Analysis of pathogen detection results of upper respiratory tract specimens from fever clinic patients

Objective: To explore the pathogen composition and distribution characteristics of pathogens in respiratory samples from patients with fever of unknown origin. Methods: A total of 96 respiratory samples of patients with unknown cause fever with respiratory symptoms were collected from four hospitals above grade II in Shijiazhuang area (Hebei Provincial Hospital of Traditional Chinese Medicine, Luancheng District People's Hospital, Luquan District People's Hospital, Shenze County Hospital) from January to April 2020, and multiplex-fluorescent polymerase chain reaction(PCR)was used to detect influenza A virus, influenza B virus, enterovirus, parainfluenza virus I/II/III/IV, respiratory adenovirus, human metapneumovirus, respiratory syncytial virus, human rhinovirus, human bocavirus, COVID-19, Mycoplasma pneumoniae, Chlamydia pneumoniae, Legionella pneumophila, Pseudomonas aeruginosa, Streptococcus pneumoniae, Klebsiella pneumoniae, Group A streptococcus, Haemophilus influenzae, Staphylococcus aureus nucleic acid detection, the results were analyzed for chi-square. Results: A total of 8 pathogens were detected in the upper respiratory tract samples of 96 fever patients, including 1 kind of virus, 6 kinds of bacterias, and Mycoplasma pneumoniae. There were 12 viruses including influenza virus and parainfluenza virus, Legionella pneumophila and Chlamydia pneumoniae were not detected. The pathogen detection rates in descending order were Streptococcus pneumoniae (58/96, 60.42%), Haemophilus influenzae(38/96, 39.58%), Klebsiella pneumoniae (14/96, 14.58%), Staphylococcus aureus (10/96, 10.42%), Mycoplasma pneumoniae (8/96, 8.33%), Pseudomonas aeruginosa (6/96, 6.25%), Group A streptococcus (4/96, 4.17%) and human rhinovirus (2/96, 2.08%). The proportions of single-pathogen infection and multi-pathogen mixed infection in fever clinic patients were similar, 41.67% (40/96) and 45.83% (44/96), respectively, and 12.50% (12/96)of the cases had no pathogens detected. The infection rate of Mycoplasma pneumoniae in female patients with fever (21.43%) was higher than that in male patients with fever (2.94%) (P < 0.05). There was no statistical difference between the distribution of of other pathogens and gender and age(P > 0.05). Conclusions: The upper respiratory tract pathogens were mainly bacterial infections, and occasional human rhinovirus and Mycoplasma pneumonia infections. In clinical diagnosis and treatment, comprehensive consideration should be given to the pathogen detection.

Burden of respiratory coinfections in haematology patients with COVID-19

Introduction: Following the lifting of generalised restrictions and universal masking, severe acute respiratory syndrome coronavirus 2 (SARS-CoV- 2)- infected patients, especially the clinically extremely vulnerable (CEV) haematology patients, are at an increased risk for other respiratory viral coinfections;therefore, physicians need to be cognizant about excluding other treatable respiratory pathogens. Here, we report coinfection with SARS-CoV- 2 and other respiratory pathogens in patients with haematological cancers presenting to a large tertiary care hospital. Method(s): From July 2022-December 2022, patients with haematological disorders were screened for SARS-CoV- 2 and other 10 common respiratory pathogens by PCR. We performed a retrospective analysis of patients with concurrent respiratory viruses and will prospectively evaluate the same from Jan 2023 to March 2023. Result(s): During this period a total of 322 inpatients had routine screening and additional 6213 swabs were done in the outpatient/ambulatory setting, of which 294 were positive in 221 patients. We excluded all patients who had a single positive PCR swab result and specifically analysed only patients with coinfections. We identified 30 patients (14%) who had respiratory coinfections with 73 viral infections/reactivations over 6 months period, which represented 25% of all positive swabs: 25 inpatients (19 symptomatic/6 asymptomatic) and 48 in outpatients (32 symptomatic/16 asymptomatic). The median age of the cohort was 47.3 years (21-77). Patients were post allograft (n = 15), autograft (n = 7), post CART (n = 5) and postchemotherapy (n = 4). Of the 30 cases, 13 patients had concurrent infections: 5 SARS-CoV2, 10 Respiratory syncytial virus (RSV), 7 Rhino and 4 Influenza A, with all patients having dual viral infection. The remaining 17 patients had multiple viral infections but separated by a median of 54 days (range 27-137 days): 16 SARS-CoV2, 5 RSV, 6 Rhino, 2 Parainfluenza, 2 Adeno and one each of Influenza A, Influenza B, and metapneumovirus. Of the treatable infections (n = 46), 22% were detected on routine asymptomatic swabbing, with 50% of SARS-CoV2 detected on routine swabs. All 8 patients with Influenza were treated with oseltamivir, of 16 RSV cases one was treated with oral ribavirin and of the 22 SARS-CoV2 patients, 5 were treated (4 Paxlovid and 1 Remdesivir). No patients needed intensive care support and no deaths were reported. Conclusion(s): The burden of respiratory coinfections in CEV cohort has a significant impact on respiratory isolation and management, including appropriate & timely initiation of therapy for treatable viral infections. Although mortality was not increased secondary to respiratory coinfections and none needed intensive care, larger prospective cohorts are needed to assess the exact impact.

An outbreak of school influenza complicated with Mycoplasma pneumoniae infection

Objective: To describe the clinical features, causal agent and transmission mode of a fever outbreak in a school in Shanghai. Methods: Field epidemiological approaches including case definition development, searching for contacts, distribution of diseases description, environmental sampling and laboratory testing. Results: A total of 16 influenza-like cases were included, all concentrated in the one class of grade two, including 15 students and 1 teacher. Among student cases, the incidence rate was 36.59%(15/41), the average age was 7.4 years, the incidence rate was 36.84%(7/19) for boys, 36.36%(8/22) for girls. The clinical course was 5-15 days, with the median of 9 days, and 18.75%(3/16) of the cases stayed studying while sick. The nasopharyngeal swab specimens in 16 cases all tested positive for influenza B, of which 11 tested positive for mycoplasma pneumoniae and 1 case also tested positive for coronavirus OC43. Body temperature, number of mononuclear cells, and treatment time of patients infected with Influenza B and mycoplasma pneumoniae were higher than those of patients infected with influenza B alone(P < 0.05). The outbreak lasted for 12 days, all sick students were treated and discharged from hospital, with no severe cases or death, and the outbreak was effectively controlled. Conclusion: This campus cluster outbreak caused by influenza B and mycoplasma pneumoniae. Patients with influenza B with mycoplasma pneumoniae have severe symptoms and a long course of illness, suggesting the importance of early management of the epidemic.

Impact of Influenza in South-East Asia

Influenza infection is asymptomatic in up to 75% of cases, but outbreaks result in significant morbidity. Reports found that severe influenza complications tend to occur among the very young (<5 years) and very old (>65 years), especially those with underlying co-morbidities like diabetes mellitus and heart disease. Even with no co-morbidity, some older persons with severe influenza may require hospitalisation or intensive care, with increased risk of myocardial infarction and stroke. In South-East Asia, influenza was often seen as a mild problem and was not deemed notifiable until the appearance of the Influenza A(H1N1) pandemic in 2009. For decades the data made available were based on extrapolated estimates collected mainly from paediatric populations, resulting in inconsistent findings. Following expanded surveillance across the region using national surveillance systems for influenza-like illness (ILI) and severe acute respiratory illness (SARI), and better diagnostic methods, improved estimates of disease burden was achieved in South-East Asia. However, two studies conducted in 2008-2010 reported findings ranging from 2-3% to 11%. With regards to increased risk of complications, the estimated global annual attack rates for influenza were 5-10% in adults and 20-30% in children, resulting in 3-5 million cases of severe illness and 290,000-650,000 deaths. A study In Singapore reported that influenza is associated with annual excess mortality rates (EMR) of 11-14.8 per 100 000 person-years, especially affecting the elderly;these rates are comparable to that of the USA. As for hospitalisation rates of children under 5 years with seasonal influenza, the USA estimated a rate of 1.4 per 100,000. Comparable rates were reported in Singapore (0.7-0.9), Thailand (2.4), Viet Nam (3.9-4.7), and the Philippines (4.7). In 2018, an updated study reported a mean annual influenza-associated respiratory EMR of 4.0-8.8 per 100 000 individuals, with South-East Asia showing a high mortality rate of 3.5-9.2 per 100,000 individuals. It was already estimated in Thailand in 2004 that influenza resulted in USD23-63 million in economic costs, with the main contribution from lost productivity due to missed workdays. Thus, comparable to countries in temperate climate, the clinical and socioeconomic impact of influenza in South-East Asia appear to be just as substantial. With the emergence of the COVID-19 pandemic in 2020, global influenza incidence dropped dramatically. In South-East Asia, the trend in influenza detections was similar to the rest of the world, with numbers slightly higher than average in early 2020, followed by a quick drop-off by the end of April 2020. After April 2020, the detection rate remained low until late July 2020, when Influenza A(H3N2) predominated in Cambodia, Malaysia, the Philippines, Singapore, Thailand and Timor-Leste;influenza B in Lao People's Democratic Republic but with an upsurge in A(H3N2) activity. Following a two-year hiatus, influenza outbreaks began to re-emerge significantly since early 2022. From February through August 2022, influenza activity in the southern hemisphere remained lower than in pre-COVID-19 pandemic years, but was at the highest level compared to similar periods since the start of the COVID-19 pandemic. Reasons for the reduction during the COVID-19 pandemic include non-pharmaceutical interventions (NPIs), reduced population mixing and reduced travel, and possibly viral interference between SARS-CoV-2 and influenza virus in the same host. In general, the reduction in influenza detections however does not appear to be associated with lack of testing. The World Health Organisation (WHO) continues to recommend that vaccination is the most effective way to prevent infection and severe outcomes caused by influenza viruses. Although influenza vaccine is not commonly used in most countries in South-East Asia, its burden is similar in other parts of the world where influenza vaccine is now routinely used. Currently, the countries in South-East Asia that are providing free influenza vacc na ion for those at high risk include Thailand, Singapore, the Philippines and Lao People's Democratic Republic.Copyright © 2023

Exposure of wild Caspian seals (Pusa caspica) to parasites, bacterial and viral pathogens, evaluated via molecular and serological assays

Disease surveillance of marine mammal populations is essential to understand the causes of strandings, identify potential threats to animal health, and to support development of conservation strategies. Here we report the first large multi-pathogen screening of prevalence for viruses, bacteria and parasites in a sample of 177 live, healthy, wild Caspian seals (Pusa caspica), captured and released during satellite telemetry studies 2007-2017. Employing molecular and serological assays we assess prevalence of pathogens known to be of significance for marine mammal health worldwide, and evaluate the results in relation to Caspian seal health and conservation. RT-PCR, and PCR assays find evidence for infection by Canine Distemper Virus (CDV), Phocine herpes virus, phocine adenovirus and Influenza A at prevalences of 5%, 6.4%, 21.7%, and 4% respectively. The genomes of CDV isolates collected in 2008 showed 99.59% identity with the 2000 Caspian seal CDV epizootic strain. A partial coding sequence for the Us2 gene from the Caspian seal herpes virus was identical to PhHV-1 isolate PB84, previously reported from a harbor seal (Phoca vitulina), while amplicon sequences for the adenovirus polymerase gene indicated a novel strain. ELISA assays detected exposure to Influenza A (55% of tested samples), adenovirus (25%), coronavirus (6%), CDV (8%), herpes virus (94%), Toxoplasma gondii (2.6%) and heartworm (1%). Hemagglutination inhibition (HI) tests detected exposure to Influenza B at a prevalence of 20%, and Leptospira microscopic agglutination tests detected suspected exposure to Leptospira serovars in 9% of tested samples. Overall, the risks, profile and prevalence of pathogens in Caspian seals appear comparable to other wild phocid seal populations. Our results suggest Caspian seals have exposure pathways to pathogens with epizootic potential or ability to cause significant morbidity, and that disease impacts could reduce the resilience of the population to other conservation threats. Caspian seals are listed as Endangered by the International Union for Conservation of Nature (IUCN), and we recommend that resources are invested to support further surveillance programs and to understand how anthropogenic pressures may influence future disease risks. A translated version of this is available in Russian and Kazakh in the Supplementary Material (Presentation 1 and Presentation 2)

Etiological structure of acute respiratory viral infections in children hospitalized in 2015-2018

Acute respiratory viral infections (ARVI) play an important role in morbidity formation among children. At the same time, studies about the ARVI etiological structure are not enough. The article presents the results of structure analyses of ARVI in children with severe and moderate degrees of disease hospitalized in the children's clinical hospital of Novosibirsk for the period 2015-2018. This research aimed to analyze the morbidity of acute respiratory viral infections with the estimation of a causal virus in children admitted to the hospital for the period 2015-2018. Material and methods. In this study, 1137 children aged between 0 and 15 years were examined. In order to determine the etiological factor in children with damage of the upper or lower respiratory tract, by using the method of RT-PCR (AmpliSensARVI-screen-FL test systems (InterLabService, Russia), mucus from the nose and throat was examined for the presence of genetic material of viruses that cause ARVI (influenza A and B viruses, parainfluenza viruses of types 1-4, respiratory syncytial virus, metapneumovirus, four types of human coronavirus, rhinovirus, adenovirus, and bocavirus). Results. The research found that the most frequently detected pathogens are respiratory syncytial virus (23.52%), influenza A and B viruses (19.73%) and rhinovirus (19.21%). Observe the dynamics some fluctuations in the detection of mentioned viral agents and increasing of mixed infections were detected. In addition, the importance of respiratory and gastrointestinal tract combined lesions, particularly for infants and preschool - age children has been noted. Conclusion. The distribution of respiratory viruses in children with severe ARVI who required hospitalization was assessed. It was shown the significance of the respiratory syncytial infection virus, influenza virus and rhinovirus in the etiological structure of hospitalized children of different ages that damage not only the respiratory tract, but also to the gastrointestinal tract. This is an important factor in optimizing the diagnosis, treatment and prevention of viral infections in children.Copyright © Infectious Diseases: News, Opinions, Training 2021.

Establishment of multi-target rapid detection method of upper repiratory susceptible viruses based on digital microfluidic technology

Objective: Provide a digital microfluidic RT-qPCR chip for rapid detection of several upper respiratory diseases. Methods: Several specific primer-probe sets were designed according to the conserved sequences of 2019 novel corona virus(2019-n COV), influenza A virus(Flu A), influenza B virus(Flu B), severe acute respiratory syndrome corona virus(SARS-Co V), Middle East respiratory syndrome corona virus(MERS-Co V), and then packaged into a digital microfluidic chip which allowed simultaneous detection of five upper respiratory tract pathogens with the help of reverse transcription quantitative PCR(RT-q PCR)technology. In the meanwhile, the detection limit, specificity and sensitivity of this digital microfluidic chip were evaluated base on the clinical specimens, plasmids and unrelated pathogens. Results: The established digital microfluidic RT-q PCR chip for 2019-n COV, Flu A, Flu B,SARS-Co V,MERS-Co V had a detection limit of 12 copies/reaction, while the detection limit of the RT-q PCR method without digital microfluidics was 15 copy/reaction;the detection limit of the two methods was basically the same. For nucleic acid samples extracted from clinical samples, the detection results of digital microfluidic RT-q PCR chips were all negative without non-specific amplification. At the same time, the RT-qPCR method and the digital microfluidic RT-qPCR chip method were used to carry out clinical comparative tests of 5 items in 20 clinical samples, total 100 tests. The results showed that the sensitivity of the digital microfluidic RT-q PCR chip reached 94%, the specificity was 100%. SPSS was used to analyze the consistency of the two methods, and the results showed that the two methods had a high degree of consistency(Kappa=0.962, P<0.05). Conclusion: Based on digital microfluidic RT-q PCR chip technology,a multi-target rapid detection method of upper respiratory tract susceptible virus was established, which could provide a new detection method for early clinical identification of respiratory pathogens.

Circulation of respiratory viruses during the COVID-19 pandemic in The Gambia

Background: In many countries, non-pharmaceutical interventions to limit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission resulted in significant reductions in other respiratory viruses. However, similar data from Africa are limited. We explored the extent to which viruses such as influenza and rhinovirus co-circulated with SARS-CoV-2 in The Gambia during the COVID-19 pandemic. Methods: Between April 2020 and March 2022, respiratory viruses were detected using RT-PCR in nasopharyngeal swabs from 1397 participants with influenza-like illness. An assay to detect SARS-CoV-2 and a viral multiplex RT-PCR assay was used as previously described to detect influenza A and B, respiratory syncytial virus (RSV) A and B, parainfluenza viruses 1-4, human metapneumovirus (HMPV), adenovirus, seasonal coronaviruses (229E, OC43, NL63) and human rhinovirus. Result(s): Overall virus positivity was 44.2%, with prevalence higher in children <5 years (80%) compared to children aged 5-17 years (53.1%), adults aged 18-50 (39.5%) and >50 years (39.9%), p<0.0001. After SARS-CoV-2 (18.3%), rhinoviruses (10.5%) and influenza viruses (5.5%) were the most prevalent. SARS-CoV-2 positivity was lower in children <5 (4.3%) and 5-17 years (12.7%) than in adults aged 18-50 (19.3%) and >50 years (24.3%), p<0.0001. In contrast, rhinoviruses were most prevalent in children <5 years (28.7%), followed by children aged 5-17 (15.8%), adults aged 18-50 (8.3%) and >50 years (6.3%), p<0.0001. Four SARS-CoV-2 waves occurred, with 36.1%-52.4% SARS-CoV-2 positivity during peak months. Influenza infections were observed in both 2020 and 2021 during the rainy season as expected (peak positivity 16.4%-23.5%). Peaks of rhinovirus were asynchronous to the months when SARS-CoV-2 and influenza peaked. Conclusion(s): Our data show that many respiratory viruses continued to circulate during the COVID-19 pandemic in The Gambia, including human rhinoviruses, despite the presence of NPIs during the early stages of the pandemic, and influenza peaks during expected months.Copyright: © 2023 Jarju S et al.

Advances in molecular diagnostic tests for community-acquired pneumonia

The use of a timely and appropriate antibiotic therapy, which requires early and accurate microorganisms' detection in pneumonia. Currently, the identification of microorganisms in pneumonia is limited by the low sensitivity and long response time of standard culture-based diagnostic tools. For this reason, treatment in pneumonia is empirical. An inadequate empirical treatment is related to poor outcomes in patients with pneumonia. The microbiological diagnosis is key to improve the outcomes in patient with pneumonia. Over the past years there was a significant advance in the molecular diagnosis of infectious diseases including pneumonia. Also the impact of the COVID-19 pandemic has impacted the development and application of these new molecular techniques. This review summarizes the advances in molecular diagnosis of community-acquired pneumonia.Copyright © 2022 EDIZIONI MINERVA MEDICA.

Influenza A and influenza B antibody determination in an Austrian cohort

Influenza is an infectious respiratory disease caused by influenza A and B, which is a virus characterized by a high mutation rate with new strains appearing regularly, making regular booster vaccinations necessary. In this study, we evaluated the immune status of Influenza A and B by using ELISA. A questionnaire was utilized to appraise the immunization anamnesis and the stance on vaccination. In total, 202 probands participated in this study. 35.6% of the probands were vaccinated, 10.9% indicated a confirmed influenza infection. 88.1% had a positive influenza A titer, whereas a positive influenza B titer was determined in only 38.6%. Additionally, a correlation between vaccination and titer could be observed. In this study, we were able to show a higher vaccination rate in our cohort than the Austrian average. Additionally, a higher percentage showed a positive influenza A titer compared to influenza B titer.Copyright © 2022

Comparative Clinical Evaluation of a Novel FluA/FluB/SARS-CoV-2 Multiplex LAMP and Commercial FluA/FluB/SARS-CoV-2/RSV RT-qPCR Assays.

Influenza and coronaviruses cause highly contagious respiratory diseases that cause millions of deaths worldwide. Public health measures implemented during the current coronavirus disease (COVID-19) pandemic have gradually reduced influenza circulation worldwide. As COVID-19 measures have relaxed, it is necessary to monitor and control seasonal influenza during this COVID-19 pandemic. In particular, the development of rapid and accurate diagnostic methods for influenza and COVID-19 is of paramount importance because both diseases have significant public health and economic impacts. To address this, we developed a multi-loop-mediated isothermal amplification (LAMP) kit capable of simultaneously detecting influenza A/B and SARS-CoV-2. The kit was optimized by testing various ratios of primer sets for influenza A/B (FluA/FluB) and SARS-CoV-2 and internal control (IC). The FluA/FluB/SARS-CoV-2 multiplex LAMP assay showed 100% specificity for uninfected clinical samples and sensitivities of 90.6%, 86.89%, and 98.96% for LAMP kits against influenza A, influenza B, and SARS-CoV-2 clinical samples, respectively. Finally, the attribute agreement analysis for clinical tests indicated substantial agreement between the multiplex FluA/FluB/SARS-CoV-2/IC LAMP and commercial AllplexTM SARS-CoV-2/FluA/FluB/RSV assays.

Fu-Zheng-Xuan-Fei formula promotes macrophage polarization and Th17/Treg cell homeostasis against the influenza B virus (Victoria strain) infection.

ETHNOPHARMACOLOGICAL RELEVANCE: Fu-Zheng-Xuan-Fei formula (FF) is a prescription that has been clinically used through the basic theory of traditional Chinese medicine (TCM) for treating viral pneumonia. Although FF possesses a prominent clinical therapeutic effect, seldom pharmacological studies have been reported on its anti-influenza B virus (IBV) activity. AIM OF THE STUDY: Influenza is an acute infectious respiratory disease caused by the influenza virus, which has high annual morbidity and mortality worldwide. With a global decline in the COVID-19 control, the infection rate of influenza virus is gradually increasing. Therefore, it is of great importance to develop novel drugs for the effective treatment of influenza virus. Apart from conventional antiviral drugs, TCM has been widely used in the clinical treatment of influenza in China. Therefore, studying the antiviral mechanism of TCM can facilitate the scientific development of TCM. MATERIALS AND METHODS: Madin-Darby canine kidney cells (MDCK) and BALB/c mice were infected with IBV, and FF was added to evaluate the anti-IBV effects of FF both in vitro and in vivo by Western blotting, immunofluorescence, flow cytometry, and pathological assessment. RESULTS: It was found that FF exhibited anti-viral activity against IBV infection both in vivo and in vitro, while inducing macrophage activation and promoting M1 macrophage polarization. In addition, FF effectively regulated the signal transducer and activator of transcription (STAT) signaling pathway-mediated Th17/Treg balance to improve the lung tissue damage caused by IBV infection-induced inflammation. The findings provided the scientific basis for the antiviral mechanism of FF against IBV infection. CONCLUSIONS: This study shows that FF is a potentially effective antiviral drug against IBV infection.

RSV circulation during SARS-CoV-2 pandemic era: what happened in Italy

Background: In the northern hemisphere, Respiratory Syncytial Virus (RSV) is more frequently detected from December to February. In Italy, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) presented a peak in incidence from the end of December 2021 to February 2022. Aim(s): To evaluate how SARS-CoV-2 pandemic has influenced RSV circulation. Method(s): We evaluated 389 children, aged 0-18 years, admitted for respiratory tract infections from September 2021 to January 2022 throughout Italy, from the north to the south. Children underwent nasal washing from 1 to 3 days after hospitalization. A (RT)-PCR was developed for detecting 15 respiratory viruses, including RSV, influenza virus A and B, human coronavirus OC43, 229E, NL-63 and HUK1, adenovirus, rhinovirus, parainfluenza virus 1-3, human bocavirus and human metapneumovirus. Result(s): We detected a virus in 338 children (86.9%): RSV was found in 267 (68.7%), other viruses in 71 (18.3%). 51 children (13.1%) resulted negative. Dividing our observational period in two-week timeframes, we found that RSV showed an early peak from October to the first half of December 2021 compared to its usual seasonality. In a previous study, we have demonstrated that RSV circulation was incredibly low from September 2020 to January 2021, in contrast with what we found in the same period in 2021-2022. Comparing RSV and SARS-CoV-2 incidences, we found that these two viruses spread in opposite ways: when SARS-CoV-2 present an incidence peak, RSV circulation reduced and viceversa. Conclusion(s): The relationship between RSV and SARS-CoV-2 showed that viral interference plays a crucial role in their epidemiology.

The Circulation of Common Respiratory Viruses and Their Co-infection with Severe Acute Respiratory Syndrome Coronavirus 2 Before and After Coronavirus Disease of 2019 Vaccination

Background: Respiratory viruses play important roles in respiratory tract infections;they are the major cause of diseases such as the common cold, bronchiolitis, pneumonia, etc., in humans that circulate more often in the cold seasons. During the COVID-19 pandemic, many strict public health measures, such as hand hygiene, the use of face masks, social distancing, and quarantines, were implemented worldwide to control the pandemic. Besides controlling the COVID-19 pandemic, these introduced measures might change the spread of other common respiratory viruses. Moreover, with COVID-19 vaccination and reducing public health protocols, the circulation of other respiratory viruses probably increases in the community. Objective(s): This study aims to explore changes in the circulation pattern of common respiratory viruses during the COVID-19 pan-demic. Method(s): In the present study, we evaluated the circulation of seven common respiratory viruses (influenza viruses A and B, rhi-novirus, and seasonal human Coronaviruses (229E, NL63, OC43, and HKU1) and their co-infection with SARS-CoV-2 in suspected cases of COVID-19 in two time periods before and after COVID-19 vaccination. Clinical nasopharyngeal swabs of 400 suspected cases of COVID-19 were tested for SARS-CoV-2 and seven common respiratory viruses by reverse transcription real-time polymerase chain reaction. Result(s): Our results showed common respiratory viruses were detected only in 10% and 8% of SARS-CoV-2-positive samples before and after vaccination, respectively, in which there were not any significant differences between them (P-value = 0.14). Moreover, common viral respiratory infections were found only in 12% and 32% of SARS-CoV-2-negative specimens before and after vaccination, respectively, in which there was a significant difference between them (P-value = 0.041). Conclusion(s): Our data showed a low rate of co-infection of other respiratory viruses with SARS-CoV-2 at both durations, before and after COVID-19 vaccination. Moreover, the circulation of common respiratory viruses before the COVID-19 vaccination was lower, probably due to non-pharmaceutical interventions (NPI), while virus activity (especially influenza virus A) was significantly in-creased after COVID-19 vaccination with reducing strict public health measures.Copyright © 2023, Author(s).

Circulation of respiratory viruses during the COVID-19 pandemic in The Gambia

Background: In many countries, non-pharmaceutical interventions to limit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission resulted in significant reductions in other respiratory viruses. However, similar data from Africa are limited. We explored the extent to which viruses such as influenza and rhinovirus co-circulated with SARS-CoV-2 in The Gambia during the COVID-19 pandemic. Method(s): Between April 2020 and March 2022, respiratory viruses were detected using RT-PCR in nasopharyngeal swabs from 1397 participants with influenza-like illness. An assay to detect SARS-CoV-2 and a viral multiplex RT-PCR assay was used as previously described to detect influenza A and B, respiratory syncytial virus (RSV) A and B, parainfluenza viruses 1-4, human metapneumovirus (HMPV), adenovirus, seasonal coronaviruses (229E, OC43, NL63) and human rhinovirus. Result(s): Overall virus positivity was 44.2%, with prevalence higher in children <5 years (80%) compared to children aged 5-17 years (53.1%), adults aged 18-50 (39.5%) and >50 years (39.9%), p<0.0001. After SARS-CoV-2 (18.3%), rhinoviruses (10.5%) and influenza viruses (5.5%) were the most prevalent. SARS-CoV-2 positivity was lower in children <5 (4.3%) and 5-17 years (12.7%) than in adults aged 18-50 (19.3%) and >50 years (24.3%), p<0.0001. In contrast, rhinoviruses were most prevalent in children <5 years (28.7%), followed by children aged 5-17 (15.8%), adults aged 18-50 (8.3%) and >50 years (6.3%), p<0.0001. Four SARS-CoV-2 waves occurred, with 36.1%-52.4% SARS-CoV-2 positivity during peak months. Influenza infections were observed in both 2020 and 2021 during the rainy season as expected (peak positivity 16.4%-23.5%). Peaks of rhinovirus were asynchronous to the months when SARS-CoV-2 and influenza peaked. Conclusion(s): Our data show that many respiratory viruses continued to circulate during the COVID-19 pandemic in The Gambia, including human rhinoviruses, despite the presence of NPIs during the early stages of the pandemic, and influenza peaks during expected months.Copyright © 2022 Jarju S et al.

Analysis of drug resistance gene in Mycoplasma pneumoniae and 13 pathogens in bronchoalveolar lavage fluid of children with Mycoplasma pneumoniae pneumonia. TT -.

Objective To investigate drug resistance gene in Mycoplasma pneumoniae (MP) and the distribution of 13 respiratory pathogens in bronchoalveolar lavage fluid(BALF) of children with Mycoplasma pneumoniae pneumonia(MPP). Methods A total of 100 BALF of children with MPP in Peking University Third Hospital and Peking University First Hospital from January 2018 to January 2019 were collected. Fluorogenic quantitative PCR was used to detect nucleic acid and it's drug resistance gene of MP and multiple PCR method was adopted to detect influenza A virus, influenza A virus - H1 N1, influenza A virus - H3 N2, influenza B, human parainfluenza virus, adenovirus, human bocavirus, human rhino virus, Chlamydia pneumoniae, human metapneumovirus, MP, human corona virus, and respiratory syncytial virus gene, and the results were compared by using Chi square test. Results In 100 BALF samples, MP and drug resistance gene were detected by fluorogenic quantitative PCR. Totally, 83 cases (83. 00%) were MP positive and 78 cases (93. 98%) were drug resistant. All of them had the point mutations A2063G in V region of 23S rRNA domain. A total of 13 kinds of respiratory pathogens were detected by multiplex PCR method, and 89 cases (89. 00%) were positive. Totally, 79 cases (79. 00%) were MP positive, of which 74 cases (74. 00%) detected only MP, and 5 cases (5. 00%) detected MP combined with other pathogens. Other pathogens were detected in 10 cases (10. 00%). The virus detection rate of 0-4 years old group was higher than that of > 4-6 years old group (P - 0. 042) and > 6 years old group (P =0. 002), and the differences were statistically significant. Conclusions MP can be detected in most BALF samples of MPP children, the drug resistance phenomenon is serious, and the main point mutation is A2063G. There were other respiratory pathogens and 2 or 3 pathogens were detected in a small number of BALF samples.Copyright © 2022 Authors. All rights reserved.

Comparison of Immunogenicity and Safety of Diphtheria-Tetanus-Pertussis-Hepatitis B-Haemophilus influenza B (Bio Farma) with Pentabio® Vaccine Primed with Recombinant Hepatitis B at Birth (Using Different Source of Hepatitis B) in Indonesian Infants.

Satisfying the needs of the national immunization program requires maintaining diphtheria-tetanus-pertussis (DTP)-hepatitis B (HB)-Haemophilus influenza B (Hib) production. Therefore, new hepatitis B sources are needed. This study aimed to evaluate the immunogenicity of the DTP-HB-Hib vaccine (Bio Farma) that used a different source of hepatitis B. A prospective randomized, double-blind, bridging study was conducted. Subjects were divided into two groups with different batch numbers. Healthy infants 6-11 weeks of age at enrollment were immunized with three doses of the DTP-HB-Hib vaccine after a birth dose of hepatitis B vaccine. Blood samples were obtained prior to vaccination and 28 days after the third dose. Adverse events were recorded until 28 days after each dose. Of the 220 subjects, 205 (93.2%) completed the study protocol. The proportion of infants with anti-diphtheria and anti-tetanus titers ≥ 0.01 IU/mL was 100%, with anti-HBsAg titers ≥ 10 mIU/mL was 100%, and with Polyribosylribitol Phosphate-Tetanus Conjugate (PRP-TT) titers > 0.15 µg/mL was 96.1%. The pertussis response rate was 84.9%. No serious adverse events related to the study vaccine occurred. The three-dose DTP-HB-Hib vaccine (Bio Farma) is immunogenic, well tolerated, and suitable to replace licensed-equivalent vaccines.

Evaluation of the Diagnostic Performance of a SARS-CoV-2 and Influenza A/B Combo Rapid Antigen Test in Respiratory Samples.

This study aimed to evaluate the performance characteristics of a rapid antigen test developed to detect SARS-CoV-2 (COVID-19), influenza A virus (IAV), and influenza B virus (IBV) (flu) compared with those of the real-time reverse transcription-polymerase chain reaction (rRT-PCR) method. One hundred SARS-CoV-2, one hundred IAV, and twenty-four IBV patients whose diagnoses were confirmed by clinical and laboratory methods were included in the patient group. Seventy-six patients, who were negative for all respiratory tract viruses, were included as the control group. The Panbio™ COVID-19/Flu A&B Rapid Panel test kit was used in the assays. The sensitivity values of the kit were 97.5%, 97.9%, and 33.33% for SARS-CoV-2, IAV, and IBV, respectively, in samples with a viral load below 20 Ct values. The sensitivity values of the kit were 16.7%, 36.5%, and 11.11% for SARS-CoV-2, IAV, and IBV, respectively, in samples with a viral load above 20 Ct. The kit's specificity was 100%. In conclusion, this kit demonstrated high sensitivity to SARS-CoV-2 and IAV for viral loads below 20 Ct values, but the sensitivity values were not compatible with PCR positivity for lower viral loads over 20 Ct values. Rapid antigen tests may be preferred as a routine screening tool in communal environments, especially in symptomatic individuals, when diagnosing SARS-CoV-2, IAV, and IBV with high caution.

The burden of viral infections in pediatric intensive care unit between endemic and pandemic coronavirus infections: A tertiary care center experience

Objectives: To measure the prevalence of viral infections, length of stay (LOS), and outcome in children admitted to the pediatric intensive care unit (PICU) during the period preceding the COVID-19 pandemic in a MERS-CoV endemic country. Methods: A retrospective chart review of children 0–14 years old admitted to PICU with a viral infection. Results: Of 1736 patients, 164 patients (9.45%) had a positive viral infection. The annual prevalence trended downward over a three-year period, from 11.7% to 7.3%. The median PICU LOS was 11.6 days. Viral infections were responsible for 1904.4 (21.94%) PICU patient-days. Mechanical ventilation was used in 91.5% of patients, including noninvasive and invasive modes. Comorbidities were significantly associated with intubation (P-value = 0.025). Patients infected with multiple viruses had median pediatric index of mortality 2 (PIM 2) scores of 4, as compared to 1 for patients with single virus infections (p < 0.001), and a median PICU LOS of 12 days, compared to 4 in the single-virus group (p < 0.001). Overall, mortality associated with viral infections in PICU was 7 (4.3%). Patients with viral infections having multiple organ failure were significantly more likely to die in the PICU (p = 0.001). Conclusion: Viral infections are responsible for one-fifth of PICU patient-days, with a high demand for mechanical ventilation. Patients with multiple viral infections had longer LOS, and higher PIM 2 scores. The downward trend in the yearly rate of PICU admissions for viral infections between the end of the MERS-CoV outbreak and the start of the COVID-19 pandemic may suggest viral interference that warrants further investigations. © 2022 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases

Performance Evaluation of STANDARD Q COVID/FLU Ag Combo for Detection of SARS-CoV-2 and Influenza A/B.

We evaluated the performance of the STANDARD Q COVID/FLU Ag Combo test (Q Ag combo test) for the detection of SARS-CoV-2, influenza A, and influenza B using a single point-of-care device compared with real-time PCR. A total of 408 individuals, 55 positives with SARS-CoV-2, 90 with influenza A, 68 with influenza B, and 195 negatives for all viruses, participated. The Q Ag combo test demonstrated a high level of sensitivity of 92.73% and a specificity of 99.49% for the detection of SARS-CoV-2. When the number of days from symptom onset (DSO) was restricted to 0 < DSO ≤ 6, the sensitivity of the Q Ag combo test to detect SARS-CoV-2 was 100%, and when the Ct value of RdRp was ≤20, the sensitivity to detect SARS-CoV-2 was 93.10%. The Q Ag combo test results also demonstrated a sensitivity of 92.22% and a specificity of 100% for influenza A, a sensitivity of 91.18%, and a specificity of 99.49% for influenza B. The agreement analysis of the Q Ag combo test with the RT-PCR results demonstrated excellent outcomes, making it useful and efficient for the detection of SARS-CoV-2, influenza A, and influenza B.