid detection tools are highly recommended.     

Fewer non-COVID-19 respiratory tract infections and gastrointestinal infections during the COVID-19 pandemic

For preventing the spread of the coronavirus disease 2019 (COVID-19) pandemic, measures like wearing masks, social distancing, and hand hygiene played crucial roles. These measures may also have affected the expansion of other infectious diseases like respiratory tract infections (RTI) and gastro-intestinal infections (GII). Therefore, we aimed to investigate non-COVID-19 related RTI and GII during the COVID-19 pandemic. Patients with a diagnosis of an acute RTI (different locations) or acute GII documented anonymously in 994 general practitioner (GP) or 192 pediatrician practices in Germany were included. We compared the prevalence of acute RTI and GII between April 2019–March 2020 and April 2020–March 2021. In GP practices, 715,440 patients were diagnosed with RTI or GII in the nonpandemic period versus 468,753 in the pandemic period; the same trend was observed by pediatricians (275,033 vs. 165,127). By GPs, the strongest decrease was observed for the diagnosis of influenza (?71%, p < 0.001), followed by acute laryngitis (?64%, p < 0.001), acute lower respiratory infections (bronchitis) (?62%, p < 0.001), and intestinal infections (?40%, p < 0.001). In contrast, the relatively rare viral pneumonia strongly increased by 229% (p < 0.001). In pediatrician practices, there was a strong decrease in infection diagnoses, especially influenza (?90%, p < 0.001), pneumonia (?73%, p < 0.001 viral; ?76%, p < 0.001 other pneumonias), and acute sinusitis (?66%, p < 0.001). No increase was observed for viral pneumonia in children. The considerable limitations concerning social life implemented during the COVID-19 pandemic to combat the spread of SARS-CoV-2 also resulted in an inadvertent but welcome reduction in other non-Covid-19 respiratory tract and gastro-intestinal infections.     

Rapid response of a medical center upon the surge of COVID-19 epidemic in Taiwan

A surge of coronavirus disease (COVID-19) cases emerged in northern Taiwan in mid-May 2021. In spite of over one-year preparedness, the medical system in this area suffered from the crisis. Far Eastern Memorial Hospital (FEMH) responded quickly with decreased total hospitalization cases (about 50%) to free manpower and space. With simple construction work, the in-hospital service capacity increases from 11 negative-pressure ward (1 unit) and 2 negative-pressure ICU (1 unit) beds to over 130 ward (5 units) and 58 ICU beds (4 units) without negative-pressure design within 3 weeks. For a period of time, FEMH takes care of 10% of all intensive care services in Taiwan. The vaccination rate of workers reaches 90% since mid-May. The amount of testing performed during the period, including PCR and rapid tests, comprised of more than 20% of tests performed in New Taipei City. Two hotels for mild/asymptomatic COVID patients were handled by FEMH workers. By mid-July, about one-fifth of COVID-19 cases in New Taipei City received services from the FEMH system. With determined leadership and concerted efforts, combined interventions can increase the capacity of medical care within weeks and help society against the COVID-19 epidemic.     

Potential risk of liver injury in epileptic patients during COVID-19 pandemic

Most of the antiseizure medications (ASMs) are metabolized in liver and many of them particularly first-generation ASMs have the potential to increase liver enzymes or induce liver injury. Hence, treatment of new onset seizures or epilepsy by ASMs during the course of coronavirus disease 2019 (COVID-19), which could potentially be complicated by hepatic dysfunction, is a challenging clinical issue. Intravenous form of levetiracetam which has no significant hepatic metabolism or drug-drug interaction is often a favorable option to control seizures in acute phase of COVID-19. Administration of enzyme inducer ASMs and valproate with the well-known hepatotoxicity and common drug interactions is not generally recommended. In patients with epilepsy who are under control with potentially hepatotoxic ASMs, close observation and cautious dose reduction or drug switch should be considered if any evidence of hepatic impairment exists. However, risks of possible breakthrough seizures should be weighed against benefits of lowering the hazard of liver injury. In patients with epilepsy who receive polytherapy with ASMs, transient dose modification with the tendency to increase the dose of ASMs with more favorable safety profile and less drug interaction and decrease the dose of drugs with main hepatic metabolism, high protein binding, potential to cause liver injury and known drug-drug reaction should be considered. Finally, decision making should be individualized based on patients’ conditions and course of illness.     

Repositive RT-PCR test in discharged COVID-19 patients during medical isolation observation

Objectives: The epidemiological and clinical characteristics of patients with coronavirus disease 2019 (COVID-19) have been researched. However, the prevalence of repositivity by real-time PCR for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains unclear.Methods: A retrospective study was conducted involving 599 discharged patients with COVID-19 in a single medical centre. The clinical features of patients during their hospitalization and 14-day post-discharge quarantine were collected.Results: A total of 122 patients (20.4%) out of 599 patients retested positive after discharge. Specifically, 94 (15.7%) retested positive within 24 h of discharge, and another 28 patients (4.7%) were repositive on day 7 after discharge, although none showed any clinical symptomatic recurrence. Both repositives and non‑repositives have similar patterns of IgG and IgM. Notably, the length of hospitalization of non-repositive patients was longer than that of 24-h repositive patients and 7-day repositive patients. In addition, the length of hospitalization of 24-h repositive patients was shorter than that of 7-day repositive patients, indicating that the length of hospitalization was also a determinant of viral shedding.Conclusion: Our study provides further information for improving the management of recovered and discharged patients, and further studies should be performed to elucidate the infectiveness of individuals with prolonged or RNA repositivity.     

First COVID-19 mortality case in Taiwan with bacterial co-infection by national surveillance of critically ill patients with influenza-negative pneumonia

A 63-year-old diabetic smoker with alcoholism was the first mortality case of coronavirus disease 2019 (COVID-19) in Taiwan. As concurrently infected with Klebsiella pneumoniae and subsequently with Klebsiella aerogenes, he was exposed by a national survey of patients with critically influenza-negative pneumonia. We recommend COVID-19 screening for patients with severe flu-like syndrome and protecting health-care workers from being infected.     

Evaluating the knowledge acquisition of lower limb anatomy among medical students during the post-acute COVID-19 era

Anatomy is the foundation of many medical and surgical specialties yet knowledge acquisition and retention among medical students is questionable. Over the years the anatomy teaching environment and teaching modalities have changed, even more so with the onset of the COVID-19 pandemic and the shift to a virtual environment. The aim of this study was to evaluate the knowledge acquisition of applied musculoskeletal lower limb clinical anatomy among first year medical students in Malta following the transition back to face-to-face lectures. The Kahoot online game-based quiz platform was used through a best out of four multiple-choice setting across four sessions. Scores generated by the platform along with frequencies of correctly answered questions were utilized to measure knowledge acquisition. The average scores for each question across sessions were statistically analyzed using ANOVA and student's t-test accordingly. Across the four sessions, the positive percentage response for clinical based questions remained higher than for pure anatomy questions. Anatomy knowledge acquisition appears to be subjective to clinical based knowledge rather than pure anatomy. There may be a plethora of reasons as to this outcome including the misconception that anatomy is not essential for clinical practice as well as the potential aftermath of the COVID-induced virtual learning environment. Further research is merit to ensure that students are provided with the best tools to enhance their knowledge acquisition, both as students and as future doctors.     

Characteristics and predictors of death among 4035 consecutively hospitalized patients with COVID-19 in Spain

ObjectivesTo analyse the characteristics and predictors of death in hospitalized patients with coronavirus disease 2019 (COVID-19) in Spain.MethodsA retrospective observational study was performed of the first consecutive patients hospitalized with COVID-19 confirmed by real-time PCR assay in 127 Spanish centres until 17 March 2020. The follow-up censoring date was 17 April 2020. We collected demographic, clinical, laboratory, treatment and complications data. The primary endpoint was all-cause mortality. Univariable and multivariable Cox regression analyses were performed to identify factors associated with death.ResultsOf the 4035 patients, male subjects accounted for 2433 (61.0%) of 3987, the median age was 70 years and 2539 (73.8%) of 3439 had one or more comorbidity. The most common symptoms were a history of fever, cough, malaise and dyspnoea. During hospitalization, 1255 (31.5%) of 3979 patients developed acute respiratory distress syndrome, 736 (18.5%) of 3988 were admitted to intensive care units and 619 (15.5%) of 3992 underwent mechanical ventilation. Virus- or host-targeted medications included lopinavir/ritonavir (2820/4005, 70.4%), hydroxychloroquine (2618/3995, 65.5%), interferon beta (1153/3950, 29.2%), corticosteroids (1109/3965, 28.0%) and tocilizumab (373/3951, 9.4%). Overall, 1131 (28%) of 4035 patients died. Mortality increased with age (85.6% occurring in older than 65 years). Seventeen factors were independently associated with an increased hazard of death, the strongest among them including advanced age, liver cirrhosis, low age-adjusted oxygen saturation, higher concentrations of C-reactive protein and lower estimated glomerular filtration rate.ConclusionsOur findings provide comprehensive information about characteristics and complications of severe COVID-19, and may help clinicians identify patients at a higher risk of death.     

Impact of COVID-19 pandemic on patients with rare disease in Hong Kong

The COVID-19 pandemic has had significant health, social, and economic consequences internationally. While the pandemic has direct implications on infected patients and families, there is a need to examine the pandemic's effect on patients with non-COVID-19-related diseases. This study examines the impact of the COVID-19 pandemic on 272 rare disease patients with 89 distinct rare diseases in Hong Kong using a cross-sectional online survey between April 10 and April 29, 2020 from the patient and caregiver perspective. The pandemic has impacted patient's health status in 46%, service use patterns in 71%, mental health in 79%, daily living in 82%, social life in 92%, and financial status in 81% of patients. Patient's health status, medical and rehabilitation, and mental health were more impacted by the COVID-19 pandemic in the group of patients with any level of dependency according to the Barthel Index for Activities of Daily Living compared with that in the group of patients who are fully independent (p < 0.0001; p < 0.0001; p = 0.0420). This study is the first study to examine the impact of COVID-19 pandemic on the rare disease population in Hong Kong, and demonstrates the pandemic's effect on service and resource utilization, and patient's physical and mental well-being.     

Prevalence of insomnia and anxiety among healthcare workers during the COVID-19 pandemic in Jilin Province

The outbreak of the 2019 novel coronavirus disease (COVID-19) has impacted the mental health of healthcare providers at the frontline. Therefore, we conducted this study to estimate the prevalence rate of anxiety and insomnia and identify associated risk factors among healthcare workers in Jilin, China, during the period from January 25 to February 25, 2020. Zung''s Self-Reported Anxiety Scale (SAS) and the Insomnia Severity Index (ISI) scale were used to diagnose anxiety and insomnia, respectively. Associated risk factors were identified through a multivariate logistic regression model. A total of 300 healthcare workers were invited and 236 completed the study. Of them, 234 (99.15%) were medical workers, 197 (83.47%) were working at frontline departments, and 159 (67.37%) were fighting against COVID-19. Fifty-seven respondents (24.15%) had anxiety (SAS index score ≥45) and 94 (39.83%) had insomnia (ISI score ≥8). Based on the multivariate analysis, contact with people from Hubei province during work (no vs not clear) [OR=0.25, 95%CI: 0.10-0.61] and personal protective equipment (PPE) (not in place vs in place) [OR=6.22, 95%CI: 2.23-17.40] were significantly correlated with anxiety. PPE (not in place vs in place) was the only significant risk factor of insomnia [OR=10.56, 95%CI: 4.00-27.87]. The prevalence of anxiety and insomnia was high in our study, reflecting the psychological impact of COVID-19 on healthcare workers. The unavailability of PPE in place was a significant risk factor of both anxiety and insomnia.     

乌鲁木齐地区冬春季小儿呼吸道感染者中呼吸道合胞病毒感染的研究

目的 了解乌鲁木齐地区冬春季节呼吸道感染患儿中呼吸道合胞病毒(RSV)的感染状况以及分子流行病学的基本情况.方法 研究对象为2006年11月-2007年4月于新疆维吾尔自治区人民医院儿科住院以及部分于门诊就诊,明确诊断为急性呼吸道感染的患儿,采集咽拭子280份,呼吸道分泌物112份.对全部标本采用反转录聚合酶链反应(RT-PCR)方法进行RSV及其亚型检测.随机取5份阳性标本测序,进行序列比较及同源性分析.结果 392份样本中共检出RSV阳性68份,阳性率17.3%(68/392),其中A基因型64份,占93.3%(64/68),B基因型4份,占6.7%(4/68).5株测序结果提示当地RSV与其他国家及地区代表株之间的同源性为63.1%～99.4%.进化树进一步显示存在A、B两个亚型.结论 RSV是引起2006-2007年冬春季该医院儿童急性呼吸道感染的重要病原体,以A亚型为主要流行株.

Abstract：

Objective To research the infections of respiratory syneytial virus(RSV)in children with respiratory tract inflammation and define its molecular epidemic features in Urumchi.Methods SamDles were collected from November 2006 to April 2007 in the People's General Hospital of Xinjiang Uygur Autonomous Region,including 112 respiratory secretions and 280 nasopharyngeal swabs. RSV and its subgroups were detected by nested PCR.The five positive amplicons selected randomly from all positive samples were sequenced and compared with other RSV in GenBank by BLAST and DNAStar.Results of all 392specimens.68 RSV G gene segments were tested.Among them,RSV lineage A occupied 93.3%,while B occuDied 6.7%.The identities between them were 63.1%-99.4%.Phylogenetic analysis defined that they belonged to two different clusters.Conclusion RSV was one of the important viruses leading to children's respiratory tract infections in the People's General Hospital of Xinjiang Uygur Autonomous Region during winter and spring from 2006 to 2007.RSV subtype A was the prevalent genotype in the hospital dunng this epidemics.