An update on respiratory syncytial virus

Respiratory syncytial virus (RSV) is a leading cause of acute respiratory infections resulting in a significant burden worldwide, particularly in children and older adults. This collection calls for original research papers that advance our understanding of the epidemiology, evolution, diagnosis, clinical management, and prevention of RSV infections.

Airborne influenza virus shedding by patients in health care units: Removal mechanisms affecting virus transmission

In this study, we characterize the distribution of airborne viruses (influenza A/B) in hospital rooms of patients with confirmed infections. Concurrently, we monitored fine particulate matter (PM2.5 & PM10) and several physical parameters including the room air exchange rate, temperature, and relative humidity to identify corresponding correlations with virus transport and removal determinants. The results continue to raise concerns about indoor air quality (IAQ) in healthcare facilities and the potential exposure of patients, staff and visitors to aerosolized viruses as well as elevated indoor PM levels caused by outdoor sources and/or re-suspension of settled particles by indoor activities. The influenza A virus was detected in 42% of 33 monitored rooms, with viruses detectible up to 1.5 m away from the infected patient. Active coughing was a statistically significant variable that contributed to a higher positive rate of virus detection in the collected air samples. Viral load across patient rooms ranged between 222 and 5,760 copies/m3, with a mean of 820 copies/m3. Measured PM2.5 and PM10 levels exceeded IAQ daily exposure guidelines in most monitored rooms. Statistical and numerical analyses showed that dispersion was the dominant viral removal pathway followed by settling. Changes in the relative humidity and the room's temperature were had a significant impact on the viral load removal. In closure, we highlight the need for an integrated approach to control determinants of IAQ in patients' rooms.

Erratum: Rotavirus Genotypes and Vaccine Effectiveness from a Sentinel, Hospital-Based, Surveillance Study for Three Consecutive Rotavirus Seasons in Lebanon

[This corrects the article DOI: 10.1371/journal.pone.0161345.].

Monkeypox (mpox) Outbreak: More queries posed as cases soar globally

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Genomic surveillance of SARS-CoV-2 in COVID-19 vaccinated healthcare workers in Lebanon

BACKGROUND

The emergence of SARS-CoV-2 variants including the Delta and Omicron along with waning of vaccine-induced immunity over time contributed to increased rates of breakthrough infection specifically among healthcare workers (HCWs). SARS-CoV-2 genomic surveillance is an important tool for timely detection and characterization of circulating variants as well as monitoring the emergence of new strains. Our study is the first national SARS-CoV-2 genomic surveillance among HCWs in Lebanon.

METHODS

We collected 250 nasopharyngeal swabs from HCWs across Lebanon between December 2021 and January 2022. Data on the date of positive PCR, vaccination status, specific occupation, and hospitalization status of participants were collected. Extracted viral RNA from nasopharyngeal swabs was converted to cDNA, library prepped using the coronaHIT method, followed by whole genome sequencing on the Illumina NextSeq 500 platform.

RESULTS

A total of 133 (57.1%) samples belonging to the Omicron (BA.1.1) sub-lineage were identified, as well as 44 (18.9%) samples belonging to the BA.1 sub-lineage, 28 (12%) belonging to the BA.2 sub-lineage, and only 15 (6.6%) samples belonging to the Delta variant sub-lineage B.1.617.2. These results show that Lebanon followed the global trend in terms of circulating SARS-CoV-2 variants with Delta rapidly replaced by the Omicron variant.

CONCLUSION

This study underscores the importance of continuous genomic surveillance programs in Lebanon for the timely detection and characterization of circulating variants. The latter is critical to guide public health policy making and to timely implement public health interventions.

Viral metagenomics analysis of stool specimens from children with unresolved gastroenteritis in Qatar

Acute gastroenteritis (AGE) is associated with significant global morbidity and mortality, especially among children under five years of age. Viruses are well established as etiologic agents of gastroenteritis since they are the most common pathogens that contribute to the disease burden in developing countries. Despite the advances in molecular diagnosis, a substantial proportion of AGE etiology remain unresolved. We implemented a viral metagenomics pipeline to determine the potential viral etiology associated with AGE among children under the age of five years in Qatar with undiagnosed etiology. Following enriching for the viral genome, ∼1.3 billion sequences were generated from 89 stool specimens using the Illumina HiSeq platform, of which 7% were mapped to viral genomes. Human viruses were detected in 34 specimens (38.2%); 14 were adenovirus, nine coxsackievirus A16, five rotavirus (G9P[8] and G4P[8]), four norovirus (GII), one influenza A virus (H3), and one respiratory syncytial virus A (RSVA). In conclusion, the viral metagenomics approach is useful for determining AGE's etiology when routine molecular diagnostic assays fail.

Three-Dimensional Cell Culture Models to Study Respiratory Virus Infections Including COVID-19

Respiratory viral infections, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are among the most common illnesses and a leading cause of morbidity and mortality worldwide. Due to the severe effects on health, the need of new tools to study the pathogenesis of respiratory viruses as well as to test for new antiviral drugs and vaccines is urgent. In vitro culture model systems, such as three-dimensional (3D) cultures, are emerging as a desirable approach to understand the virus host interactions and to identify novel therapeutic agents. In the first part of the article, we address the various scaffold-free and scaffold-based 3D culture models such as hydrogels, bioreactors, spheroids and 3D bioprinting as well as present their properties and advantages over conventional 2D methods. Then, we review the 3D models that have been used to study the most common respiratory viruses including influenza, parainfluenza, respiratory syncytial virus (RSV) and coronaviruses. Herein, we also explain how 3D models have been applied to understand the novel SARS-CoV-2 infectivity and to develop potential therapies.

Uptake rates, knowledge, attitudes, and practices toward seasonal influenza vaccination among healthcare workers in Lebanon

Despite recommendations and their occupational risk to influenza infection vaccine hesitancy remains a challenge among healthcare workers (HCWs). No studies have been conducted in Lebanon to assess the influenza vaccine's acceptance among HCWs. We conducted a survey to assess factors associated with vaccine uptake and practices among HCWs in Lebanon. Only 40.4% of the HCWs reported receiving the 2018-2019 seasonal vaccine and 1 out 5 routinely received the seasonal vaccine. One-third of the HCWs reported having free access to the influenza vaccine. The willingness to receive the vaccine decreased had it been offered for a fee. Self, family and community protection (55.5%) was a key vaccination enabler. While, viral evolution, concerns regarding vaccine efficacy and side effects, and cost of vaccine ranked as top vaccination barriers. The majority of the HCWs (75%) recommended the vaccine to their patients. Past influenza vaccination (Odds ratio (OR) = 2.37, CI 1.48,3.79), willingness to receive the vaccine for free (OR = 6.93, CI 4.27-11.34) or having diagnosed influenza (OR = 1.81, CI 1.12-2.92) were significantly associated with HCWs' willingness to recommend the vaccine to patients. Better knowledge about influenza and vaccination was strongly associated with the willingness to receive and recommend the vaccine (p < .001). The vaccination rate among HCWs in Lebanon was suboptimal despite the positive attitudes toward the influenza vaccine. Interventions that enhance vaccine accessibility and knowledge are warranted to improve vaccination coverage among HCWs.

No association between the SARS-CoV-2 variants and mortality rates in the Eastern Mediterranean Region

As the novel coronavirus SARS-CoV-2 continues to spread in all countries, there is a growing interest in monitoring and understanding the impact of emerging strains on virus transmission and disease severity. Here, we analyzed SARS-CoV-2 genomic sequences reported in the Eastern Mediterranean Region (EMR) countries, as of 1 January 2021. The majority (~75%) of these sequences originated from three out of 22 EMR countries, and 65.8% of all sequences belonged to GISAID clades GR, GH, G and GV. A delay ranging between 30 and 150 days from sample collection to sequence submission was observed across all countries, limiting the utility of such data in informing public health policies. We identified ten common non-synonymous mutations represented among SARS-CoV-2 in the EMR and several country-specific ones. Two substitutions, spike_D614G and NSP12_P323L, were predominantly concurrent in most countries. While the single incidence of NSP12_P323L was positively correlated with higher case fatality rates in EMR, no such association was established for the double (spike_D614G and NSP12_P323L) concurrent variant across the region. Our study identified critical data gaps in EMR highlighting the importance of enhancing surveillance and sequencing capacities in the region.

Repurposing Ivermectin for COVID-19: Molecular Aspects and Therapeutic Possibilities

As of January 2021, SARS-CoV-2 has killed over 2 million individuals across the world. As such, there is an urgent need for vaccines and therapeutics to reduce the burden of COVID-19. Several vaccines, including mRNA, vector-based vaccines, and inactivated vaccines, have been approved for emergency use in various countries. However, the slow roll-out of vaccines and insufficient global supply remains a challenge to turn the tide of the pandemic. Moreover, vaccines are important tools for preventing the disease but therapeutic tools to treat patients are also needed. As such, since the beginning of the pandemic, repurposed FDA-approved drugs have been sought as potential therapeutic options for COVID-19 due to their known safety profiles and potential anti-viral effects. One of these drugs is ivermectin (IVM), an antiparasitic drug created in the 1970s. IVM later exerted antiviral activity against various viruses including SARS-CoV-2. In this review, we delineate the story of how this antiparasitic drug was eventually identified as a potential treatment option for COVID-19. We review SARS-CoV-2 lifecycle, the role of the nucleocapsid protein, the turning points in past research that provided initial 'hints' for IVM's antiviral activity and its molecular mechanism of action- and finally, we culminate with the current clinical findings.

Detection of influenza virus in air samples of patient rooms

BACKGROUND

Understanding the transmission and dispersal of influenza virus and respiratory syncytial virus (RSV) via aerosols is essential for the development of preventative measures in hospital environments and healthcare facilities.

METHODS

During the 2017-2018 influenza season, patients with confirmed influenza or RSV infections were enrolled. Room air samples were collected close (0.30 m) to and distant (2.20 m) from patients' heads. Real-time polymerase chain reaction was used to detect and quantify viral particles in the air samples. The plaque assay was used to determine the infectiousness of the detected viruses.

FINDINGS

Fifty-one air samples were collected from the rooms of 29 patients with laboratory-confirmed influenza; 51% of the samples tested positive for influenza A virus (IAV). Among the IAV-positive patients, 65% were emitters (had at least one positive air sample), reflecting a higher risk of nosocomial transmission compared with non-emitters. The majority (61.5%) of the IAV-positive air samples were collected 0.3 m from a patient's head, while the remaining IAV-positive air samples were collected 2.2 m from a patient's head. The positivity rate of IAV in air samples was influenced by distance from the patient's head and day of sample collection after hospital admission. Only three patients with RSV infection were recruited and none of them were emitters.

CONCLUSION

Influenza virus can be aerosolized beyond 1 m in patient rooms, which is the distance considered to be safe by infection control practices. Further investigations are needed to determine the extent of infectivity of aerosolized virus particles.

COVID-19 in-vitro Diagnostics: State-of-the-Art and Challenges for Rapid, Scalable, and High-Accuracy Screening

The world continues to grapple with the devastating effects of the current COVID-19 pandemic. The highly contagious nature of this respiratory disease challenges advanced viral diagnostic technologies for rapid, scalable, affordable, and high accuracy testing. Molecular assays have been the gold standard for direct detection of the presence of the viral RNA in suspected individuals, while immunoassays have been used in the surveillance of individuals by detecting antibodies against SARS-CoV-2. Unlike molecular testing, immunoassays are indirect testing of the viral infection. More than 140 diagnostic assays have been developed as of this date and have received the Food and Drug Administration (FDA) emergency use authorization (EUA). Given the differences in assasy format and/or design as well as the lack of rigorous verification studies, the performance and accuracy of these testing modalities remain unclear. In this review, we aim to carefully examine commercialized and FDA approved molecular-based and serology-based diagnostic assays, analyze their performance characteristics and shed the light on their utility and limitations in dealing with the COVID-19 global public health crisis.

Neurological and Neuropsychological Changes Associated with SARS-CoV-2 Infection: New Observations, New Mechanisms

SARS-CoV-2 infects cells through angiotensin-converting enzyme 2 (ACE2), a ubiquitous receptor that interacts with the virus' surface S glycoprotein. Recent reports show that the virus affects the central nervous system (CNS) with symptoms and complications that include dizziness, altered consciousness, encephalitis, and even stroke. These can immerge as indirect immune effects due to increased cytokine production or via direct viral entry into brain tissue. The latter is possible through neuronal access via the olfactory bulb, hematogenous access through immune cells or directly across the blood-brain barrier (BBB), and through the brain's circumventricular organs characterized by their extensive and highly permeable capillaries. Last, the COVID-19 pandemic increases stress, depression, and anxiety within infected individuals, those in isolation, and high-risk populations like children, the elderly, and health workers. This review surveys the recent updates of CNS manifestations post SARS-CoV-2 infection along with possible mechanisms that lead to them.

Platforms Exploited for SARS-CoV-2 Vaccine Development

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the only zoonotic-origin coronavirus (CoV) that has reached the pandemic stage. The virus uses its spike (S) glycoprotein to attach to the host cells and initiate a cascade of events that leads to infection. It has sternly affected public health, economy, education, and social behavior around the world. Several scientific and medical communities have mounted concerted efforts to limit this pandemic and the subsequent wave of viral spread by developing preventative and potential vaccines. So far, no medicine or vaccine has been approved to prevent or treat coronavirus disease 2019 (COVID-19). This review describes the latest advances in the development of SARS-CoV-2 vaccines for humans, mainly focusing on the lead candidates in clinical trials. Moreover, we seek to provide both the advantages and the disadvantages of the leading platforms used in current vaccine development, based on past vaccine delivery efforts for non-SARS CoV-2 infections. We also highlight the population groups who should receive a vaccine against COVID-19 in a timely manner to eradicate the pandemic rapidly.

The origins of G12P[6] rotavirus strains detected in Lebanon

The G12 rotaviruses are an increasingly important cause of severe diarrhoea in infants and young children worldwide. Seven human G12P[6] rotavirus strains were detected in stool samples from children hospitalized with gastroenteritis in Lebanon during a 2011-2013 surveillance study. Complete genomes of these strains were sequenced using VirCapSeq-VERT, a capture-based high-throughput viral-sequencing method, and further characterized based on phylogenetic analyses with global RVA and vaccine strains. Based on the complete genomic analysis, all Lebanese G12 strains were found to have Wa-like genetic backbone G12-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1. Phylogenetically, these strains fell into two clusters where one of them might have emerged from Southeast Asian strains and the second one seems to have a mixed backbone between North American and Southeast Asian strains. Further analysis of these strains revealed high antigenic variability compared to available vaccine strains. To our knowledge, this is the first report on the complete genome-based characterization of G12P[6] emerging in Lebanon. Additional studies will provide important insights into the evolutionary dynamics of G12 rotaviruses spreading in Asia.

Macrophage responses associated with COVID-19: A pharmacological perspective

COVID-19 has caused worldwide death and economic destruction. The pandemic is the result of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has demonstrated high rates of infectivity leading to great morbidity and mortality in vulnerable populations. At present, scientists are exploring various approaches to curb this pandemic and alleviate its health consequences, while racing to develop a vaccine. A particularly insidious aspect of COVID-19 is the delayed overactivation of the body's immune system that is manifested as the cytokine storm. This unbridled production of pro-inflammatory cytokines and chemokines can directly or indirectly cause massive organ damage and failure. Systemic vascular endothelial inflammation and thrombocytopenia are potential consequences as well. In the case of COVID-19, the cytokine storm often fits the pattern of the macrophage activation syndrome with lymphocytopenia. The basis for the imbalance between the innate and adaptive immune systems is not clearly defined, but highlights the effect of SARS-CoV-2 on macrophages. Here we discuss the potential underlying basis for the impact of SARS-CoV-2 on macrophages, both direct and indirect, and potential therapeutic targets. These include granulocyte-macrophage colony-stimulating factor (GM-CSF), interleukin 6 (IL-6), interferons, and CXCL10 (IP-10). Various biopharmaceuticals are being repurposed to target the cytokine storm in COVID-19 patients. In addition, we discuss the rationale for activating the macrophage alpha 7 nicotinic receptors as a therapeutic target. A better understanding of the molecular consequences of SARS-CoV-2 infection of macrophages could lead to novel and more effective treatments for COVID-19.

Burden of influenza B virus infection and considerations for clinical management

Influenza B viruses cause significant morbidity and mortality, particularly in children, but the awareness of their impact is often less than influenza A viruses partly due to their lack of pandemic potential. Here, we summarise the biology, epidemiology and disease burden of influenza B, and review existing data on available antivirals for its management. There has long been uncertainty surrounding the clinical efficacy of neuraminidase inhibitors (NAIs) for influenza B treatment. In this article, we bring together the existing data on NAIs and discuss these alongside recent large randomised controlled trial data for the new polymerase inhibitor baloxavir in high-risk influenza B patients. Finally, we offer considerations for the clinical management of influenza B, with a focus on children and high-risk patients where disease burden is highest.

Detection of influenza virus in air samples of patient rooms

BACKGROUND

Understanding the transmission and dispersal of influenza virus and respiratory syncytial virus (RSV) via aerosols is essential for the development of preventative measures in hospital environments and healthcare facilities.

METHODS

During the 2017-2018 influenza season, patients with confirmed influenza or RSV infections were enrolled. Room air samples were collected close (0.30 m) to and distant (2.20 m) from patients' heads. Real-time polymerase chain reaction was used to detect and quantify viral particles in the air samples. The plaque assay was used to determine the infectiousness of the detected viruses.

FINDINGS

Fifty-one air samples were collected from the rooms of 29 patients with laboratory-confirmed influenza; 51% of the samples tested positive for influenza A virus (IAV). Among the IAV-positive patients, 65% were emitters (had at least one positive air sample), reflecting a higher risk of nosocomial transmission compared with non-emitters. The majority (61.5%) of the IAV-positive air samples were collected 0.3 m from a patient's head, while the remaining IAV-positive air samples were collected 2.2 m from a patient's head. The positivity rate of IAV in air samples was influenced by distance from the patient's head and day of sample collection after hospital admission. Only three patients with RSV infection were recruited and none of them were emitters.

CONCLUSION

Influenza virus can be aerosolized beyond 1 m in patient rooms, which is the distance considered to be safe by infection control practices. Further investigations are needed to determine the extent of infectivity of aerosolized virus particles.

Epidemiology and clinical characteristics of viral infections in hospitalized children and adolescents with cancer in Lebanon

Background

Viral infections in children and adolescents with malignancy are commonly encountered and have a significant impact on morbidity and mortality. Studies and epidemiological data regarding viral infections in children with cancer in developing countries are lacking. This retrospective cohort study aims to assess the burden of viral infections in children and adolescents with cancer, by assessing prevalence, risk factors, as well as morbidity and mortality of common viruses over a period of 8 years.

Methods and findings

Medical records of cancer patients treated at the Children Cancer Center of Lebanon were reviewed and 155 participants under the age of 21 were identified with at least one documented viral infection during the period from July 2009 to November 2017. This subset included 136 participants with active malignancy and 19 participants with a history of cancer who underwent hematopoietic stem cell transplantation [HSCT] and were in remission; the latter group was analyzed separately. Information regarding participant characteristics, hospital course, and complications were obtained. Associations between viral infections and certain factors were assessed. In the cohort, 64% were male, 81% were Lebanese. In participants with active malignancy, 90% received chemotherapy in the 6 months preceding the viral infection episode, 11% received radiotherapy. 51% of participants were neutropenic at the time of viral detection, and 77% were lymphopenic. 17% experienced a bacterial co-infection, and 3 experienced a viral co-infection. Among 162 viral infection episodes, clinically diagnosed skin infections, mainly herpes simplex virus type 1 and varicella-zoster virus, were the most common [44% of cases]. These were followed by laboratory-proven systemic herpes infections: cytomegalovirus [14%] and Epstein-Barr virus [6%]. Respiratory viruses: influenza and respiratory syncytial virus, accounted for 9% and 4%, respectively, whereas rotavirus represented 11% and BK virus represented 3% of cases. Acute lymphocytic leukemia was the most prevalent neoplasia [57%]. Fever was the most common presenting symptom [55%] and febrile neutropenia was the reason for admission in 24% of cases. The mean length of stay was significantly longer in participants with cytomegalovirus infections and significantly lower in rotavirus infection. Admission to the ICU occurred in 9%, complications in 8%, and mortality in 5%. Participants with viral infections post-HSCT were noted to have a significantly longer length of hospital stay compared to non-HSCT participants, with no other significant differences in clinical course and outcome. The study was limited by its retrospective nature and by the late introduction and underuse of multiplex PCR panels, which may have led to underdiagnosis of viral infections.

Conclusions

Viral infections were prevalent in our sample of cancer patients and may have contributed to morbidity and mortality. Newly available viral diagnostics are likely to vastly increase the number and scope of detectable viral infections in this population. Prospective studies using multiplex PCR technology with systematic testing of patients will be more helpful in defining the burden of viral infections. Furthermore, efforts at antimicrobial stewardship would benefit from the identification of viral causes of infection and limit the unnecessary use of antibiotics in the pediatric cancer population.

Seasonality of Respiratory Viral Infections: Will COVID-19 Follow Suit?

Respiratory viruses, including coronaviruses, are known to have a high incidence of infection during winter, especially in temperate regions. Dry and cold conditions during winter are the major drivers for increased respiratory tract infections as they increase virus stability and transmission and weaken the host immune system. The novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) emerged in China in December 2020 and swiftly spread across the globe causing substantial health and economic burdens. Several countries are battling with the second wave of the virus after a devastating first wave of spread, while some are still in the midst of their first wave. It remains unclear whether SARS-CoV-2 will eventually become seasonal or will continue to circulate year-round. In an attempt to address this question, we review the current knowledge regarding the seasonality of respiratory viruses including coronaviruses and the viral and host factors that govern their seasonal pattern. Moreover, we discuss the properties of SARS-CoV-2 and the potential impact of meteorological factors on its spread.

COVID-19 Therapeutic Options Under Investigation

Since its emergence in China in December 2019, COVID-19 has quickly spread around the globe causing a pandemic. Vaccination or the development of herd immunity seems the only way to slow down the spread of the virus; however, both are not achievable in the near future. Therefore, effective treatments to mitigate the burden of this pandemic and reduce mortality rates are urgently needed. Preclinical and clinical studies of potential antiviral and immunomodulatory compounds and molecules to identify safe and efficacious therapeutics for COVID-19 are ongoing. Two compounds, remdesivir, and dexamethasone have been so far shown to reduce COVID-19-associated death. Here, we provide a review of the potential therapeutic agents being considered for the treatment and management of COVID-19 patients.

Molecular Insights Into SARS COV-2 Interaction With Cardiovascular Disease: Role of RAAS and MAPK Signaling

In December 2019, reports of viral pneumonia came out of Wuhan city in Hubei province in China. In early 2020, the causative agent was identified as a novel coronavirus (CoV) sharing some sequence similarity with SARS-CoV that caused the severe acute respiratory syndrome outbreak in 2002. The new virus, named SARS-CoV-2, is highly contagious and spread rapidly across the globe causing a pandemic of what became known as coronavirus infectious disease 2019 (COVID-19). Early observations indicated that cardiovascular disease (CVD) patients are at higher risk of progression to severe respiratory manifestations of COVID-19 including acute respiratory distress syndrome. Moreover, further observations demonstrated that SARS-CoV-2 infection can induce de novo cardiac and vascular damage in previously healthy individuals. Here, we offer an overview of the proposed molecular pathways shared by the pathogenesis of CVD and SARS-CoV infections in order to provide a mechanistic framework for the observed interrelation. We examine the crosstalk between the renin-angiotensin-aldosterone system and mitogen activated kinase pathways that potentially links cardiovascular predisposition and/or outcome to SARS-CoV-2 infection. Finally, we summarize the possible effect of currently available drugs with known cardiovascular benefit on these pathways and speculate on their potential utility in mitigating cardiovascular risk and morbidity in COVID-19 patients.

The burden of laboratory-confirmed influenza infection in Lebanon between 2008 and 2016: a single tertiary care center experience

BACKGROUND

Influenza is a major cause of morbidity and mortality worldwide. Following the 2009 pandemic, there was widened interest in studying influenza burden in all regions. However, since data from the World Health Organization (WHO) Middle East and North Africa (MENA) region remain limited, we aimed to contribute to the understanding of influenza burden in Lebanon.

METHODS

A retrospective chart review extending over a period of 8 seasons from Jan 1st, 2008 till June 30th, 2016 at a tertiary care center in Beirut was performed. All cases confirmed to have influenza based on rapid antigen detection or/and polymerase chain reaction on a respiratory sample were included for analysis. Data on epidemiology, clinical presentation, complications, antiviral use and mortality were collected for analysis.

RESULTS

A total of 1829 cases of laboratory-confirmed influenza were identified. Average annual positivity rate was 14% (positive tests over total requested). Both influenza A and B co-circulated in each season with predominance of influenza A. Influenza virus started circulating in December and peaked in January and February. The age group of 19-50 years accounted for the largest proportion of cases (22.5%) followed by the age group of 5-19 years (18%). Pneumonia was the most common complication reported in 33% of cases. Mortality reached 3.8%. The two extremes of age (< 2 years and ≥ 65 years) were associated with a more severe course of disease, hospitalization, intensive care unit (ICU) admission, complications, and mortality rate. Of all the identified cases, 26% were hospitalized. Moderate-to-severe disease was more likely in influenza B cases but no difference in mortality was reported between the two types. Antivirals were prescribed in 68.8% and antibiotics in 41% of cases. There seemed to be an increasing trend in the number of diagnosed and hospitalized cases over the years of the study.

CONCLUSION

Patients with laboratory-confirmed influenza at our center had a high rate of hospitalization and mortality. A population based prospective surveillance study is needed to better estimate the burden of Influenza in Lebanon that would help formulate a policy on influenza control.

Depletion of Host and Viral Sphingomyelin Impairs Influenza Virus Infection

Influenza A virus (IAV) is a major human respiratory pathogen causing annual epidemics as well as periodic pandemics. A complete understanding of the virus pathogenesis and host factors involved in the viral lifecycle is crucial for developing novel therapeutic approaches. Sphingomyelin (SM) is the most abundant membrane sphingolipid. It preferentially associates with cholesterol to form distinct domains named lipid rafts. Sphingomyelinases, including acid sphingomyelinase (ASMase), catalyzes the hydrolysis of membrane SM and consequently transform lipid rafts into ceramide-enriched membrane platforms. In this study, we investigated the effect of SM hydrolysis on IAV propagation. Depleting plasma membrane SM by exogenous bacterial SMase (bSMase) impaired virus infection and reduced virus entry, whereas exogenous SM enhanced infection. Moreover, the depletion of virus envelope SM also reduced virus infectivity and impaired its attachment and internalization. Nonetheless, inhibition of ASMase by desipramine did not affect IAV infection. Similarly, virus replication was not impaired in Niemann-Pick disease type A (NPA) cells, which lack functional ASMase. IAV infection in A549 cells was associated with suppression of ASMase activity starting at 6 h post-infection. Our data reveals that intact cellular and viral envelope SM is required for efficient IAV infection. Therefore, SM metabolism can be a potential target for therapeutic intervention against influenza virus infection.

A three-dimensional A549 cell culture model to study respiratory syncytial virus infections

BACKGROUND

Respiratory syncytial virus (RSV) is a primary cause of morbidity and mortality worldwide, affecting infants, young children, and immune-compromised patients; however, currently no vaccine is available for prevention of RSV infections. The overwhelming majority of our knowledge of how RSV causes infection is based upon studies that have been carried out using traditional 2D methods, with cells cultured on flat plastic dishes. Although these simplified culture systems are essential to gain an insight into the fundamentals of host-pathogen interactions, cells in 2D are not exposed to the same conditions as cells in 3D tissues in the body and are therefore a poor representation of thein vivo microenvironment. In this study, we aim to develop the first 3D culture model for RSV infection using A549 cells to test its utility for RSV pathogenesis.

METHODS

To generate spheroids, A549 cells were cultured using ultra-low attachment plates to generate 25 × 10³ cell spheroids. The viability of the spheroids was assessed by trypan blue exclusion assay and flow cytometry showing prominent live cells throughout the spheroids confirming high viability over seven days of incubation.

RESULTS

Immunostaining of A549 spheroids inoculated with RSV, showed time-dependent dissemination of the viral antigen RSV-F within the spheroid, resulting in syncytia formation and a 3-fold increase in mucin secretion compared to the uninfected cells. Additionally, RSV successfully replicated in the spheroids producing infectious virus as early as day one post-inoculation and was sustained for up to 7 days post-inoculation.

CONCLUSIONS

Results show that A549 spheroids are susceptible and permissive for RSV since they exhibit the characteristics of RSV infection including syncytia formation and mucin overexpression, suggesting that A549 spheroids can be used a promising model for studying RSV in vitro.

Review of seasonal influenza vaccination in the Eastern Mediterranean Region: Policies, use and barriers

Vaccination is the main control measure for influenza and its severe complications. To better understand the influenza vaccination situation in the Eastern Mediterranean Region, we conducted an extensive review of literature published between 2006 and 2016 in the region on influenza vaccine policies, use, recommendations and coverage. Forty-eight articles met the inclusion criteria. These originated from 11 of the 22 countries of the region, with most being from Saudi Arabia and Iran. The review revealed knowledge gaps and misconceptions about influenza and its vaccines even among healthcare workers. Most of the papers reviewed reported low coverage in the target populations. Limited literature on the number of countries with concrete national influenza vaccination policies was available, which may not accurately represent the situation in the Region. In conclusion, lack of awareness and knowledge are the main barriers to influenza vaccination, which remains very low in the Eastern Mediterranean Region. Countries of the region need to promote and invest in research on influenza vaccination, which is critical to inform evidence-based programmes and policies to improve vaccination rates and control influenza.

Genetic Diversity of Human Rotavirus A Among Hospitalized Children Under-5 Years in Lebanon

Human rotavirus remains a major cause of gastroenteritis worldwide despite the availability of effective vaccines. In this study, we investigated the genetic diversity of rotaviruses circulating in Lebanon. We genetically characterized the VP4 and VP7 genes encoding the outer capsid proteins of 132 rotavirus-associated gastroenteritis specimens, previously identified in hospitalized children (<5 years) from 2011 to 2013 in Lebanon. These included 43 vaccine-breakthrough specimens and the remainder were from non-vaccinated subjects. Phylogenetic analysis of VP4 and VP7 genes revealed distinct clustering compared to the vaccine strains, and several substitutions were identified in the antigenic epitopes of Lebanese specimens. No unique changes were identified in the breakthrough specimens compared to non-breakthroughs that could explain the occurrence of infection in vaccinated children. Further, we report the emergence of a rare P[8] OP354-like strain with a G9 VP7 in Lebanon, possessing high genetic variability in their VP4 compared to vaccine strains. Therefore, human rotavirus strains circulating in Lebanon and globally have accumulated numerous substitutions in their antigenic sites compared to those currently used in the licensed vaccines. The successful spread and continued genetic drift of these strains over time might undermine the effectiveness of the vaccines. The effect of such changes in the antigenic sites on vaccine efficacy remains to be assessed.

Hepatitis A Virus Genotype IB Outbreak among Internally Displaced Persons, Syria

In 2018, a hepatitis A virus outbreak was identified among internally displaced persons in Syria. Sequence analysis based on the viral protein 1/2A junction revealed that the causative virus belonged to genotype IB. A high displacement rate, deteriorated sanitary and health conditions, and poor water quality likely contributed to this outbreak.

Molecular epidemiology and genetic characterization of influenza B virus in Lebanon during 2016-2018

BACKGROUND

Influenza B viruses are a major cause of serious acute respiratory infections in humans.

METHODS

Nasopharyngeal swabs were collected from subjects with influenza-like illness during October 2016-June 2018 and screened for influenza A and B. The hemagglutinin (HA) and neuraminidase (NA) genes of the Lebanese influenza B specimens were sequenced and phylogenetically compared with the vaccine strains and specimens from the Eastern Mediterranean Region and Europe.

RESULTS

Influenza A and B viruses co-circulated between October and May and peaked between January and March. During the 2016-2017 season, A/H3N2 (33.4%) and B/Yamagata (29.7%) were the predominantly circulating viruses followed by B/Victoria and A/H1N1pdm09 viruses. During the 2017-2018 season, A/H3N2 (31.5%) and A/H1Npdm09 (29.3%) were most prevalent with co-circulation of B/Yamagata and to a lesser extent B/Victoria viruses. The B/Yamagata specimens belonged to clade-3 while the B/Victoria belonged to clade-1A. None of the analyzed specimens had a mutation known to confer resistance to NA inhibitors (NAIs).

CONCLUSION

Multiple subtypes of influenza co-circulate each year in Lebanon with a peak between January and March. The trivalent vaccine included a B/Victoria strain which mismatched the B/Yamagata lineage that predominated during the study period, highlighting the importance of quadrivalent vaccines.

Epidemiological, Molecular, and Clinical Features of Norovirus Infections among Pediatric Patients in Qatar

BACKGROUND

Norovirus (NoV) is recognized as the second most important etiological agent leading to acute gastroenteritis globally. In order to determine the burden and characteristics of NoV infections in children in Qatar, profiling of circulating genotypes and their correlation with demographics and clinical manifestations were evaluated.

METHODS

A total of 177 NoV-positive fecal samples were collected from children suffering from acute gastroenteritis (AGE) during two-year period between June 2016 and June 2018. The age of the subjects ranged between 3 months and 12 years (median of 15 months). Genotyping was performed by amplifying and sequencing parts of viral VP1 and RNA-dependent RNA polymerase (RdRp) regions. Phylogenetic analysis and evolutionary relationships were performed using MEGA7.0. Fisher's exact test was used to run statistical analysis for the clinical and demographical characteristics of circulating strains.

RESULTS

Overall, NoV infections were relatively higher in males than females with a ratio of 1.3:1 (p = 0.0073). Most of the NoV infections were reported in children between 1 and 3 years old (49.7%), followed by those <1 and >3 years of age (41.2% and 9.1%, respectively). NoV infections occurred throughout the year, with a noticeable increase in summer (36.6%) and drop in winter (25.4%). Nearly all (98.8%) NoV-infected children were positive for genogroup II (GII) compared to only two samples (1.2%) being positive for genogroup I (GI): GI.3 and GI.4. NoV genotype GII.4 (62.2%), GII.2 (15.8%), and GII.3 (13.5%) were predominant in our study. The detected strains shared >98% sequence homology with emerging recombinant strain of GII.P16-GII.4/RUS/Novosibirsk/2017 (MG892929), GII.P16-GII.4 Sydney/2012 (KY887601), GII.4 Sydney/2012, recombinant GII.P4 New Orleans /2009/GII.4 Sydney 2012 (MG585810.1), and the emerging strain GII.P16-GII.2 CHN/2017 (MH321823). Severe clinical illness (vesikari score >10) was reported in children infected with genotypes sharing homology with the above emerging strains. While GII.4 was reported in all age groups, NoV GII.3 infections were higher in children <1 year of age. Both genogroups (GII.4 and GII.3) in addition to GII.2 reported higher incidence in Qatari subjects compared to other nationalities (p = 0.034).

CONCLUSION

This is the first report about NoV molecular epidemiology in Qatar. The most detected NoV strain was genogroup GII, which is the dominant genotype in the Middle East region. Further, we report GII.4, GII.2, and GII.3 as the most predominant NoV genotypes in our study. Moreover, disease severity scores were higher among children genotyped with genogroup GI (GI.4) and genogroup GII (GII.4, GII.2, GII.3, GII.6, and GII.7).

Prevalence and characteristics of acute respiratory virus infections in pediatric cancer patients

Background

Patients with pediatric cancer have a higher risk of morbidity and mortality because of respiratory viral infections than other patient populations.

Objectives

To investigate the causative viruses of respiratory infections and their burden among patients with pediatric cancer in Lebanon.

Study design

Nasopharyngeal swabs along with clinical and demographic data were collected from patients with pediatric cancer presenting febrile episodes with upper respiratory tract symptoms. Total nucleic acid was extracted from specimens followed by the real‐time PCR analysis targeting 14 respiratory viruses to estimate the frequency of infections.

Results

We obtained 89 nasopharyngeal swabs from patients with pediatric cancer (mean age, 5.8 ± 4.2 years). Real‐time PCR confirmed viral infection in 77 swabs (86.5%). Among these, 151 respiratory viruses were detected. Several viruses cocirculated within the same period; respiratory syncytial virus (RSV) being the most common (45.45%), followed by parainfluenza virus (PIV; 26%), influenza type B (26%), human metapneumovirus (24.6%), and human coronavirus (HCoV; 24.6%). Coinfections were detected in 55% of the subjects, and most of them involved RSV with one or more other viruses. A strong correlation was found between PIV, Flu (influenza of any type), RSV, and HCoV with the incidence of coinfections. RSV was associated with lower respiratory tract infections, nasal congestion, bronchitis, and bacteremia. HCoV was associated with bronchiolitis; rhinovirus was associated with hospital admission.

Conclusion

Patients with pediatric cancer have a high burden of respiratory viral infections and a high incidence of coinfections. Molecular diagnostics can improve management of febrile episodes and reduce antibiotic use.

Respiratory viruses are leading cause of ARTI in pediatric cancer patients.

Coinfections are common among febrile pediatric cancer patients.

RSV was the most common in mono‐ and coinfections among pediatric cancer patients.

RSV, PIV, Flu, HCoV are associated with coinfections.

Molecular diagnostics permit rapid and sensitive diagnostics and limit antibiotic abuse.

Detection of ON1 and novel genotypes of human respiratory syncytial virus and emergence of palivizumab resistance in Lebanon

Respiratory syncytial virus (RSV) is a common cause of respiratory tract infections in children and immunocompromised individuals. A multi-center surveillance of the epidemiologic and molecular characteristics of RSV circulating in Lebanon was performed. The attachment (G) and fusion (F) glycoproteins were analyzed and compared to those reported regionally and globally. 16% (83/519) of the nasopharyngeal swabs collected during the 2016/17 season tested positive for RSV; 50% (27/54) were RSV-A and 50% (27/54) were RSV-B. Phylogenetic analysis of the G glycoprotein revealed predominance of the RSVA ON1 genotype, in addition to two novel Lebanese genotype variants, hereby named LBA1 and LBA2, which descended from the ON1 and NA2 RSV-A genotypes, respectively. RSV-B strains belonged to BA9 genotype except for one BA10. Deduced amino acid sequences depicted several unique substitutions, alteration of glycosylation patterns and the emergence of palivizumab resistance among the Lebanese viruses. The emergence of ON1 and other novel genotypes that are resistant to palivizumab highlights the importance of monitoring RSV globally.

Seasonal influenza vaccination policies in the Eastern Mediterranean Region: Current status and the way forward

BACKGROUND

The World Health Organization recommends annual influenza vaccination, especially in high-risk groups. Little is known about the adoption and implementation of influenza vaccination policies in the Eastern Mediterranean Region.

METHODS

A survey was distributed to country representatives at the ministries of health of the 22 countries of the Region between December 2016 and February 2017 to capture data on influenza immunization policies, recommendations, and practices in place.

RESULTS

Of the 20 countries that responded to the survey, 14 reported having influenza immunization policies during the 2015/2016 influenza season. All countries with an influenza immunization policy recommended vaccination for people with chronic medical conditions, healthcare workers and pilgrims. Two of the 20 countries did not target pregnant women. Eight countries used the northern hemisphere formulation, one used the southern hemisphere formulation and nine used both. Vaccination coverage was not monitored by all countries and for all target groups. Where reported, coverage of a number of target groups (healthcare workers, children) was generally low. Data on the burden of influenza and vaccine protection are scarce in the Region.

CONCLUSIONS

Despite widespread policy recommendations on influenza vaccination, attaining high coverage rates remains a challenge in the Eastern Mediterranean Region. Tackling disparities in influenza vaccine accessibility and strengthening surveillance systems may increase influenza vaccine introduction and use.

Effectiveness of the quadrivalent inactivated influenza vaccine in Japan during the 2015-2016 season: A test-negative case-control study comparing the results by real time PCR, virus isolation

Background

We estimated influenza vaccine effectiveness (VE) in 2015–2016 season against medically attended, laboratory-confirmed influenza, when quadrivalent inactivated vaccine (IIV4) was first introduced in Japan, using test-negative case-control design. Influenza A(H1N1)pdm09 cocirculated with B/Yamagata and B/Victoria during the study period in Japan.

Method

We based our case definition on two laboratory tests, real-time reverse transcription polymerase chain reaction (RT PCR), and virus isolation and compared VEs based on these tests. In addition, VE was evaluated by rapid diagnostic test (RDT). Nasopharyngeal swabs were collected from outpatients who visited clinics with influenza-like illness (ILIs) in Hokkaido, Niigata, Gunma and Nagasaki prefectures.

Results

Among 713 children and adults enrolled in this study, 578 were influenza positive by RT PCR including, 392 influenza A and 186 influenza B, while 135 were tested negative controls. The adjusted VE by RT PCR for all ages against any influenza was low protection of 36.0% (95% confidence interval [CI], 3.1% to 58.6%), for influenza A was 30.0% (95% CI: −10.0% to 55.5%), and influenza B was moderate 50.2% (95% CI: 13.3% to 71.4%). Adjusted VE for virus isolation for A(H1N1)pdm09 was 37.1% (95% CI: 1.7% to 59.7%), Yamagata lineage 51.3% (95% CI: 6.4% to 74.7%) and Victoria lineage 21.3% (95% CI: −50.0% to 58.9%). VE was highest and protective in 0–5 years old group against any influenza and influenza A and B/Yamagata, but the protective effect was not observed for other age groups and B/Victoria. RDT demonstrated concordant results with RT PCR and virus isolation. Sequencing of hemagglutinin gene showed that all A(H1N1)pdm09 belong to clade 6B including 31 strains (88.6%), which belong to clade 6B.1 possessing S162N mutations that may alter antigenicity and affect VE for A(H1N1)pdm09.

Conclusions

IIV4 influenza vaccine during 2015–2016 was effective against A(H1N1)pdm09 and the two lineages of type B. Younger children was more protected than older children and adults by vaccination.

Phylogeographic analysis of human influenza A and B viruses in Myanmar, 2010-2015

We investigated the circulation patterns of human influenza A and B viruses in Myanmar between 2010 and 2015 by analyzing full HA genes. Upper respiratory tract specimens were collected from patients with symptoms of influenza-like illness. A total of 2,860 respiratory samples were screened by influenza rapid diagnostic test, of which 1,577 (55.1%) and 810 (28.3%) were positive for influenza A and B, respectively. Of the 1,010 specimens that were positive for virus isolation, 370 (36.6%) were A(H1N1)pdm09, 327 (32.4%) were A(H3N2), 130 (12.9%) B(Victoria), and 183 (18.1%) were B(Yamagata) viruses. Our data showed that influenza epidemics mainly occurred during the rainy season in Myanmar. Our three study sites, Yangon, Pyinmana, and Pyin Oo Lwin had similar seasonality and circulating type and subtype of influenza in a given year. Moreover, viruses circulating in Myanmar during the study period were closely related genetically to those detected in Thailand, India, and China. Phylogeographic analysis showed that A(H1N1)pdm09 viruses in Myanmar originated from Europe and migrated to other countries via Japan. Similarly, A(H3N2) viruses in Myanmar originated from Europe, and disseminated to the various countries via Australia. In addition, Myanmar plays a key role in reseeding of influenza B viruses to Southeast Asia and East Asia as well as Europe and Africa. Thus, we concluded that influenza virus in Myanmar has a strong link to neighboring Asian countries, Europe and Oceania.

Review of seasonal influenza vaccination in the Eastern Mediterranean Region: Policies, use and barriers

Vaccination is the main control measure for influenza and its severe complications. To better understand the influenza vaccination situation in the Eastern Mediterranean Region, we conducted an extensive review of literature published between 2006 and 2016 in the region on influenza vaccine policies, use, recommendations and coverage. Forty-eight articles met the inclusion criteria. These originated from 11 of the 22 countries of the region, with most being from Saudi Arabia and Iran. The review revealed knowledge gaps and misconceptions about influenza and its vaccines even among healthcare workers. Most of the papers reviewed reported low coverage in the target populations. Limited literature on the number of countries with concrete national influenza vaccination policies was available, which may not accurately represent the situation in the Region. In conclusion, lack of awareness and knowledge are the main barriers to influenza vaccination, which remains very low in the Eastern Mediterranean Region. Countries of the region need to promote and invest in research on influenza vaccination, which is critical to inform evidence-based programmes and policies to improve vaccination rates and control influenza.

Incidence of antiviral drug resistance markers among human influenza A viruses in the Eastern Mediterranean Region, 2005-2016

BACKGROUND

Two classes of antiviral drugs are available for influenza antiviral therapy: the adamantanes and the neuraminidase inhibitors (NAIs). Due to the emergence of adamantane-resistant variants, the use of these drugs has been largely limited in the world. The NAIs became the drugs of choice for treatment of influenza A infections. However, amino acid substitutions in the NA protein might lead to reduced sensitivity to NAIs.

METHODS

The frequency and distribution of matrix protein 2 (M2) and neuraminidase (NA) variants which confer resistance to antiviral drugs was investigated in the Eastern Mediterranean Region (EMR) between 2005 and 2016. A total of 314 M2 and 1209 NA protein sequences from influenza A/H1N1, A/H1N1pdm09, A/H3N2, and A/H5N1 available in the public database were analyzed.

RESULTS

Eighty-six percent of the influenza A viruses detected in the EMR were resistant to adamantanes, among which, H3 strains exhibited the highest (95.32%) level of adamantane resistance. Approximately 98.51% (265/269) of influenza A/H1N1 and H3N2 resistant viruses had the S31N substitution in their M2 sequences. The V27A mutation was the only resistance marker found in A/H5N1 viruses and was detected at a frequency of 7.40% among the investigated viruses. Other resistant mutations L26F, A30T, G34E, and L38F were not detected in any of the variants. We found that 2.81% (n = 34) of the detected NA sequences from influenza A viruses possessed at least one NAI-resistant mutation and the vast majority of resistant viruses 79.41% (27/34) bear the H274Y mutation. The frequency of NAI-resistant viruses was 3.29% (24/729) for the H1N1pdm09, 10.64% (5/47) for the seasonal H1N1, and 4.06% (5/123) for H5N1 viruses. None of the H3N2 viruses analyzed during the study period were resistant to NAIs.

CONCLUSION

Our study reveals the emergence and spread of antiviral drug resistant influenza A viruses in the EMR and emphasizes the importance of continuous surveillance to maintain the effective use of the current antivirals.

Influenza vaccination situation in Middle-East and North Africa countries: Report of the 7th MENA Influenza Stakeholders Network (MENA-ISN)

Background

The Middle East and North Africa (MENA) region faces a dual challenge with regard to influenza infection due to severe zoonotic influenza outbreaks episodes and the circulation of Northern Hemisphere human influenza viruses among pilgrims.

Methods

The MENA Influenza Stakeholder Network (MENA-ISN) was set-up with the aim of increasing seasonal influenza vaccination coverage by (i) enhancing evidence-based exchanges, and (ii) increasing awareness on the safety and benefits of seasonal vaccination. During the 7th MENA-ISN meeting, representatives from 8 countries presented their influenza surveillance, vaccination coverage and actions achieved and provided a list of country objectives for the upcoming 3 years.

Results

MENA-ISN countries share the goal to reduce influenza related morbidity and mortality. Participants admitted that lack of knowledge about influenza, its consequences in terms of morbidity, mortality and economy are the major barrier to attaining higher influenza vaccination coverage in their countries. The cost of the vaccine is another key barrier that could contribute to low vaccination coverage. Participants drew a list of strategic interventions to bridge gaps in the knowledge of influenza burden in this region.

Conclusions

Participating countries concluded that despite an increase in vaccine uptake observed during the last few years, influenza vaccination coverage remains relatively low. Priority areas should be identified and action plans tailored to each country situation set-up to investigate the best way to move forward.

Diagnostic tools of caprine and ovine anaplasmosis: a direct comparative study

Background

The diagnosis of anaplasmosis is rather conflicting with other haemoprotozoans. Hence, the study aimed to compare and evaluate the efficiency of competitive ELISA (cELISA), indirect fluorescence antibody (IFA), and Polymerase chain reaction (PCR) for precise diagnosis of Anaplasma spp. and to assess their concordance with microscopic examination (ME).

Results

A total of 312 blood samples (189 sheep and 123 goats) were examined for Anaplasma infection during a 1 year period. Giemsa-stained blood smears were examined under the microscope. IFA and cELISA were used for the detection of Anaplasma spp. antibodies. PCR was used as a standard of truth and for the identification of Anaplasma species. Using cELISA assay, 47.4% (148) were positive (93 sheep and 55 goats) with a sensitivity and specificity of 91.9, and 86.9%, respectively. Using IFA, it was found that 57.4% (179)were positive (113 sheep and 66 goats) with a sensitivity and specificity of 100, and 93.3%, respectively. PCR assay identified A. ovis in 49 (25.3%) sheep and 30 (15.5%) goats, and A. phagocytophilumin 74 (38.1%) sheep and 41 (20.8%) goats.

Conclusions

High sensitivity and specificity values of IFA and ELISA tests compared to microscopic examination strongly support their utility in the diagnosis of Anaplasma infection. PCR was a more specific diagnostic tool that allows to discriminate between Anaplasma subspecies, which makes it the method of choice for anaplasmosis diagnosis.

Pityriasis rosea-like eruption associated with ondansetron use in pregnancy

A 30-year-old pregnant female presented with a 2-week history of pityriasis rosea-like eruption. The rash started 2 days after the patient had started taking ondansetron 8 mg for alleviation of moderate-to-severe nausea and vomiting of pregnancy. Physical examination revealed erythematous papulosquamous lesions characterized by annular scaly margins and a dusky centre over the arms, chest, abdomen, lower back and legs. The rash did not involve the palms, sole or mucous membranes, and no lesions were observed on the lymph nodes. Ondansetron was discontinued. The rash ceased to spread and started to disappear within 2 weeks with full resolution noted after 1 month. Analysis of the case using the Naranjo adverse drug reaction probability scale indicated that ondansetron was the probable cause of the pityriasis rosea-like eruption. This is the first case report of pityriasis rosea related to ondansetron therapy.

Neuraminidase inhibitor susceptibility and evolutionary analysis of human influenza B isolates from three Asian countries during 2012-2015

Influenza B viruses of both the Yamagata and the Victoria lineages are implicated in a large proportion of the morbidity and mortality associated with influenza outbreaks. In this study, we characterized the full genomes of 53 influenza B viruses isolated during 2012-2015 in three Asian countries: Japan, Myanmar, and Vietnam. Analysis of the hemagglutinin (HA) genes revealed co-circulation of both the Yamagata and Victoria lineages within the same season in these countries. Our analysis revealed, that a large proportion of viruses circulating during 2013-2014 in Japan and Vietnam were mismatched to the vaccine supporting the rationale for using quadrivalent vaccines. Molecular analysis of the neuraminidase (NA) genes did not reveal any of the previously reported substitutions associated with reduced susceptibility to neuraminidase inhibitors (NAIs). However, one isolate from Nagasaki displayed reduced inhibition by NAIs, associated with an NA-M426I substitution (N2-numbering). Phylogenetic analysis of the eight genome segments identified a 6 + 2 reassortant strain belonging to the Victoria lineage that circulated in Japan during the 2013-2014 season. This strain appears to have evolved from a descendent of a B/Brisbane/60/2008-like strain in an intra-lineage reassortment event involving the nucleoprotein (NP) and nonstructural (NS) genes. Therefore, influenza B strains circulating worldwide continue to evolve via complex reassortment events, which contribute to their survival and the emergence of new strains. These findings highlight the need for ongoing genome-wide studies of circulating viruses and assessing the implications of these evolutionary events on the vaccines.

Molecular epidemiology of human respiratory syncytial virus among children in Japan during three seasons and hospitalization risk of genotype ON1

We investigated the genetic diversity, the circulation patterns, and risk for hospital admission of human respiratory syncytial virus (HRSV) strains in Japan between 2012 through 2015. During the study period, 744 HRSV-positive cases were identified by rapid diagnostic test. Of these, 572 samples were positive by real-time PCR; 400 (69.9%) were HRSV-A, and 172 (30.1%) were HRSV-B. HRSV-A and -B alternated as the dominant strain in the subsequent seasons. Phylogenetic tree analysis of the second hyper-variable region of the G protein classified the HRSV-A specimens into NA1 (n = 242) and ON1 (n = 114) genotypes and the HRSV-B specimens into BA9 (n = 60), and BA10 (n = 27). The ON1 genotype, containing a 72-nucleotide duplication in the G protein’s second hyper-variable region, was first detected in the 2012–2013 season but it predominated and replaced the older NA1 HRSV-A in the 2014–2015 season, which also coincided with a record number of HRSV cases reported to the National Infectious Disease Surveillance in Japan. The risk of hospitalization was 6.9 times higher for the ON1 genotype compared to NA1. In conclusion, our data showed that the emergence and predominance of the relatively new ON1 genotype in Japan was associated with a record high number of cases and increased risk for hospitalization.

Investigation of viral and bacterial enteropathogens of diarrheic sheep and goats in Medina, Saudi Arabia

Diarrhea is a serious problem in sheep and goat farming, causing great economic losses. Most viral and bacterial enteropathogens of diarrheic sheep and goats are considered foodborne pathogens with a potential to be zoonotic. The present study investigated the prevalence of some viral and bacterial enteropathogens in diarrheic sheep and goats between October 2015and February 2016 in Medina, Saudi Arabia. A total of 310 fecal samples were collected from diarrheic sheep (n=193) and goats (n=117). The samples were screened for the presence of rotavirus and bovine coronavirus (BCoV) using Sandwich (ELISA) technique. The bacterial enteropathogens were isolated and identified biochemically and the virulence factors of Escherichia coli were determined by using PCR. Escherichia coli was the most prevalent agent in both sheep and goats (34.7% and 30.7%, respectively). According to the expressed virulence genes, Enterotoxigenic Escherichia coli (ETEC) was detect in 34.3% of sheep isolates and 30.6% of goats isolates. Salmonella species was isolated from 3.6% of sheep and 2.6% of goats. Klebsiella species was isolated from 1.6% of sheep but not from goats. Regarding viral agents, rotavirus was found in 31.6% of sheep and 27.4% of goats, while BCoV was detected in 19.6% of the sheep and 16.2% of the goats. The prevalence of bacterial and viral enteropathogens was significantly higher in the 0-12 months age group compared to the older age groups. Double infection was the most common (53.0%) infection pattern compared to single (37.5%) and triple (9.5%) infections. Rotavirus infection was significantly associated with ETEC infection. In conclusion, we report high prevalence of rotavirus and ETEC in sheep and goats, which are of veterinary and public health importance. This study provides valuable data on the prevalence of viral and bacterial enteropathogens in sheep and goats in Medina, Saudi Arabia that will be useful to develop control measures for these pathogens.