New respiratory viruses and the elderly

Does the variant positivity and negativity affect the clinical course in COVID-19?: A cohort study

The primary aim of the current study is to analyze the clinical, laboratory, and demographic data comparing the patients with Coronavirus Disease 2019 (COVID-19) admitted to our intensive care unit before and after the UK variant was first diagnosed in December 2020. The secondary objective was to describe a treatment approach for COVID-19. Between Mar 12, 2020, and Jun 22, 2021, 159 patients with COVID-19 were allocated into 2 groups: the variant negative group (77 patients before December 2020) and the variant positive group (82 patients after December 2020). The statistical analyses included early and late complications, demographic data, symptoms, comorbidities, intubation and mortality rates, and treatment options. Regarding early complications, unilateral pneumonia was more common in the variant (-) group (P = .019), whereas bilateral pneumonia was more common in the variant (+) group (P < .001). Regarding late complications, only cytomegalovirus pneumonia was observed more frequently in the variant (-) group (P = .023), whereas secondary gram (+) infection, pulmonary fibrosis (P = .048), acute respiratory distress syndrome (ARDS) (P = .017), and septic shock (P = .051) were more common in the variant (+) group. The therapeutic approach showed significant differences in the second group such as plasma exchange and extracorporeal membrane oxygenation which is more commonly used in the variant (+) group. Although mortality and intubation rates did not differ between the groups, severe challenging early and late complications were observed mainly in the variant (+) group, necessitating invasive treatment options. We hope that our data from the pandemic will shed light on this field. Regarding the COVID-19 pandemic, it is clear that there is much to be done to deal with future pandemics.

The Potential Use of Carnosine in Diabetes and Other Afflictions Reported in Long COVID Patients

Carnosine is a dipeptide expressed in both the central nervous system and periphery. Several biological functions have been attributed to carnosine, including as an anti-inflammatory and antioxidant agent, and as a modulator of mitochondrial metabolism. Some of these mechanisms have been implicated in the pathophysiology of coronavirus disease-2019 (COVID-19). COVID-19 is caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2). The clinical manifestation and recovery time for COVID-19 are variable. Some patients are severely affected by SARS-CoV-2 infection and may experience respiratory failure, thromboembolic disease, neurological symptoms, kidney damage, acute pancreatitis, and even death. COVID-19 patients with comorbidities, including diabetes, are at higher risk of death. Mechanisms underlying the dysfunction of the afflicted organs in COVID-19 patients have been discussed, the most common being the so-called cytokine storm. Given the biological effects attributed to carnosine, adjuvant therapy with this dipeptide could be considered as supportive treatment in patients with either COVID-19 or long COVID.

The long-term prognostic value of serum 25(OH)D, albumin, and LL-37 levels in acute respiratory diseases among older adults

Background

Older adults are more susceptible to respiratory tract infection than healthy working age adults. The increased susceptibility of older adults is thought to be interlinked with vitamin D status, nourishment, and immunological state in general. Data are scarce whether these parameters could serve as prognostic markers.

Aim

To study whether serum 25(OH)D, albumin, and LL-37 level could give prognostic value of long-term survival in the older adults with multimorbidity and acute respiratory infection.

Methods

Consecutive episodes of hospital care of patients 65 years and older with respiratory symptoms were prospectively studied as a cohort. Standard clinical questionnaire was filled by the study physician. Laboratory markers included serum levels of 25(OH)D, albumin and LL-37, C-reactive protein (CRP), white blood cell count (WBC) and polymerase chain reaction diagnostics for 14 respiratory viruses. Pneumonia was confirmed by chest radiographs. Respiratory illness severity, death at ward, length of hospital stays, and 5-year survival were used as outcomes.

Results

In total, 289 older adult patients with mean age of 83 years were included in the study. Serum 25(OH)D deficiency (< 50 nmol/liter) was present in 59% and hypoalbuminemia (< 3.5 g/dL) in 55% of the study patients. Low serum albumin level was associated to one, two- and five-year mortality after hospital stay (all P < .05). In addition, it was associated with pneumonia, dyspnea, over 13-night long stay at ward and death at ward (all P < .05). No associations were seen between serum 25(OH)D and LL-37 levels and disease severity, short-term clinical outcome, or long-term survival. Associations between serum 25(OH)D, albumin, and LL-37 levels and respiratory virus presence were not seen.

Conclusions

Serum albumin level on admission seems to give valuable information about the patients’ general health and recovery potential in treating older adults with respiratory symptoms. Serum 25(OH)D and LL-37 had no associations with disease severity or long- and short-term prognosis among older adults hospitalized with respiratory symptoms.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12877-022-02836-8.

Respiratory syncytial virus acute respiratory infections in ≥ 65-year-old adults in long-term care facilities in the Czech Republic

OBJECTIVES

Due to immunosenescence and presence of comorbidities, respiratory syncytial virus (RSV) disease burden is a major health concern in older adults, which is expected to increase with the life expectancy rise. Data on RSV burden are scarce in older adults residing in long-term care facilities, a vulnerable population living in crowded settings. Therefore, two independent prospective studies were conducted during the 2003-2004 and 2004-2005 RSV seasons to assess RSV acute respiratory illnesses (ARIs) and lower respiratory tract infections (LRTIs) in ≥ 65-year-old adults residing in long-term care facilities in the Czech Republic.

METHODS

RSV ARI episodes were confirmed by polymerase chain reaction in nasal swabs collected within 3 days of symptoms onset. The mortality and morbidity of RSV-confirmed ARIs, as well as the risk factors associated with RSV-confirmed ARIs were evaluated.

RESULTS

Among 1,251 participants in the 2003-2004 season (ARI surveillance between October and March), there were no RSV-positive cases in 255 ARI and 105 LRTI episodes. Among 1,280 participants in the 2004-2005 season (ARI surveillance between October and April), there were 39 and 26 RSV-positive cases in 335 ARI and 217 LRTI episodes, respectively, and RSV-positive ARI and LRTI episode incidence rates were 45.82 and 30.40 per 1,000 person-years. Among 290 RSV-negative and 39 RSV-positive ARI cases in the 2004-2005 season, 15 and 4 hospitalizations, 188 and 26 LRTIs, and 11 and 3 deaths were reported. Risk factors associated with RSV-positive ARI were female gender (odds ratio: 4.98), chronic heart failure class II (odds ratio: 2.31) and diabetes requiring insulin treatment (odds ratio: 9.82).

CONCLUSIONS

These studies showed that RSV was an important cause of ARI in older adults living in long-term care facilities in the 2004-2005 season, with fluctuating yearly incidences.

Serological survey following SARS-COV-2 outbreaks at long-term care facilities in metro Vancouver, British Columbia: Implications for outbreak management and infection control policies

A cross-sectional serological survey was carried out in two long-term care facilities that experienced COVID-19 outbreaks in order to evaluate current clinical COVID-19 case definitions. Among individuals with a negative or no previous COVID-19 diagnostic test, myalgias, headache, and loss of appetite were associated with serological reactivity. The US CDC probable case definition was also associated with seropositivity. Public health and infection control practitioners should consider these findings for case exclusion in outbreak settings.

Respiratory-tract infections among geriatrics: prevalence and factors associated with the treatment outcomes

Background:

Geriatric individuals are more susceptible to different infections, especially respiratory-tract infections (RTIs) due to their compromised immune system. Hence, the objectives of the present study were to evaluate the prevalence, medication regimen complexity and factors associated with the treatment outcomes of different RTIs among geriatrics.

Methods:

A retrospective cross-sectional study (5 years) was conducted at the respiratory department, Hospital Pulau Pinang. Patients aged ⩾65 years with confirmed diagnosis of RTI were included in the study.

Results:

A total of 474 patients were included, and the most prevalent RTIs were community-acquired pneumonia (65.6%) followed by chronic obstructive pulmonary disease (20.7%), bronchitis (8.2%) and hospital-acquired pneumonia (5.5%). Amoxicillin/clavulanate (69.8%), ampicillin/sulbactam (9.1%) and cefuroxime (6.5%) are the most common antibiotics prescribed to treat RTIs among geriatrics. Smoking, alcohol consumption, polypharmacy and presence of other co-morbidities are statistically significant factors associated with treatment outcomes of RTIs among geriatrics.

Conclusion:

Prevalence of community-acquired pneumonia (65.6%) among older patients aged 65 years and older higher than other RTIs. Smoking, alcohol use, presence of polypharmacy and other co-morbidities are important factors associated with the treatment outcomes of RTIs.

The reviews of this paper are available via the supplemental material section.

COVID-19: A Review on the Novel Coronavirus Disease Evolution, Transmission, Detection, Control and Prevention

Three major outbreaks of the coronavirus, a zoonotic virus known to cause respiratory disease, have been reported since 2002, including SARS-CoV, MERS-CoV and the most recent 2019-nCoV, or more recently known as SARS-CoV-2. Bats are known to be the primary animal reservoir for coronaviruses. However, in the past few decades, the virus has been able to mutate and adapt to infect humans, resulting in an animal-to-human species barrier jump. The emergence of a novel coronavirus poses a serious global public health threat and possibly carries the potential of causing a major pandemic outbreak in the naïve human population. The recent outbreak of COVID-19, the disease caused by SARS-CoV-2, in Wuhan, Hubei Province, China has infected over 36.5 million individuals and claimed over one million lives worldwide, as of 8 October 2020. The novel virus is rapidly spreading across China and has been transmitted to 213 other countries/territories across the globe. Researchers have reported that the virus is constantly evolving and spreading through asymptomatic carriers, further suggesting a high global health threat. To this end, current up-to-date information on the coronavirus evolution and SARS-CoV-2 modes of transmission, detection techniques and current control and prevention strategies are summarized in this review.

COVID-19: A Review on the Novel Coronavirus Disease Evolution, Transmission, Detection, Control and Prevention

Three major outbreaks of the coronavirus, a zoonotic virus known to cause respiratory disease, have been reported since 2002, including SARS-CoV, MERS-CoV and the most recent 2019-nCoV, or more recently known as SARS-CoV-2. Bats are known to be the primary animal reservoir for coronaviruses. However, in the past few decades, the virus has been able to mutate and adapt to infect humans, resulting in an animal-to-human species barrier jump. The emergence of a novel coronavirus poses a serious global public health threat and possibly carries the potential of causing a major pandemic outbreak in the naïve human population. The recent outbreak of COVID-19, the disease caused by SARS-CoV-2, in Wuhan, Hubei Province, China has infected over 36.5 million individuals and claimed over one million lives worldwide, as of 8 October 2020. The novel virus is rapidly spreading across China and has been transmitted to 213 other countries/territories across the globe. Researchers have reported that the virus is constantly evolving and spreading through asymptomatic carriers, further suggesting a high global health threat. To this end, current up-to-date information on the coronavirus evolution and SARS-CoV-2 modes of transmission, detection techniques and current control and prevention strategies are summarized in this review.

Impact of COVID-19 Pandemic and Lockdown Measures on the Mental Health of the General Population in the Gulf Cooperation Council States: A Cross-Sectional Study

Background: In the Gulf Cooperation Council (GCC) countries (Kuwait, Qatar, Saudi Arabia, Bahrain, United Arab Emirates, and Oman), as in the rest of the world, the COVID-19 has been spreading since 2019, and it had a significant impact on various aspects of life. The outbreak and the restrictive measures imposed by countries to stop the spread of the virus could harm the mental health condition of the general population. This cross-sectional study aims to assess the impact of the pandemic on mental health and investigate the potential risk factors. Methods: An online survey was collected from individuals in GCC countries from May to October 2020. The final sample included 14,171 participants, 67.3% females and 60.4% younger than 35 years old. The survey consisted of depression, Anxiety, Insomnia, and post-traumatic stress questionnaires. Crude and adjusted Odds ratios are calculated using simple and multivariable logistic regressions to investigate the association between risk factors and mental health issues. Results: Endorsement rates for depression were 11,352 (80.1%), 9,544 (67.3%) for anxiety, 8,845 (63.9%) for insomnia and 9,046 (65.2%) for post-traumatic stress. Being female and younger age were associated with a higher likelihood of developing depression, anxiety, insomnia, and post-traumatic stress. In addition, participants with underlying psychological problems were three times more likely to develop depressive and post-traumatic stress symptoms. Conclusion: According to the findings, women, youth, singles, divorced individuals, and individuals with pre-existing psychological and medical conditions are subject to a higher risk of mental health problems during the pandemic, which policy-makers should consider when imposing restrictive measures.

Respiratory viral infections in the elderly

With the global over 60-year-old population predicted to more than double over the next 35 years, caring for this aging population has become a major global healthcare challenge. In 2016 there were over 1 million deaths in >70 year olds due to lower respiratory tract infections; 13-31% of these have been reported to be caused by viruses. Since then, there has been a global COVID-19 pandemic, which has caused over 2.3 million deaths so far; increased age has been shown to be the biggest risk factor for morbidity and mortality. Thus, the burden of respiratory viral infections in the elderly is becoming an increasing unmet clinical need. Particular challenges are faced due to the interplay of a variety of factors including complex multimorbidities, decreased physiological reserve and an aging immune system. Moreover, their atypical presentation of symptoms may lead to delayed necessary care, prescription of additional drugs and prolonged hospital stay. This leads to morbidity and mortality and further nosocomial spread. Clinicians currently have limited access to sensitive detection methods. Furthermore, a lack of effective antiviral treatments means there is little incentive to diagnose and record specific non-COVID-19 viral infections. To meet this unmet clinical need, it is first essential to fully understand the burden of respiratory viruses in the elderly. Doing this through prospective screening research studies for all respiratory viruses will help guide preventative policies and clinical trials for emerging therapeutics. The implementation of multiplex point-of-care diagnostics as a mainstay in all healthcare settings will be essential to understand the burden of respiratory viruses, diagnose patients and monitor outbreaks. The further development of novel targeted vaccinations as well as anti-viral therapeutics and new ways to augment the aging immune system is now also essential.The reviews of this paper are available via the supplemental material section.

Clinical Courses and Outcomes of Patients with Chronic Obstructive Pulmonary Disease During the COVID-19 Epidemic in Hubei, China

Purpose

In this study, we investigated the acute exacerbation and outcomes of COPD patients during the outbreak of COVID-19 and evaluated the prevalence and mortality of COPD patients with confirmed COVID-19.

Methods

A prospectively recruited cohort of 489 COPD patients was retrospectively followed-up for their conditions during the COVID-19 pandemic from December 2019 to March 2020 in Hubei, China. In addition, the features of 821 discharged patients with confirmed COVID-19 were retrospectively analyzed.

Results

Of the 489 followed-up enrolled COPD patients, 2 cases were diagnosed as confirmed COVID-19, and 97 cases had exacerbations, 32 cases of which were hospitalized, and 14 cases died. Compared with the 6-month follow-up results collected 1 year ago, in 307 cases of this cohort, the rates of exacerbations and hospitalization of the 489 COPD patients during the last 4 months decreased, while the mortality rate increased significantly (2.86% vs 0.65%, p=0.023). Of the 821 patients with COVID-19, 37 cases (4.5%) had pre-existing COPD. Of 180 confirmed deaths, 19 cases (10.6%) were combined with COPD. Compared to COVID-19 deaths without COPD, COVID-19 deaths with COPD had higher rates of coronary artery disease and/or cerebrovascular diseases. Old age, low BMI and low parameters of lung function were risk factors of all-cause mortality for COVID-19 patients with pre-existing COPD.

Conclusion

Our findings imply that acute exacerbations and hospitalizations of COPD patients were infrequent during the COVID-19 pandemic. However, COVID-19 patients with pre-existing COPD had a higher risk of all-cause mortality.

T. cruzi infection among aged rats: Melatonin as a promising therapeutic molecule

Although T. cruzi was identified as the cause of Chagas disease more than 100 years ago, satisfactory treatments still do not exist, especially for chronic disease. Here we review work suggesting that melatonin could have promise as a Chagas therapeutic. Melatonin has remarkably diverse actions. It is an immunomodulator, an anti-inflammatory, an antioxidant, a free radical scavenger, and has antiapoptotic and anti-aging effects. The elderly (aged 60 years or more) as a group are growing faster than any other age group. Here we discuss the major effects and the mechanisms of action of melatonin on aged T. cruzi-infected rats. Melatonin's protective effects may be consequences of its cooperative antioxidant and immunomodulatory actions. Melatonin modulates oxidative damage, inducing an antioxidant response and reversing age-related thymus regression. Its protective actions could be the result of its anti-apoptotic activity, and by its counteracting the excessive production of corticosterone. This review describes our work showing that host age plays an important and variable influence on the progression of systemic T. cruzi infection and supporting the hypothesis that melatonin should be considered as a powerful therapeutic compound with multiple activities that can improve host homeostasis during experimental T. cruzi infection.

Respiratory tract virus infections in the elderly with pneumonia

BACKGROUND

In children suffering from severe lower airway illnesses, respiratory virus detection has given good prognostic information, but such reports in the elderly are scarce. Therefore, our aim was to study whether the detection of nasopharyngeal viral pathogens and conventional inflammatory markers in the frail elderly correlate to the presence, signs and symptoms or prognosis of radiographically-verified pneumonia.

METHODS

Consecutive episodes of hospital care of patients 65 years and older with respiratory symptoms (N = 382) were prospectively studied as a cohort. Standard clinical questionnaire was filled by the study physician. Laboratory analyses included PCR diagnostics of nasopharyngeal swab samples for 14 respiratory viruses, C-reactive protein (CRP) and white blood cell count (WBC). Chest radiographs were systematically analysed by a study radiologist. The length of hospital stay, hospital revisit and death at ward were used as clinical endpoints.

RESULTS

Median age of the patients was 83 years (range 76-90). Pneumonia was diagnosed in 112/382 (29%) of the studied episodes. One or more respiratory viruses were detected in 141/382 (37%) episodes and in 34/112 (30%) episodes also diagnosed with pneumonia. Pneumonia was associated with a WBC over 15 × 10⁹/L (P = .006) and a CRP value over 80 mg/l (P < .05). A virus was detected in 30% of pneumonia episodes and in 40% of non-pneumonia episodes, but this difference was not significant (P = 0.09). The presence of a respiratory virus was associated with fewer revisits to the hospital (P < .05), whereas a CRP value over 100 mg/l was associated with death during hospital stay (P < .05). Respiratory virus detections did not correlate to WBC or CRP values, signs and symptoms or prognosis of radiographically-verified pneumonia episodes.

CONCLUSION

Among the elderly with respiratory symptoms, respiratory virus detection was not associated with an increased risk of pneumonia or with a more severe clinical course of the illness. CRP and WBC remain important indicators of pneumonia, and according to our findings, pneumonia should be treated as a bacterial disease regardless of the virus findings. Our data does not support routine virus diagnostics for the elderly patients with pneumonia outside the epidemic seasons.

Crystal structure of the post-fusion core of the Human coronavirus 229E spike protein at 1.86 Å resolution

Human coronavirus 229E (HCoV‐229E) usually causes mild upper respiratory infections in heathy adults, but may lead to severe complications or mortality in individuals with weakened immune systems. Virus entry of HCoV‐229E is mediated by its spike (S) protein, where the S1 domain facilitates attachment to host cells and the S2 domain is involved in subsequent fusion of the virus and host membranes. During the fusion process, two heptad repeats, HR1 and HR2, in the S2 domain assemble into a six‐helix membrane‐fusion structure termed the fusion core. Here, the complete fusion‐core structure of HCoV‐229E has been determined at 1.86 Å resolution, representing the most complete post‐fusion conformation thus far among published human alphacoronavirus (α‐HCoV) fusion‐core structures. The overall structure of the HCoV‐229E fusion core is similar to those of SARS, MERS and HCoV‐NL63, but the packing of its 3HR1 core differs from those of SARS and MERS in that it contains more noncanonical `x' and `da' layers. Side‐by‐side electrostatic surface comparisons reveal that the electrostatic surface potentials are opposite in α‐HCoVs and β‐HCoVs at certain positions and that the HCoV‐229E surface also appears to be the most hydrophobic among the various HCoVs. In addition to the highly conserved hydrophobic interactions between HR1 and HR2, some polar and electrostatic interactions are also well preserved across different HCoVs. This study adds to the structural profiling of HCoVs to aid in the structure‐based design of pan‐coronavirus small molecules or peptides to inhibit viral fusion.

Viral respiratory infections in a nursing home: a six-month prospective study

BACKGROUND

The knowledge on viral respiratory infections in nursing home (NH) residents and their caregivers is limited. The purpose of the present study was to assess and compare the incidence of acute respiratory infections (ARI) in nursing home (NH) residents and staff, to identify viruses involved in ARI and to correlate viral etiology with clinical manifestations of ARI.

METHODS

The prospective surveillance study was accomplished in a medium-sized NH in Slovenia (central Europe). Ninety NH residents and 42 NH staff were included. Nasopharyngeal swabs were collected from all participants at enrollment (December 5th, 2011) and at the end of the study (May 31st, 2012), and from each participant that developed ARI within this timeframe. Molecular detection of 15 respiratory viruses in nasopharyngeal swab samples was performed.

RESULTS

The weekly incidence rate of ARI in NH residents and NH staff correlated; however, it was higher in staff members than in residents (5.9 versus 3.8/1,000 person-days, P = 0.03), and was 2.5 (95 % CI: 1.36-4.72) times greater in residents without dementia than in residents with dementia. Staff members typically presented with upper respiratory tract involvement, whereas in residents lower respiratory tract infections predominated. Respiratory viruses were detected in 55/100 ARI episodes. In residents, influenza A virus, respiratory syncytial virus, and human metapneumovirus were detected most commonly, whereas in NH staff rhinovirus and influenza A virus prevailed. 38/100 ARI episodes (30/56 in residents, 8/44 in staff) belonged to one of three outbreaks (caused by human metapneumovirus, influenza A virus and respiratory syncytial virus, respectively). NH residents had higher chances for virus positivity within outbreak than HN staff (OR = 7.4, 95 % CI: 1.73-31.48, P < 0.01).

CONCLUSIONS

ARI are common among NH residents and staff, and viruses were detected in a majority of the episodes of ARI. Many ARI episodes among NH residents were outbreak cases and could be considered preventable.

TRIAL REGISTRATION

The study was registered on the 1^th of December 2011 at ClinicalTrials ( NCT01486160 ).

Human bocavirus: Current knowledge and future challenges

Human bocavirus (HBoV) is a parvovirus isolated about a decade ago and found worldwide in both respiratory samples, mainly from early life and children of 6-24 mo of age with acute respiratory infection, and in stool samples, from patients with gastroenteritis. Since then, other viruses related to the first HBoV isolate (HBoV1), namely HBoV2, HBoV3 and HBoV4, have been detected principally in human faeces. HBoVs are small non-enveloped single-stranded DNA viruses of about 5300 nucleotides, consisting of three open reading frames encoding the first two the non-structural protein 1 (NS1) and nuclear phosphoprotein (NP1) and the third the viral capsid proteins 1 and 2 (VP1 and VP2). HBoV pathogenicity remains to be fully clarified mainly due to the lack of animal models for the difficulties in replicating the virus in in vitro cell cultures, and the fact that HBoV infection is frequently accompanied by at least another viral and/or bacterial respiratory and/or gastroenteric pathogen infection. Current diagnostic methods to support HBoV detection include polymerase chain reaction, real-time PCR, enzyme-linked immunosorbent assay and enzyme immunoassay using recombinant VP2 or virus-like particle capsid proteins, although sequence-independent amplification techniques combined with next-generation sequencing platforms promise rapid and simultaneous detection of the pathogens in the future. This review presents the current knowledge on HBoV genotypes with emphasis on taxonomy, phylogenetic relationship and genomic analysis, biology, epidemiology, pathogenesis and diagnostic methods. The emerging discussion on HBoVs as true pathogen or innocent bystander is also emphasized.

Evaluation of custom multiplex real - time RT - PCR in comparison to fast - track diagnostics respiratory 21 pathogens kit for detection of multiple respiratory viruses

BACKGROUND

Severe acute respiratory infections in children can be fatal, rapid identification of the causative agent and timely treatment can be life saving. Multiplex real time RT-PCR helps in simultaneous detection of multiple viruses saving cost, time and labour. Commercially available multiplex real time RT-PCR kits are very expensive. Therefore the aim of the present study was to develop a cost effective multiplex real time RT-PCR for the detection of 18 respiratory viruses and compare it with an in-vitro diagnostics approved Fast Track Diagnostic Respiratory Pathogens 21 Kit (FTD).

METHODS

Nasopharyngeal aspirates and throat swabs were collected and processed for extraction of nucleic acid using an automated extraction system and multiplex real time RT-PCR was performed using the FTD kit and a custom assay on 356 samples.

RESULTS

Custom and FTD assays detected one or more respiratory viruses in 268 (75.29 %) and 262 (73.60 %) samples respectively. The concordance between the custom assay and the FTD assay was 100 % for HCoV OC43, HCoV 229E, HPIV-1, HPIV-2, HBoV, HPeV, Flu A, and Influenza A(H1N1)pdm09 and 94.66 - 99.71 % for the remaining viruses; Flu B (99.71 %), HRV (99.71 %), HPIV-3 (98.87 %), HPIV-4 (99.43 %), HCoV NL63 (99.71 %), HMPV A/B (99.71 %), RSV A/B (94.66 %), EV (98.31 %), HCoV HKU1 (99.71 %), HAdV (99.71 %). Major discrepancy was observed for RSV A/B, which was over detected in 18 samples by the custom assay as compared to the FTD assay. The custom assay was much cheaper than the FTD assay and the time taken was only 29 min more.

CONCLUSION

The custom primer and probe mix was found to be comparable to the FTD assay with good concordance but was much cheaper and the time taken for reporting was only 29 min more. The low cost custom multiplex RT-PCR can be a useful alternative to the costly FTD kit for rapid identification of viral aetiology in resource limited settings.

Lung Infection by Human Bocavirus Induces the Release of Profibrotic Mediator Cytokines In Vivo and In Vitro

Human Bocavirus subtype 1 (HBoV1) is associated with respiratory diseases and may contribute to chronic lung diseases by persisting in the infected host. Here the question was addressed if HBoV infections could contribute to fibrogenesis processes as suggested by previously published clinical observations. Cytokine profiles induced by HBoV infection in CuFi-8 air-liquid interphase cell cultures and in bronchoalveolar lavage fluid (BALF) of 20 HBoV-positive and 12 HBoV-negative patients were analysed by semi-quantitative Western spot blot analyses. Although lots of cytokines were regulated independently of HBoV status, several cytokines associated with lung fibrosis and tumour development, e.g., EGF, VEGF, TARC (CCL17), TNF-α, TNF-β, TIMP-1, were clearly upregulated in the HBoV-positive cohort. These findings suggest that the development of lung fibrosis might be triggered by HBoV induced cytokine expression.

Case Report: Human Bocavirus Associated Pneumonia as Cause of Acute Injury, Cologne, Germany

Although the human bocavirus (HBoV) is known since a decade, limited information about its pathogenesis is available due to the lack of an animal model. Thus, clinical cases and studies are the major source of novel information about the course of infection and the related pathophysiology.In this context, a clinical case of an adult patient suffering from severe HBoV-pneumonia is described that was associated with loss of consciousness followed by acute rib fracture and subsequent neurological disorder.Following initial global respiratory dysfunction the clinical respiratory symptoms recovered but the neurological symptoms maintained after weaning and intensive care in the stroke unit. During the initial phase, an acute active HBoV infection was confirmed by positive polymerase chain reactions from bronchoalveolar lavage fluid and serum.The case further demonstrates that HBoV can cause severe pneumonia, induce secondary disease also in adults, and may be associated with neurological symptoms as previously assumed.

Viral Respiratory Tract Infections in Adult Patients Attending Outpatient and Emergency Departments, Taiwan, 2012-2013: A PCR/Electrospray Ionization Mass Spectrometry Study

Viral etiologies of respiratory tract infections (RTIs) have been less studied in adult than in pediatric populations. Furthermore, the ability of PCR/electrospray ionization mass spectrometry (PCR/ESI-MS) to detect enteroviruses and rhinoviruses in respiratory samples has not been well evaluated. We sought to use PCR/ESI-MS to comprehensively investigate the viral epidemiology of adult RTIs, including testing for rhinoviruses and enteroviruses. Nasopharyngeal or throat swabs from 267 adults with acute RTIs (212 upper RTIs and 55 lower RTIs) who visited a local clinic or the outpatient or emergency departments of a medical center in Taiwan between October 2012 and June 2013 were tested for respiratory viruses by both virus isolation and PCR/ESI-MS. Throat swabs from 15 patients with bacterial infections and 27 individuals without active infections were included as control samples. Respiratory viruses were found in 23.6%, 47.2%, and 47.9% of the 267 cases by virus isolation, PCR/ESI-MS, and both methods, respectively. When both methods were used, the influenza A virus (24.3%) and rhinoviruses (9.4%) were the most frequently identified viruses, whereas human coronaviruses, human metapneumovirus (hMPV), enteroviruses, adenoviruses, respiratory syncytial virus, and parainfluenza viruses were identified in small proportions of cases (<5% of cases for each type of virus). Coinfection was observed in 4.1% of cases. In the control group, only 1 (2.4%) sample tested positive for a respiratory virus by PCR/ESI-MS. Patients who were undergoing steroid treatment, had an active malignancy, or suffered from chronic obstructive pulmonary disease (COPD) were at risk for rhinovirus, hMPV, or parainfluenza infections, respectively. Overall, immunocompromised patients, patients with COPD, and patients receiving dialysis were at risk for noninfluenza respiratory virus infection. Rhinoviruses (12.7%), influenza A virus (10.9%), and parainfluenza viruses (7.3%) were the most common viruses involved in the 55 cases of lower RTIs. The factors of parainfluenza infection, old age, and immunosuppression were independently associated with lower RTIs. In conclusion, PCR/ESI-MS improved the diagnostic yield for viral RTIs. Non-influenza respiratory virus infections were associated with patients with comorbidities and with lower RTIs. Additional studies that delineate the clinical need for including non-influenza respiratory viruses in the diagnostic work-up in these populations are warranted.

Molecular identification and quantification of human rhinoviruses in respiratory samples

PCR-based molecular assays have become standard diagnostic procedures for the identification and quantification of human rhinoviruses (HRVs) and other respiratory pathogens in most, if not all, clinical microbiology laboratories. Molecular assays are significantly more sensitive than traditional culture-based and serological methods. This advantage has led to the recognition that HRV infections are common causes for not only upper airway symptoms but also more severe lower respiratory illnesses. In addition, molecular assays improve turnaround time, can be performed by technicians with ordinary skills, and can easily be automated. This chapter describes two highly sensitive and specific PCR-based methods for identifying and quantifying HRVs. The first is a two-step PCR method for the detection and typing of HRV. The second is a pan-HRV real-time quantitative (q) PCR method for measuring viral loads in respiratory samples.

Development of an efficient qRT-PCR assay for quality control and cellular quantification of respiratory samples

BACKGROUND

Sample quality is a fundamental parameter for the successful diagnosis of respiratory viruses. This parameter depends upon the concentration of epithelial cells. Respiratory samples are usually heterogeneous, which makes relative quantification of the viral load, against the quantity of cells, the most suitable measurement. The quantification of viral load in the field of respiratory viruses is a vital piece of information. Quantification is required from RNA or DNA viral genomes extracted.

OBJECTIVES

To design (RT-)PCR assays for reference genes, which show stable expression during viral infection, to be used as cellular controls and cellular quantification tools.

STUDY DESIGN

Assays were designed for two reference genes: hypoxanthine phosphoribosyltransferase 1 (HPRT1) and ubiquitin C (UBC). The glyceraldehyde-3-phosphate dehydrogenase gene (GAPDH) was used as a reference for this study. The transcriptional activity of the three genes was studied during infection with respiratory syncytial virus and adenovirus. The HPRT1 q(RT-)PCR assay was used on clinical samples.

RESULTS

All the analysis methods concluded that the three reference genes were stably expressed during viral infection. The HPRT1 q(RT-)PCR assay indicated that the majority of clinical samples (n=301, 69%) had a cellular load of between 100 and 10,000 cells/PCR. The data showed that the concentration decreased as the age of patient increased.

CONCLUSIONS

A new tool has been developed and commercialized for quality control and evaluation of cellular concentration in respiratory samples.

Respiratory viruses associated with patients older than 50 years presenting with ILI in Senegal, 2009 to 2011

Background

In Africa, especially in West Africa, studies about the prevalence and diversity of respiratory viruses (influenza and others) in elderly people are largely lacking. In studies done elsewhere, it is well established that older people, when compared with younger adults, are at greater risk of significant morbidity and mortality from complications arising from influenza. The main aim of this study was to determine the prevalence and the diversity of respiratory viruses associated with ILI cases in adults over 50 years old in Senegal.

Methods

The recruitment period of this study was from January 2009 to December 2011. 232 patients aged 50 years and above presenting ILI cases were enrolled. Nasal-pharyngeal and/or oral pharyngeal swabs were collected from patients. RNA was extracted from 200 μl of each sample followed by a two-step real-time RT-PCR. The Anyplex™ II RV16 Detection kit was used for viral detection. The kit enabled the simultaneous detection of the presence of 16 respiratory viruses.

Results

150 viruses were detected: influenza viruses (44.7%) and rhinoviruses (26.7%) were the most prevalent. We detected 13 human parainfluenza viruses (8.7%), 7 human respiratory syncytial viruses (4.7%), 6 coronaviruses (4%), 5 human metapneumoviruses (3.3%), 5 human adenoviruses (3.3%) and 1 human bocavirus (0.7%). 14 cases (6%) of dual virus infections and one triple viral detection case were encountered. 56 (56.6%) viruses detected were found in the 50-64 year old age group, 59 (76.6%; P < 0.001) from 65–74 year old age group and 35 (62.5%) were detected in the ≥75 year old age group. The viral co-infections were more frequent in the 65-74 age group (9/15).

Conclusions

This pilot study demonstrates a variety of respiratory viruses in the elderly. It also highlights a high prevalence of these viruses in this age group. We speculate from these results that the impact of respiratory viruses other than influenza on the elderly has been considerably underestimated. A more exhaustive study seems necessary in order to provide a more complete picture of the burden of respiratory viruses on morbidity among adults over 50 years old in the sub-Saharan context.

Respiratory syncytial virus and other respiratory viral infections in older adults with moderate to severe influenza-like illness

Background. Few studies have prospectively assessed viral etiologies of acute respiratory infections in community-based elderly individuals. We assessed viral respiratory pathogens in individuals ≥65 years with influenza-like illness (ILI).

Methods. Multiplex reverse-transcriptase polymerase chain reaction identified viral pathogens in nasal/throat swabs from 556 episodes of moderate-to-severe ILI, defined as ILI with pneumonia, hospitalization, or maximum daily influenza symptom severity score (ISS) >2. Cases were selected from a randomized trial of an adjuvanted vs nonadjuvanted influenza vaccine conducted in elderly adults from 15 countries.

Results. Respiratory syncytial virus (RSV) was detected in 7.4% (41/556) moderate-to-severe ILI episodes in elderly adults. Most (39/41) were single infections. There was a significant association between country and RSV detection (P = .004). RSV prevalence was 7.1% (2/28) in ILI with pneumonia, 12.5% (8/64) in ILI with hospitalization, and 6.7% (32/480) in ILI with maximum ISS > 2. Any virus was detected in 320/556 (57.6%) ILI episodes: influenza A (104/556, 18.7%), rhinovirus/enterovirus (82/556, 14.7%), coronavirus and human metapneumovirus (each 32/556, 5.6%).

Conclusions. This first global study providing data on RSV disease in ≥65 year-olds confirms that RSV is an important respiratory pathogen in the elderly. Preventative measures such as vaccination could decrease severe respiratory illnesses and complications in the elderly.

Human Bocavirus

Human bocavirus 1 (HBoV1), family Parvoviridae, subfamily Parvovirinae, genus Bocavirus, is a recently described respiratory virus with a worldwide distribution. It is recognized as one of the most frequently detected respiratory viruses in hospitalized children below 5 years of age and mainly detected in children between 6 and 24 months of age. The severe clinical course of HBoV1 infection can be seen in prematurely born children or children, but rarely adults, with other underlying medical conditions. The seroepidemiological studies show that most of the children are infected with HBoV1 by the age of 6 and that the IgG antibodies remain for life. The routine laboratory diagnostics of HBoV1 infections is almost exclusively based on detection of HBoV1 DNA in respiratory samples by PCR. Due to frequent coinfections with other respiratory viruses, PCR of plasma samples and detection of specific IgM might aid in determining the etiology of infection.

Aging affects the proportions of T and B cells in a group of elderly men in a developing country--a pilot study from Pakistan

Immune status is different in the elderly and the young, but whether age-associated differences are similar in developing and industrialized countries is unclear. To approach this question, peripheral blood immune cell phenotypes were analyzed by polychromatic flow cytometry in 50 young and 50 elderly men in a pilot study in a rural area of Pakistan. As a group, the elderly had a significantly lower CD4:CD8 ratio, a lower percentage of CD8+ naïve T cells, and significantly higher percentage of late-differentiated memory cells than the young. No age-associated differences were seen in B cells or NK cells. CD8+ cells as a percentage of CD3+ T cells were positively associated with plasma CRP levels but not other factors. We conclude that there are differences between the peripheral immune cell phenotypes of young and elderly Pakistani men and that these seem broadly similar to those more extensively documented in industrialized countries, despite the marked societal, nutritional, and many other differences in these populations.

Rhinoviruses as an underestimated cause of influenza-like illness in pregnancy during the 2009-2010 influenza pandemic

During the 2009-2010 influenza pandemic, pregnant women were identified at high risk for severe infection. In case of influenza-like illness they were systematically treated with oseltamivir. When performed, virological diagnosis showed that some of these women were not influenza-infected. The objectives of the study were to identify viruses which could induce an influenza-like illness in pregnant women during the 2009-2010 pandemic, then to establish possible links between detected viruses and symptoms, and then characterize human rhinoviruses (HRV) strains detected in some samples. Nasal swabs from 78 pregnant women presenting with influenza-like illness and previously tested for influenza virus by RT-PCR in 2009-2010 were further assayed by multiplex RespiFinder assay and bocavirus PCR to search for 13 other viruses. Genotyping of HRV strains was carried out using partial genomic sequencing in the VP4/VP2 region. Influenza A virus infection was confirmed in 33 women (42%). Non-influenza viruses were detected in 18 additional cases (23%). Rhinoviruses were the most numerous (13%) and belonged to 9 different genotypes distributed between the 3 genogroups. When comparing symptoms observed in influenza-infected women and women infected by other viruses, shivers were more frequent in the former group (P=0.02), and expectorations in the latter (P=0.03). During the influenza pandemic 2009-2010, non-influenza viruses and mostly rhinoviruses were an underestimated cause of influenza-like illness in pregnant women. Viral diagnosis should help to stop empiric oseltamivir therapy in influenza-negative patients and antibiotic treatment in patients infected with a non-influenza virus.

New molecular virus detection methods and their clinical value in lower respiratory tract infections in children

During the past decade, several new respiratory viruses and their subgroups have been discovered. All these new viruses, as well as previously known respiratory viruses, can be detected by sensitive PCR methods, which have become popular in the diagnostic workup of respiratory viral infections. Currently, respiratory viruses can be detected in up to 95% of children with lower respiratory tract illness. On the other hand, virus detection rates in asymptomatic children are also high (up to 68%), as are coinfection rates in symptomatic children (up to 43%) and justified concerns of causality have been raised. Imposing progress has been made in developing multiplex quantitative PCR assays; here, several primer sets are run within a single PCR mixture. These PCR assays give a better understanding of the dominant viral infection, of viral infections that may be incipient and of any waning infections than does a single-target PCR. Multiplex PCR assays are also gaining popularity due to their cost-effectiveness and short throughput time compared to multiple single-target PCRs. Our understanding of the indications of virus PCRs and our ability to interpret the results from a clinical point of view have improved. This paper reviews the progress in PCR assays and discusses their role in the diagnosis of lower respiratory tract infections in children.

The role of infections and coinfections with newly identified and emerging respiratory viruses in children

Acute respiratory infections are a major cause of morbidity in children both in developed and developing countries. A wide range of respiratory viruses, including respiratory syncytial virus (RSV), influenza A and B viruses, parainfluenza viruses (PIVs), adenovirus, rhinovirus (HRV), have repeatedly been detected in acute lower respiratory tract infections (LRTI) in children in the past decades. However, in the last ten years thanks to progress in molecular technologies, newly discovered viruses have been identified including human Metapneumovirus (hMPV), coronaviruses NL63 (HcoV-NL63) and HKU1 (HcoV-HKU1), human Bocavirus (HBoV), new enterovirus (HEV), parechovirus (HpeV) and rhinovirus (HRV) strains, polyomaviruses WU (WUPyV) and KI (KIPyV) and the pandemic H1N1v influenza A virus. These discoveries have heavily modified previous knowledge on respiratory infections mainly highlighting that pediatric population is exposed to a variety of viruses with similar seasonal patterns. In this context establishing a causal link between a newly identified virus and the disease as well as an association between mixed infections and an increase in disease severity can be challenging. This review will present an overview of newly recognized as well as the main emerging respiratory viruses and seek to focus on the their contribution to infection and co-infection in LRTIs in childhood.

Microbes and asthma: the missing cellular and molecular links

PURPOSE OF REVIEW

In this review, we describe the 'state-of-the-art' in our knowledge of asthma and what gaps exist, which can be exploited in the future for effective translation of our knowledge from the bench or population studies to diagnosis and therapy.

RECENT FINDINGS

The advent of microbiome research has expanded the potential role of microbes in asthma. There has been a significant increase in our understanding of the pathologic, genetic, cellular and molecular mechanisms of asthma. Nonetheless, the contribution of microbes to the genesis, exacerbation and treatment of asthma are poorly understood.

SUMMARY

Asthma is a complex chronic disease of the lung whose incidence is growing at all ages despite the progress that has been made in the areas of diagnosis and treatment of asthma. The complexity is partly due to the environmental insults such as allergens and microbial infections that play differential roles in the pathogenesis of childhood vis-à-vis elderly asthma. Microbes may play important roles in the exacerbation of asthma and hence in the comorbidities due to asthma, and also in the causation of asthma.

Severity of human rhinovirus infection in immunocompromised adults is similar to that of 2009 H1N1 influenza

This retrospective chart review of patients at a tertiary referral center compares characteristics and clinical features of patients diagnosed with human rhinovirus (HRV) infection to those of patients with 2009 H1N1 influenza A (pH1N1) during the pandemic respiratory season of 2009 to 2010. Hospital admission rates, intensive care unit (ICU) admissions, and mortality were not statistically different between the HRV and pH1N1 groups; however, more patients in the HRV group were considered immunocompromised.