Baseline characteristics and clinical symptoms related to respiratory viruses identified among patients presenting with influenza-like illness in primary care

High incidence of pneumonia cases observed in children seen in general practice consultations during the 2023-2024 season, France

BACKGROUND

An increase in hospitalizations for respiratory illnesses due to Mycoplasma pneumoniae was reported in France in late October 2023. Data in primary care are scarce and microbiological or radiological investigations are not routinely recommended for community-acquired pneumonia.

METHODS

We computed weekly incidence rates of pneumonia and bronchiolitis cases from the electronic records of French general practitioners from January 2016 to August 2024. These weekly incidences were described in the light of the Covid-19 pandemic, overall and by age group. For better interpretation, the weekly incidences of pneumonia and bronchiolitis were compared with virological surveillance data of acute respiratory infections observed in general practice.

RESULTS

During the 2016-2024 period, 108,539 cases of pneumonia and 46,411 cases of bronchiolitis were identified from 51,351,414 consultations. The incidence of pneumonia consultations in general practice during the 2022-2023 and 2023-2024 seasons is similar to that observed before the Covid-19 pandemic, after two seasons of low incidence (2020-2021 and 2021-2022). However, the 2023-2024 pneumonia epidemic is the strongest ever observed in children (0-14 years, and especially among the 5-14 years) in general practice since 2016, with an earlier onset. Regarding the incidence of bronchiolitis in children, the 2023-2024 season was in line with the 2021-2022, 2022-2023 and pre-pandemic seasons. No abnormal circulation of classical seasonal viruses was observed during the 2023-2024 season.

CONCLUSIONS

The sharp increase in pneumonia cases observed this season among children in primary care settings requires the implementation of studies to understand the cause and to confirm or refute the possible association with M. pneumoniae as observed in hospitals. Given the impact of the Covid-19 pandemic on the circulation of pathogens, it would be useful to extend, even on a temporary basis, the traditional microbiological surveillance in primary care to include common bacterial pathogens affecting the upper and lower respiratory tract, such as M. pneumoniae, S. pneumoniae or Streptococcus A.

Respiratory Symptoms and Health Outcomes of Rhinovirus and Influenza Virus Infections: Implications of Asthma, Diabetes Mellitus and Allergic Rhinitis in Rhinovirus C Infection

Rhinovirus (RV), classified into RV-A, RV-B, and RV-C, is a prevalent cause of respiratory tract infections (RTIs). Here, we analysed RV infection and its clinical implications among outpatients with acute upper RTIs. Demographic data, baseline comorbidities, clinical symptoms, and health outcomes of RV-infected patients (n = 849) were compared with influenza (n = 417). Multivariable logistic regression was employed to evaluate predictors and health outcomes over a 1-year follow-up period. RV infections predominantly presented with cough, nasal discharge, and sore throat, whereas fever was more prevalent in influenza cases. RV-C-infected individuals with diabetes mellitus (adjusted odds ratio [aOR] 3.6; 95% CI 1.7-7.2; p = 0.001) and asthma (aOR 1.9; 95% CI 1.0-3.5; p = 0.047) showed a higher likelihood of experiencing severe acute respiratory symptoms. RV-C patients with comorbidities were twice more likely to have primary care visits due to RTIs within 1 year (aOR 2.4; 95% CI 1.4-4.4; p = 0.003). Asthma (aOR 3.8; 95% CI 1.9-7.2; p < 0.0001) and allergic rhinitis (aOR 2.9; 95% CI 1.0-8.0; p = 0.042) were key predictors of increased RTI-related primary care visits. RV infection, particularly in individuals with asthma, allergic rhinitis and diabetes, poses a significant disease burden similar to that of influenza.

A new pathogen pattern of acute respiratory tract infections in primary care after COVID-19 pandemic: a multi-center study in southern China

BACKGROUND

After the coronavirus disease 2019 (COVID-19) pandemic, no studies on bacterial and atypical pathogens were conducted in primary care. We aimed to describe the etiological composition of acute respiratory tract infections (ARTIs) presenting to primary care with limited resources after the pandemic.

METHODS

1958 adult patients with ARTIs from 17 primary care clinics were recruited prospectively from January 2024 to March 2024. 17 and 62 pathogens in throat swab samples were tested using polymerase chain reaction (PCR) and targeted next-generation sequencing (tNGS), respectively. We analyzed the pathogen spectrum and co-infectious pattern of viral, bacterial or atypical pathogens. Then, the associations between clinical characteristics and pathogens were investigated.

RESULTS

In PCR test, the positive rate of any pathogens was 80.3%, consisting of 60.2% for viruses, 41.8% for bacteria and 21.7% for viral-bacterial co-infection. In tNGS test, the positive rate was 89.1%, consisting of 64.7% for viruses, 55.2% for bacteria and 30.9% for viral-bacterial co-infection. Influenza virus B (18.2%), influenza virus A (16.8%) and severe acute respiratory syndrome coronavirus 2 (14.1%) were the three leading viral pathogens, and H. influenzae (36.1%), S. anginosus (15.7%) and S. pneumoniae (8.4%) were the three leading bacterial pathogens. Few M. pneumoniae (1.6%) were detected. The mixed bacterial or mixed viral-bacterial co-infections were the most common co-infectious patterns. The mixed bacterial or mixed viral-bacterial co-infections were the most common co-infectious patterns. Overall, patients with viral infection or viral-bacterial co-infection had more clinical symptoms, and patients with bacterial infection had higher inflammatory indicators.

CONCLUSIONS

After the COVID-19 pandemic, the main viral pathogens of ARTIs were unevenly distributed, and less bacterial and atypical pathogens were detected in primary care. The microbiological evidences can optimize the precision diagnosis and treatment of ARTIs in primary care with limited resources.

Prospective cohort study of patient demographics, viral agents, seasonality, and outcomes of influenza-like illness in Mexico in the late H1N1-pandemic and post-pandemic years (2010-2014)

Objectives

Influenza-like illness (ILI) caused by respiratory viruses results in various respiratory clinical manifestations. The ILI002 prospective observational cohort study aimed to describe viral agents, seasonality, and outcomes of patients with ILI during four seasons in the influenza H1N1-pandemic and post-pandemic years (2010-2014).

Methods

Patients from six Mexican hospitals were enrolled from April 2010 to March 2014. Clinical data and nasopharyngeal swabs were obtained and tested for viral respiratory pathogens by real-time reverse-transcription polymerase chain reaction.

Results

Of the 5662 enrolled participants, 64.9% were adults and 35.1% were children. Among the 5629 participants with single-pathogen detection, rhinovirus (20.2%), influenza virus (11.2%), respiratory syncytial virus (RSV) (7.2%), and coronavirus (6.8%) were the most frequent pathogens. Co-infection occurred in 14.5% of cases; 49.3% of participants required hospitalization, particularly in RSV cases (42.9% adults, 89.6% children). The mortality rate was 2.8% higher among older adult participants and those with comorbidities. Influenza H1N1 had the highest mortality rate, yet almost half of the deceased had no pathogen. Rhinovirus persisted year-round, while influenza, coronavirus, and RSV peaked during cooler months.

Conclusions

Analyses showed that some viruses causing ILI may lead to severe disease and hospitalization irrespective of comorbidities. These findings may help in decision-making about public health policies on prevention measures, vaccination, treatment, and administration of health care.

SARS-CoV-2, influenza A/B and respiratory syncytial virus positivity and association with influenza-like illness and self-reported symptoms, over the 2022/23 winter season in the UK: a longitudinal surveillance cohort

BACKGROUND

Syndromic surveillance often relies on patients presenting to healthcare. Community cohorts, although more challenging to recruit, could provide additional population-wide insights, particularly with SARS-CoV-2 co-circulating with other respiratory viruses.

METHODS

We estimated the positivity and incidence of SARS-CoV-2, influenza A/B, and RSV, and trends in self-reported symptoms including influenza-like illness (ILI), over the 2022/23 winter season in a broadly representative UK community cohort (COVID-19 Infection Survey), using negative-binomial generalised additive models. We estimated associations between test positivity and each of the symptoms and influenza vaccination, using adjusted logistic and multinomial models.

RESULTS

Swabs taken at 32,937/1,352,979 (2.4%) assessments tested positive for SARS-CoV-2, 181/14,939 (1.2%) for RSV and 130/14,939 (0.9%) for influenza A/B, varying by age over time. Positivity and incidence peaks were earliest for RSV, then influenza A/B, then SARS-CoV-2, and were highest for RSV in the youngest and for SARS-CoV-2 in the oldest age groups. Many test positives did not report key symptoms: middle-aged participants were generally more symptomatic than older or younger participants, but still, only ~ 25% reported ILI-WHO and ~ 60% ILI-ECDC. Most symptomatic participants did not test positive for any of the three viruses. Influenza A/B-positivity was lower in participants reporting influenza vaccination in the current and previous seasons (odds ratio = 0.55 (95% CI 0.32, 0.95)) versus neither season.

CONCLUSIONS

Symptom profiles varied little by aetiology, making distinguishing SARS-CoV-2, influenza and RSV using symptoms challenging. Most symptoms were not explained by these viruses, indicating the importance of other pathogens in syndromic surveillance. Influenza vaccination was associated with lower rates of community influenza test positivity.

Genetic diversity and characterization of rhinoviruses from Chinese clinical samples with a global perspective

IMPORTANCE

Based on clinical samples collected in China, we detected and reported 22 types for the first time in China, as well as three types for the first time in Asia, and reported their genetic characteristics and diversity. We identified a novel type of Rhinovirus (RV), A110, highlighting its unique genetic features. We annotated the genomic structure and serotype of all the existing RV sequences in the database, and four novel RV types were identified and their genetic diversity reported. Combined with the sequence annotation, we constructed a complete VP1 data set of RV and conducted the first large-scale evolutionary dynamics analysis of RV. Based on a high-quality data set, we conducted a comprehensive analysis of the guanine-cytosine (GC) content variations among serotypes of RVs. This study provides crucial theoretical support and valuable data for understanding RV's genetic diversity and developing antiviral strategies.

Positive and negative viral associations in patients with acute respiratory tract infections in primary care: the ECOVIR study

Introduction

Acute respiratory infections (ARIs) are the most common viral infections encountered in primary care settings. The identification of causal viruses is still not available in routine practice. Although new strategies of prevention are being identified, knowledge of the relationships between respiratory viruses remains limited.

Materials and methods

ECOVIR was a multicentric prospective study in primary care, which took place during two pre-pandemic seasons (2018-2019 and 2019-2020). Patients presenting to their General practitioner (GP) with ARIs were included, without selecting for age or clinical conditions. Viruses were detected on nasal swab samples using a multiplex Polymerase Chain Reaction test focused on 17 viruses [Respiratory Syncytial Virus-A (RSV-A), RSV-B, Rhinovirus/Enterovirus (HRV), human Metapneumovirus (hMPV), Adenovirus (ADV), Coronaviruses (CoV) HKU1, NL63, 229E, OC43, Influenza virus (H1 and H3 subtypes), Influenza virus B, Para-Influenza viruses (PIVs) 1-4, and Bocavirus (BoV)].

Results

Among the 668 analyzed samples, 66% were positive for at least one virus, of which 7.9% were viral codetections. The viral detection was negatively associated with the age of patients. BoV, ADV, and HRV occurred more significantly in younger patients than the other viruses (p < 0.05). Codetections were significantly associated with RSV, HRV, BoV, hMPV, and ADV and not associated with influenza viruses, CoV, and PIVs. HRV and influenza viruses were negatively associated with all the viruses. Conversely, a positive association was found between ADV and BoV and between PIVs and BoV.

Conclusion

Our study provides additional information on the relationships between respiratory viruses, which remains limited in primary care.

Influenza-like illness in individuals treated with immunosuppressants, biologics, and/or systemic corticosteroids for autoimmune or chronic inflammatory disease: A crowdsourced cohort study, France, 2017-2018

BACKGROUND

Influenza-like illness (ILI) incidence estimates in individuals treated with immunosuppressants and/or biologics and/or corticosteroid for an autoimmune or chronic inflammatory disease are scarce. We compared the ILI incidence among immunocompromised population and the general population.

METHOD

We conducted a prospective cohort study during the 2017-2018 seasonal influenza epidemic, on the GrippeNet.fr electronic platform, which allows the collection of epidemiological crowdsourced data on ILI, directly from the French general population. The immunocompromised population were adults treated with systemic corticosteroids, immunosuppressants, and/or biologics for an autoimmune or chronic inflammatory disease, recruited directly on GrippeNet.fr and also among patients of the departments of a single university hospital that were asked to incorporate GrippeNet.fr. The general population consisted of adults reporting none of the above treatments or diseases participating in GrippeNet.fr. The incidence of ILI was estimated on a weekly basis and compared between the immunocompromised population and the general population, during the seasonal influenza epidemic.

RESULTS

Among the 318 immunocompromised patients assessed for eligibility, 177 were included. During the 2017-2018 seasonal influenza epidemic period, immunocompromised population had 1.59 (95% CI: 1.13-2.20) higher odds to experience an ILI episode, compared to the general population (N = 5358). An influenza vaccination was reported by 58% of the immunocompromised population, compared to 41% of the general population (p < 0.001).

CONCLUSION

During a seasonal influenza epidemic period, the incidence of influenza-like illness was higher in patients treated with immunosuppressants, biologics, and/or corticosteroids for an autoimmune or chronic inflammatory disease, compared to the general population.

Can Some Viral Respiratory Infections Observed Before the Pandemic Announcement Be Related to SARS-CoV-2?

OBJECTIVE

There have been doubts that SARS-CoV-2 has been circulating before the first case was announced. The aim of this study was to evaluate the possibility of COVID-19 in some cases diagnosed to be viral respiratory tract infection in the pre-pandemic period in our center.

MATERIAL AND METHODS

Patients who were admitted to our hospital's pulmonary diseases, infectious diseases, and intensive care clinics with the diagnosis of viral respiratory system infection within a 6-month period between October 2019 and March 12, 2020, were screened. Around 248 archived respiratory samples from these patients were analyzed for SARS-CoV-2 ribonucleic acid by real-timequantitative polymerase chain reaction. The clinical, laboratory, and radiological data of the patients were evaluated.

RESULTS

The mean age of the study group was 47.5 (18-89 years); 103 (41.5%) were female and 145 (58.4%) were male. The most common presenting symptoms were cough in 51.6% (n = 128), fever in 42.7% (n = 106), and sputum in 27.0% (n = 67). Sixty-nine percent (n = 172) of the patients were pre-diagnosed to have upper respiratory tract infection and 22.0% (n = 55) had pneumonia, one-third of the patients (n = 84, 33.8%) were followed in the service. Respiratory viruses other than SARS-CoV-2 were detected in 123 (49.6%) patients. Influenza virus (31.9%), rhinovirus (10.5%), and human metapneumovirus (6.5%) were the most common pathogens, while none of the samples were positive for SARS-CoV-2 RNA. Findings that could be significant for COVID-19 pneumonia were detected in the thorax computed tomography of 7 cases.

CONCLUSION

The negative SARS-CoV-2 real-time-quantitative polymerase chain reaction results in the respiratory samples of the cases followed up in our hospital for viral pneumonia during the pre-pandemic period support that there was no COVID-19 among our cases during the period in question. However, if clinical suspicion arises, both SARS and non-SARS respiratory viral pathogens should be considered for differential diagnosis.

DIFFERENT CLINICAL PRESENTATIONS OF HUMAN RHINOVIRUS (HRV) SPECIES INFECTION IN CHILDREN AND ADULTS IN MEXICO

Background

Human rhinoviruses (HRVs) are a common cause of influenza-like illness, with the ability to infect the upper and lower respiratory tracts. In this study we aim to describe the clinical and molecular features of HRV infection in Mexican children and adults.

Methods

We performed a hospital-based, 4-year multicenter prospective observational cohort study of patients with influenza-like illness. Participants who tested positive for HRV were included. We described demographic, clinical, and laboratory characteristics and the association between HRV types, illness severity, and clinical outcomes.

Results

Of the 5662 subjects recruited, 1473 (26%) had HRV; of those, 988 (67.1%) were adults (≥18 years) and 485 (32.9%) were children. One hundred sixty-seven (11.33%) samples were sequenced; 101 (60.5%) were rhinovirus species A (HRV-A), 22 (13.2%) were rhinovirus species B (HRV-B), and 44 (26.3%) were rhinovirus species C (HRV-C). Among children and adults, 30.5% and 23.5%, respectively, were hospitalized (non–intensive care unit [ICU]). The odds of HRV-C are higher than HRV-A for participants in the ICU (compared to outpatient) and when platelets, lymphocytes, white blood cells, and lactate dehydrogenase are increased. The odds of HRV-C are higher than HRV-A and HRV-B with shortness of breath. The odds of HRV-A are higher than HRV-B, and the odds of HRV-B are higher than HRV-C, when mild symptoms like muscle ache and headache occur.

Conclusions

Rhinoviruses are a common cause of influenza-like illness. It is necessary to improve the surveillance, testing, and species identification for these viruses to understand different clinical presentations and risk factors associated with worse outcomes.

Clinical Trials Registration. NCT01418287.

Respiratory syncytial virus in pediatric influenza-like illness cases in Lombardy, Northern Italy, during seven consecutive winter seasons (from 2014-2015 to 2020-2021)

Introduction

Respiratory syncytial virus (RSV) is the major cause of lower respiratory tract illness in young children and can also cause influenza‐like illness (ILI). Here we investigated the epidemiological features of RSV infection in pediatric ILI cases in Lombardy (a region in Northern Italy accounting nearly 10 million inhabitants) from 2014–2015 to 2020–2021 winter seasons.

Material and Methods

Data for this study were retrieved and statistically analyzed from the database of virological influenza surveillance of the regional reference laboratory for Lombardy within the Italian influenza surveillance network (InfluNet).

Results

RSV accounted for nearly 19% of pediatric ILI with a risk of infection nearly two‐fold greater than that of individuals ≥15 years. RSV positivity rate increased to 28% considering 0–5 years old children. Although in children ≤5 years the risk of infection from influenza viruses resulted nearly two‐fold higher than the risk of RSV infection, the age group 4–6 months and 7–12 months showed a five‐fold greater risk of infection from RSV than from influenza. Children ≤5 years of age with pre‐existing underlying health conditions had a nearly five‐fold greater risk of getting RSV infection than otherwise healthy 0–5 years old children. RSV was identified in ILI cases <15 years of age in all considered winter seasons except in the 2020–2021 season.

Discussion

Sentinel surveillance of ILI allowed us to identify groups at higher risk of RSV and influenza infection and to define the start, duration, timing, and intensity of the RSV and influenza community circulation. This surveillance approach can be implemented to assess the RSV circulation and impact in a real‐time manner.

Dietary Supplementation with Biobran/MGN-3 Increases Innate Resistance and Reduces the Incidence of Influenza-like Illnesses in Elderly Subjects: A Randomized, Double-Blind, Placebo-Controlled Pilot Clinical Trial

Influenza-like illness (ILI) remains a major cause of severe mortality and morbidity in the elderly. Aging is associated with a decreased ability to sense pathogens and mount effective innate and adaptive immune responses, thus mandating the development of protective nutraceuticals. Biobran/MGN-3, an arabinoxylan from rice bran, has potent anti-aging and immunomodulatory effects, suggesting that it may be effective against ILI. The objective of the current study was to investigate the effect of Biobran/MGN-3 on ILI incidence, natural killer (NK) cell activity, and the expressions of RIG-1 (retinoic acid-inducible gene 1), MDA5 (melanoma differentiation-associated protein 5), and their downstream signaling genes ISG-15 (interferon-stimulated genes 15) and MX1 (myxovirus (influenza) resistance 1, interferon-inducible). A double-blind, placebo-controlled clinical trial included eighty healthy older adults over 55 years old, 40 males and 40 females, who received either a placebo or Biobran/MGN-3 (500 mg/day) for 3 months during known ILI seasonality (peak incidence) in Egypt. The incidence of ILI was confirmed clinically according to the WHO case definition criteria. Hematological, hepatic, and renal parameters were assessed in all subjects, while the activity of NK and NKT (natural killer T) cells was assessed in six randomly chosen subjects in each group by the degranulation assay. The effect of Biobran/MGN-3 on RIG-1 and MDA5, as well as downstream ISG15 and MX1, was assessed in BEAS-2B pulmonary epithelial cells using flow cytometry. The incidence rate and incidence density of ILI in the Biobran/MGN-3 group were 5.0% and 0.57 cases per 1000 person-days, respectively, compared to 22.5% and 2.95 cases per 1000 person-days in the placebo group. Furthermore, Biobran/MGN-3 ingestion significantly enhanced NK activity compared to the basal levels and to the placebo group. In addition, Biobran/MGN-3 significantly upregulated the expression levels of RIG-1, MDA5, ISG15, and MX1 in the human pulmonary epithelial BEAS-2B cell lines. No side effects were observed. Taken together, Biobran/MGN-3 supplementation enhanced the innate immune response of elderly subjects by upregulating the NK activity associated with reduction of ILI incidence. It also upregulated the intracellular RIG-1, MDA5, ISG15, and MX1 expression in pulmonary epithelial tissue cultures. Biobran/MGN-3 could be a novel agent with prophylactic effects against a wide spectrum of respiratory viral infections that warrants further investigation.

Management of hospitalized influenza A patients during the season 2018/19 : Comparison of three medical departments and the effect on outcome and antibiotic usage

BACKGROUND

Diagnosis and treatment of influenza patients are often provided across several medical specialties. We compared patient outcomes at an infectious diseases (ID), a rheumatology (Rheu) and a pulmonology (Pul) department.

MATERIAL AND METHODS

In this prospective observational multicenter study we included all influenza positive adults who were hospitalized and treated at flu isolation wards in three hospitals in Vienna during the season 2018/2019.

RESULTS

A total of 490 patients (49% female) with a median age of 73 years (interquartile range [IQR] 61-82) were included. No differences regarding age, sex and most underlying diseases were present at admission. Frequencies of the most common complications differed: acute kidney failure (ID 12.7%, Rheu 21.2%, Pulm 37.1%, p < 0.001), acute heart failure (ID 4.3%, Rheu 17.1%, Pulm 14.4%, p < 0.001) and respiratory insufficiency (ID 45.1%, Rheu 41.5%, Pulm 56.3%, p = 0.030). Oseltamivir prescription was lowest at the pulmonology flu ward (ID 79.6%, Rheu 90.5%, Pulm 61.7%, p < 0.001). In total 176 patients (35.9%) developed pneumonia. Antibiotic selection varied between the departments: amoxicillin/clavulanic acid (ID 28.9%, Rheu 63.8%, Pulm 5.9%, p < 0.001), cefuroxime (ID 28.9%, Rheu 1.3%, Pulm 0%, p < 0.001), 3rd generation cephalosporins (ID 4.4%, Rheu 5%, Pulm 72.5%, p < 0.001), doxycycline (ID 17.8%, Rheu 0%, Pulm 0%, p < 0.001). The median length of stay was significantly different between wards: ID 6 days (IQR 5-8), Rheu 6 days (IQR 5-7) and Pulm 7 days (IQR 5-9.5, p = 0.034). In-hospital mortality was 4.3% and did not differ between specialties.

CONCLUSION

We detected differences in oseltamivir usage, length of in-hospital stay and antibiotic choices for pneumonia. Influenza-associated mortality was unaffected by specialty.

Epidemiological and clinical characteristics of respiratory viruses in 4403 pediatric patients from multiple hospitals in Guangdong, China

Background

Acute respiratory infections (ARI) cause considerable morbidity and mortality worldwide, especially in children. Unfortunately, there are limited multi-center data on common viral respiratory infections in south China.

Methods

A total of 4403 nasal swabs were collected from children in 10 cities in Guangdong, China in 2019. Seven respiratory viruses, influenza A virus (IFA), influenza B virus (IFB), respiratory syncytial virus (RSV), adenoviruses (ADV) and parainfluenza virus types 1–3 (PIV1, PIV2 and PIV3), were detected by direct immunofluorescence antibody assay. The personal information and clinical characteristics were recorded and analyzed.

Results

The results showed that at least one virus was detected in 1099 (24.96 %) samples. The detection rates of RSV, IFA, ADV, PIV3, PIV1 and PIV2 were 7.13 % (314/4403), 5.31 % (234/4403), 4.02 % (177/4403), 3.04 % (134/4403), 1.70 % (75/4403) and 1.16 % (51/4403), respectively. The detection rate of RSV was highest in 0–6-month-old children at 18.18 % (106/583), while the detection rate of IFA was highest in 12–18-year-old children at 20.48 % (17/83). The total detection rates in winter and spring were 35.67 % (219/614) and 34.56 % (403/1166), higher than those in summer, 17.41 % (284/1631), and autumn, 19.46 % (193/992).

Conclusions

RSV and IFA were the main respiratory viruses in children. With increasing age the detection rate of RSV decreased in children, but the trends for the detection rates of IFA and IFB were the opposite. This study provided the viral etiology and epidemiology of pediatric patients with ARI in Guangdong, China.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12887-021-02759-0.

Are Posterior Oropharyngeal Saliva Specimens an Acceptable Alternative to Nasopharyngeal Sampling for the Monitoring of SARS-CoV-2 in Primary-Care Settings?

Background: The present study was set up to evaluate the efficacy of virological surveillance using posterior oropharyngeal saliva samples to monitor the COVID-19 pandemic in general practice. Methods: Posterior oropharyngeal saliva samples were collected without restriction on timing or alimentation by general practitioners from patients with acute respiratory infection (ARI) seen in consultation. Saliva samples were tested by real-time reverse transcription polymerase chain reaction for SARS-CoV-2 and 21 other respiratory pathogens. Results for SARS-CoV-2 in saliva samples were compared to results obtained using a nasopharyngeal swab (NPS) collected in a certified medical laboratory before or after the ARI consultation. Results: Overall, 143 ARI patients were enrolled between 6 June 2020, and 19 January 2021. SARS-CoV-2 RNA was detected in 37.0% (n = 53) of saliva samples and in 39.0% (n = 56) of NPS. Both saliva and NPS were positive in 51 patients. Positive and negative results were concordant between saliva samples and NPS in 51 (96.2%) and in 85 (94.4%) patients, respectively, with a Cohen’s Kappa coefficient of 0.89 (95% CI 0.82–0.97, p < 0.001). Other respiratory viruses were detected in 28.0% (n = 40) of the 143 saliva samples. Conclusions: Findings suggest that saliva samples could represent an attractive alternative to NPS for surveillance of SARS-CoV-2 in patients consulting for an ARI in primary care.

Impact of the lockdown on the burden of COVID-19 in outpatient care in France, spring 2020

BACKGROUND

To limit the spread of SARS-CoV-2 several countries implemented measures to reduce the number of contacts such as a national lockdown. We estimated the impact of the first lockdown on the burden of COVID-19 in the community in France.

METHODS

Physicians participating in the French Sentinelles network reported the number of patients with an acute respiratory infection (ARI) seen in consultation and performed nasopharyngeal swabs in a sample of these patients (first patient of the week). The swabs were tested by RT-PCR for the presence of SARS-CoV-2. Clinical and virological data were combined to estimate ARI incidence attributable to SARS-CoV-2 from 17 March to 10 May 2020.

RESULTS

The incidence of ARI attributable to COVID-19 decreased after the second week of the lockdown period from 142 (95%CI [101; 183]) to 41 (95%CI [21; 60]) per 100,000 population. A decrease was observed in all areas in metropolitan France. The youngest age groups (<15-years-old) were least affected with a cumulated incidence estimated to 14 per 100,000 population during the study period.

CONCLUSIONS

The data collected in primary care suggests that the first lockdown implemented in France during spring 2020 significantly reduced the incidence of acute respiratory infections including COVID-19 in France and limited the geographic spread of SARS-CoV-2.

Estimation of influenza-attributable burden in primary care from season 2014/2015 to 2018/2019, France

Influenza viruses cause seasonal epidemics whose intensity varies according to the circulating virus type and subtype. We aim to estimate influenza-like illness (ILI) incidence attributable to influenza viruses in France from October 2014 to May 2019. Physicians participating in the French Sentinelles network reported the number of patients with ILI seen in consultation and performed nasopharyngeal swabs in a sample of these patients. The swabs were tested by RT-PCR for the presence of influenza viruses. These clinical and virological data were combined to estimate ILI incidence attributable to influenza viruses by subtypes and age groups. Influenza incidence rates over seasons ranged from 1.9 (95% CI, 1.9; 2.0) to 3.4% (95% CI, 3.2; 3.6) of the population. Each season, more than half of ILI cases were attributable to influenza. Children under 15 years were the most affected, with influenza incidence rates ranging from 3.0 (95% CI, 2.8;3.3) to 5.7% (95% CI, 5.3;6.1). Co-circulation of several (sub)types of influenza viruses was observed each year, except in 2016/2017 where A(H3N2) viruses accounted for 98.0% of the influenza cases. Weekly ILI incidences attributable to each influenza virus (sub)type were mostly synchronized with ILI incidence, except in 2014/2015 and 2017/2018, where incidence attributable to type B viruses peaked few weeks later. The burden of medically attended influenza among patients with ILI is significant in France, varying considerably across years and age groups. These results show the importance of influenza surveillance in primary care combining clinical and virological data.

Characteristics associated with COVID-19 or other respiratory viruses' infections at a single-center emergency department

Background

Rapid identification of patients with high suspicion of COVID-19 will become a challenge with the co-circulation of multiple respiratory viruses (RVs). We have identified clinical or biological characteristics to help distinguish SARS-CoV-2 from other RVs.

Methods

We used a prospective cohort including all consecutive patients admitted through the emergency department’s (ED) and presenting respiratory symptoms from November 2019 to April 2020. Patients were tested for RV using multiplex polymerase chain reaction (mPCR) and SARS-CoV-2 RT-PCR.

Results

203/508 patients were positive for an RV during the non-SARS-CoV-2 epidemic period (November to February), and 268/596 patients were SARS-CoV-2 positive during the SARS-CoV-2 epidemic (March to April). Younger age, male gender, fever, absence of expectoration and absence of chronic lung disease were statistically associated with SARS-CoV-2 detection. Combining these variables allowed for the distinguishing of SARS-CoV-2 infections with 83, 65, 75 and 76% sensitivity, specificity, PPV and NPV, respectively.

Conclusion

Patients’ characteristics associated with a positive PCR are common between SARS-CoV-2 and other RVs, but a simple discrimination of strong SARS-CoV-2 suspicion with a limited set of clinical features seems possible. Such scoring could be useful but has to be prospectively evaluated and will not eliminate the need for rapid PCR assays.

Respiratory syncytial virus in influenza-like illness cases: Epidemiology and molecular analyses of four consecutive winter seasons (2014-2015/2017-2018) in Lombardy (Northern Italy)

BACKGROUND

Besides seasonal influenza viruses (IV), several other pathogens-including respiratory syncytial virus (RSV)-are involved in clinically undistinguished influenza-like illnesses (ILIs). This study aimed at investigating the contribution of RSV in ILI cases in Lombardy (Northern Italy) during four consecutive winter seasons.

MATERIALS AND METHODS

In the framework of influenza surveillance, respiratory samples from ILI outpatients were collected from 2014-2015 to 2017-2018 season. IV-negative swabs were included in the study and analyzed to detect and molecularly characterize RSV-A and RSV-B.

RESULTS

A total of 12.9% (135/1047) of samples were positive to RSV that was mostly detected among children ≤5 years (51/183, 27.8%) and those aged 6 to 15 years (30/158, 18.9%), whereas elderly >65 years accounted for 12% of RSV cases (15/125). The median start of RSV epidemic was in the end of November, with a peak in mid-February and a width of nearly 4 months, almost overlapping seasonal influenza epidemic. RSV-A and RSV-B co-circulated in all considered seasons, with RSV-B predominating on RSV-A (63.6% vs 36.4%; P < .001). Most (85.2%) RSV-A belonged to genotype ON1 and the remaining to NA1. All RSV-B clustered within the BA genotype.

CONCLUSIONS

In this study, RSV significantly contributed to ILI cases, especially among pediatric population (<15 years), although it was detected in all age groups. RSV-B predominated on RSV-A, and the most recent evolved genotypes (BA and ON1, respectively) circulated. Investigating the epidemiological and molecular characteristics of RSV in ILI cases can increase baseline epidemiological information before the introduction of RSV vaccination.

Manifestations and Risk Factors in Children Hospitalized with Respiratory Syncytial Virus Infection

Background: Acute lower respiratory infection (ALRI) is one of the main causes of morbidity and mortality in children under five years of age, and the respiratory syncytial virus (RSV) remains its leading etiological factor. Although RSV infections occur in all age groups, the most severe course is observed among children. The clinical manifestations include both mild upper respiratory infections and severe infections of the lower tract, such as bronchiolitis and pneumonia that can lead to hospitalization and severe complications, including respiratory failure. Objectives: The study aimed to evaluate the manifestations of RSV infection in hospitalized children younger than 18 months of age and predictors of disease severity, as well as their comparison with the same age group hospitalized due to ALRI of different etiology. Methods: A retrospective analysis was performed on medical records of 448 children hospitalized due to ALRI. The analysis was performed on the total study group and subgroups of children with positive and negative results of the nasal swab for RSV detection. In each group, clinical data, laboratory test results, and imaging results were analyzed. Results: The most common manifestation was pneumonia (n = 82; 63.08%). Otitis media was observed mainly in children under six months of age with lowered inflammatory markers (P < 0.05), conjunctivitis in those with a positive family history of allergies (P < 0.05), and pneumonia in children under six months of age, with lower blood oxygen saturation and inflammatory markers, features of acidosis, and fever-free course (P < 0.05). Respiratory failure affected 13 children (10%). However, no predictors of this complication were noted. Conclusions: As pneumonia was the most common manifestation in children with both RSV-positive and RSV-negative ALRI, it seems advisable to perform the imaging of the lungs on admission and carefully monitor the child’s condition during hospitalization. In both groups, special attention should be paid to the youngest children with low inflammatory markers on hospital admission, increased clinical symptoms, and family history of allergies. Nevertheless, widely known risk factors of RSV infection itself do not reflect the risk of developing pneumonia or respiratory failure in its course.

Clinical characteristics and outcomes in adult patients hospitalized with influenza, respiratory syncytial virus and human metapneumovirus infections

Objectives: To compare the clinical characteristics and outcomes of patients hospitalized with respiratory syncytial virus (RSV), human metapneumovirus (hMPV), and influenza infections.Methods: This study prospectively enrolled 594 patients hospitalized with influenza-like illness (ILI) and laboratory-confirmed RSV, hMPV, or influenza infections over three consecutive influenza seasons at a tertiary hospital in China.Results: While certain clinical features were of value as predictors of infection type, none exhibited good predictive performance as a means of discriminating between these three infections (area under the receiver-operating characteristic curve < 0.70). After controlling for potential confounding variables, RSV infections in pneumonia patients were found to be associated with a 30-day mortality risk comparable to that of influenza patients [odds ratio (OR) 1.016, 95% confidence interval (CI) 0.267-3.856, p = 0.982], whereas hMPV infection was associated with a reduced risk of mortality (OR 0.144, 95% CI 0.027-0.780, p = 0.025). Among those without pneumonia, the 30-day mortality risk in patients with influenza was comparable to that in patients infected with RSV (OR 1.268, 95% CI 0.172-9.355, p = 0.816) or hMPV (OR 1.128, 95% CI 0.122-10.419, p = 0.916).Conclusion: Disease severity associated with these three types of viral infection was inconsistent when comparing patients with and without pneumonia, highlighting the importance of etiologic testing.

New loss of smell and taste: Uncommon symptoms in COVID-19 patients on Nord Franche-Comte cluster, France

BACKGROUND

New loss of smell or taste was not included as common symptoms of COVID-19 until March 2020 when the pandemic started in Western countries. We want to describe the prevalence and features of anosmia and dysgeusia in COVID-19 patients.

METHODS

We retrospectively investigated the clinical features of confirmed cases of COVID-19 in Nord Franche-Comté Hospital, Trevenans, France, between March, 1st and March, 14th 2020. We used SARS-CoV-2 real time RT-PCR in respiratory samples to confirm the cases.

RESULTS

Of 70 patient enrolled, the mean age was 57.0 years and 29 patients (41%) were men. Median Charlson comorbidity index was 1.70(±2.5). Twenty-seven (39%) patients had pneumonia. Fatigue (93% [65]), cough (80% [55]) and fever (77% [54]) were the three main symptoms. Neurologic symptoms were present in more than half of the patients: anosmia (53% [37]) and dysgeusia (48% [34]). The mean duration of anosmia was 7.4 (±5, [1-21]) days, 51% (36/70) recovered before 28 days of evolution. Only one patient with anosmia had not recovered at the end of the follow-up. Patients with anosmia had less often a pneumonia (10/37 vs 17/33, p = 0.036), were less often hospitalized (13/37 vs 20/33, p = 0.033) and needed less often oxygen therapy (6/37 vs 17/33, p = 0.002) than patients without anosmia. There were no statistically differences for viral load between patients with anosmia and patients without anosmia (5.5 [2.0-8.6] vs 5.3 [2.1-8.5] log copies/ml respectively, p = 0.670). The fatality of COVID-19 in our study was 6% with four deaths.

CONCLUSIONS

Anosmia and dysgeusia are present in half of COVID-19 patients. The mean duration of anosmia was 7 days and the outcome seems favorable in less than 28 days.

Clinical features of COVID-19 and influenza: a comparative study on Nord Franche-Comte cluster

Clinical descriptions about influenza-like illnesses (ILI) in COVID-19 seem non-specific. We aimed to compare the clinical features of COVID-19 and influenza. We retrospectively investigated the clinical features and outcomes of confirmed cases of COVID-19 and influenza in Nord Franche-Comté Hospital between February 26th and March 14th 2020. We used SARS-CoV-2 RT-PCR and influenza virus A/B RT-PCR in respiratory samples to confirm the diagnosis. We included 124 patients. The mean age was 59 (±19 [19-98]) years with 69% female. 70 patients with COVID-19 and 54 patients with influenza A/B. Regarding age, sex and comorbidities, no differences were found between the two groups except a lower Charlson index in COVID-19 group (2 [±2.5] vs 3 [±2.4],p = 0.003). Anosmia (53% vs 17%,p < 0.001), dysgeusia (49% vs 20%,p = 0.001), diarrhea (40% vs 20%,p = 0.021), frontal headache (26% vs 9%,p = 0.021) and bilateral cracklings sounds (24% vs 9%,p = 0.034) were statistically more frequent in COVID-19. Sputum production (52% vs 29%,p = 0.010), dyspnea (59% vs 34%,p = 0.007), sore throat (44% vs 20%,p = 0.006), conjunctival hyperhemia (30% vs 4%,p < 0.001), tearing (24% vs 6%,p = 0.004), vomiting (22% vs 3%,p = 0.001) and rhonchi sounds (17% vs 1%,p = 0.002) were more frequent with influenza infection. We described several clinical differences which can help the clinicians during the co-circulation of influenza and SARS-CoV-2.

A comparative study on the clinical features of COVID-19 with non-SARS-CoV-2 respiratory viral infections

During this coronavirus disease 2019 (COVID-19) pandemic, physicians have the important task of risk stratifying patients who present with acute respiratory illnesses. Clinical presentation of COVID-19, however, can be difficult to distinguish from other respiratory viral infections. Thus, identifying clinical features that are strongly associated with COVID-19 in comparison to other respiratory viruses can aid risk stratification and testing prioritization especially in situations where resources for virological testing and resources for isolation facilities are limited. In our retrospective cohort study comparing the clinical presentation of COVID-19 and other respiratory viral infections, we found that anosmia and dysgeusia were symptoms independently associated with COVID-19 and can be important differentiating symptoms in patients presenting with acute respiratory illness. On the other hand, laboratory abnormalities and radiological findings were not statistically different between the two groups. In comparing outcomes, patients with COVID-19 were more likely to need high dependency or intensive care unit care and had a longer median length of stay. With our findings, we emphasize that epidemiological risk factors and clinical symptoms are more useful than laboratory and radiological abnormalities in differentiating COVID-19 from other respiratory viral infections.

Respiratory Complications in Children Hospitalized with Respiratory Syncytial Virus Infection

The goal of this study was to define the prevalence of respiratory complications, other than bronchiolitis, such as pneumonia, acute otitis media, and conjunctivitis in children treated in a hospital due to respiratory syncytial virus (RSV) infection, with reference to the plausible risk factors. The study included 111 children, aged up to 22 months (median 3 months). Complications were observed in 68 (61%) children, with 32 (29%) children presenting more than one. The most frequent complication was acute otitis media in 53 (48%), pneumonia in 37 (33%), and conjunctivitis in 12 (11%) out of the 111 children. Children with complications were older than those without complications and had fever that lasted for a significantly longer time, both before and during hospitalization, and the fever was stronger. They also presented a significantly lower breathing rate at admission. The age over 3 months was a single risk factor associated with the development of otitis media (OR = 9.8, 95%CI: 3.6-26.7) and pneumonia (OR = 2.8, 95%CI: 1.1-7.3). Other factors such as prematurity, birth weight below 2500 g, exposure to tobacco smoke during pregnancy, and the cessation of breastfeeding below age 6 months were statistically irrelevant to this end. We conclude that complications are very frequent in hospitalized children with RSV infection and their risk increases with the infant age.

Performance and ease of use of a molecular point-of-care test for influenza A/B and RSV in patients presenting to primary care

Annual influenza epidemics cause substantial morbidity and mortality, and the majority of patients with influenza-like illness present to primary care. Point-of-care influenza tests could support treatment decisions. It is critical to establish analytic performance of these platforms in real-life patient samples before uptake can be considered. We aimed to assess the analytical performance and ease of use of the cobas® Liat® PCR POCT in detecting influenza A/B and RSV in samples collected from patients with influenza-like illness in primary care. Sensitivity and specificity of the cobas® Liat® POCT are calculated in comparison with a commercial laboratory-based PCR test (Fast-Track Respiratory Pathogens 21 Plus kit (Fast-Track Diagnostics)). Samples with discordant results were analysed additionally by the RespiFinder 2Smart (PathoFinder) using an Extended Gold Standard (EGS). Acceptability was scored on a five-point Likert scale as well as a failure mode analysis of the cobas® Liat® POCT was performed. Nasal and oropharyngeal swabs were obtained from 140 children and nasopharyngeal swabs from 604 adults (744 patients). The cobas® Liat® POCT had a sensitivity and specificity of 100% (95% CI 99-100%) and 98.1% (95%CI 96.3-99%) for influenza A, 100% (95% CI 97.7-100%) and 99.7% (95%CI 98.7-99.9%) for influenza B and 100% (95% CI 87.1-100%) and 99.4% (95%CI 98.6-99.8%) for RSV, respectively. According to trained lab technicians, the cobas® Liat® POCT was considered easy-to-use, with a fast turn-around-time. Cobas® Liat® POCT is a promising decentralised test platform for influenza A/B and RSV in primary care as it provides fairly rapid results with excellent analytic performance. Point-of-care influenza tests could support treatment decisions in primary care. Cobas® Liat® POCT is a promising decentralised test platform for influenza A/B and RSV in primary care as it provides fairly rapid results with excellent analytic performance.

Excess cases of influenza-like illnesses synchronous with coronavirus disease (COVID-19) epidemic, France, March 2020

Several French regions where coronavirus disease (COVID-19) has been reported currently show a renewed increase in ILI cases in the general practice-based Sentinelles network. We computed the number of excess cases by region from 24 February to 8 March 2020 and found a correlation with the number of reported COVID-19 cases so far. The data suggest larger circulation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the French population than apparent from confirmed cases.

Characteristics of human metapneumovirus infection in adults hospitalized for community-acquired influenza-like illness in France, 2012-2018: a retrospective observational study

Objectives

To describe the prevalence, clinical features and complications of human metapneumovirus (hMPV) infections in a population of adults hospitalized with influenza-like illness (ILI).

Methods

This was a retrospective, observational, multicenter cohort study using prospectively collected data from adult patients hospitalized during influenza virus circulation, for at least 24 h, for community-acquired ILI (with symptom onset <7 days). Data were collected from five French teaching hospitals over six consecutive winters (2012–2018). Respiratory viruses were identified by multiplex reverse transcription polymerase chain reaction (RT-PCR) on nasopharyngeal specimens. hMPV + patients were compared with hMPV– patients, influenza+ and respiratory syncytial virus (RSV)+ patients using multivariate logistic regressions. Primary outcome was the prevalence of hMPV in patients hospitalized for ILI.

Results

Among the 3148 patients included (1449 (46%) women, 1988 (63%) aged 65 and over; 2508 (80%) with chronic disease), at least one respiratory virus was detected in 1604 (51%, 95% confidence interval (CI) 49–53), including 100 cases of hMPV (100/3148, 3% 95% CI 3–4), of which 10 (10%) were viral co-infection. In the hMPV + patients, mean length of stay was 7 days, 62% (56/90) developed a complication, 21% (14/68) were admitted to intensive care unit and 4% (4/90) died during hospitalization. In comparison with influenza + patients, hMPV + patients were more frequently >65 years old (adjusted odds ratio (aOR) = 3.3, 95% CI 1.9–6.3) and presented more acute heart failure during hospitalization (aOR = 1.8, 95% CI 1.0–2.9). Compared with RSV + patients, hMPV + patients had less cancer (aOR = 0.4, 95% CI 0.2–0.9) and were less likely to smoke (aOR = 0.5, 95% CI 0.2–0.9) but had similar outcomes, especially high rates of respiratory and cardiovascular complications.

Conclusions

Adult hMPV infections mainly affect the elderly and patients with chronic conditions and are responsible for frequent cardiac and pulmonary complications similar to those of RSV infections. At-risk populations would benefit from the development of antivirals and vaccines targeting hMPV.