mteb/CovidQA huggingface dataset:
To determine the viral load in the lung of the infected mice, plaque assays and qPCR were performed. The pulmonary viral titers in the EAP (25 mg/kg) group were significantly lower than the titers in the mice that received PBS at day 3 postinfection (Figures 2(c) and 2(d) ). These data clearly indicate that intranasal administration of EAP controls H5N1 viral replication and improves survival rates in a mouse model. The protective effect of EAP against H5N1 virus is likely due to its immunomodulatory properties. To detect IL-6, TNF-, and IFN-expression, lungs of five mice per group were collected at day 0 before infection and tested by qPCR and ELISA. The mRNA levels in the EAP group (25 mg/kg) were significantly higher than those in the PBS control (naive mice) (Figures 3(a)-3(c) ). Soluble cytokine levels at day 0 were measured by ELISA, and results were consistent with the qPCR results, even though IFN-production in the EAP group was not significantly higher than that of the PBS
group ( = 0.0599) (Figures 3(g)-3(i) ). These results suggest that EAP increases the IL-6, TNF-, and IFN-production.
IL-6, TNF-, and IFN-expression at day 3 postinfection was determined by qPCR. In contrast, TNF-mRNA levels following EAP (25 mg/kg) treatment were significantly lower than those in the PBS group (Figure 3(e) ), while IL-6 and IFN-expression were only slightly lower (not significant) (Figures 3(d) and 3(f) ). These results may be explained by a higher viral load, and the more severe inflammatory response in PBS treated mice.
Excessive inflammation can cause severe lung lesions during H5N1 influenza infection. To evaluate histopathological changes in the lungs of infected mice, tissues of each group at day 3 postinfection were examined. The lungs of PBS treated mice exhibited a severe inflammation response, characterized by interstitial edema, inflammatory cellular infiltration around small blood vessels, alveolar lumen flooded with edema fluid mixed with exfoliated alveolar epithelial cells, and a thickening of alveolar walls (Figures 4(c) and 4(d) ). The lungs of EAP (25 mg/kg) treated mice exhibited milder lesions than those receiving PBS, characterized by signs of bronchopneumonia with interstitial edema, and inflammatory cell infiltration around small blood vessels (Figures 4(a) and 4(b) ). Viral loads and inflammatory cytokine production in the lung were correlated; suggesting that EAP treatment reduces lung lesions in H5N1 infected mice.
Polysaccharides derived from many plants enhance the secretion of cytokines and chemokines, such as TNF-, IL-6, IL-8, and IL-12 [11] . This immunomodulatory effect is mediated mainly through recognition of polysaccharide polymers by several pattern recognition receptors (PRRs). To determine which receptor contributes directly to the innate immune recognition of EAP, Toll-like receptor 2 (TLR2), TLR4, Dectin-1, and mannose receptor (MR) were examined by qPCR both in vivo and in vitro. Mice were treated with EAP at a dose of 25 mg/kg body weight intranasally once daily for 5 days, with control mice receiving PBS. Lung total RNA was prepared for qPCR. The expression of Dectin-1 and MR in EAP treated mice was significantly elevated compared with controls, while expression of TLR2 and TLR4 were slightly higher, but not statistically significant (Figure 5(a) ). In vitro assay showed similar trends. As shown in Figure 5 (b), Raw264.7 cells were treated with 200 g/mL EPA for 36 h before qPCR.
Dectin-1 and MR levels were significantly higher, while expression of TLR2 and TLR4 did not change. These data suggest that EAP recognition occurred mainly via the Dectin-1 and MR pathway.
In this study, we evaluated the immunomodulatory activities and protective effect of EAP against H5N1 influenza infection in a mouse model. To our knowledge, these findings are the first to show the anti-H5N1 effect of EAP. Intranasal administration of EAP prior to H5N1 viral challenge improved survival rates of infected mice with a corresponding reduction of pulmonary viral load. The anti-H5N1 effect was very likely due to the innate immune recognition of EAP and the secretion of innate immune mediators (IL-6, TNFand IFN-) before infection. Furthermore, the effect of EAP on PRR expression (including TLR2, TLR4, Dectin-1, and MR) was determined both in vivo and in vitro. These results suggest that the innate immune recognition of EAP was dependent upon the activation of the Dectin-1 and MR pathways. Our data demonstrate the feasibility of using EAP as a novel immunomodulatory agent against influenza infection. Unfortunately, the sugar composition of EAP has not been characterized.
The emergence of new drug-resistant strains resulting from antigenic drift limits the therapeutic benefits of vaccination and antiviral agents in controlling influenza [6, 21, 22] . Thus, development of novel broad-spectrum antiinfluenza strategies is urgently needed. Most botanical polysaccharides are ideal candidates for novel immunomodulatory agents due to their nontoxic properties and fewer side effects compared with bacterially derived polysaccharides. A number of polysaccharides isolated from plant and fungi exhibit effective antiviral benefits against influenza A virus (including H1N1 and H3N2 subtypes) [12] [13] [14] [15] . The use of polysaccharides as immunomodulatory agent in anti-H5N1 studies is rare. In this paper, our data show the immunomodulatory activities of EAP both in vivo and in vitro. EAP treatment elevated the production of IL-6, TNF-, and IFNand provides a survival advantage in H5N1 infected mice. The survival rate following EAP pretreatment (25 mg/kg body
weight) was significantly higher than in mice receiving PBS (50% to 0%).
In previous reports, high levels of proinflammatory cytokines and chemokines (including TNF-, IL-6 and IFN-) were detected during H5N1 infection [23, 24] . This "cytokine storm" leads to the severe respiratory symptoms and host immune injury. Thus, H5N1-induced cytokine storms are hypothesized to be the main cause of mortality, and the use of anti-inflammatory agents may therefore provide a therapeutic effect [25, 26] . However, it is unclear whether the lack of proinflammatory cytokines (such as TNFand IL-6) facilitates viral clearance. Interestingly, knockout 8
Evidence-Based Complementary and Alternative Medicine mice deficient in TNF-, TNF-receptor, IL-6, MIP-1 , and IL-1R or steroid-treated, wild-type mice did not have a survival advantage compared with wild-type mice following H5N1 influenza infection [27, 28] . Interestingly, prophylactic treatment of TLR3 agonist PolyICLC, which strongly upregulates cytokine production, provides protection against H1N1 and H5N1 infections [29, 30] . These conflicting studies may be explained in that the inflammatory response helps clear the virus, while aggravating host pathological damage. Elevated production of cytokines, such as IL-6, TNF-, and IFNare very important for viral clearance in the early stage of infection by activating the innate immune system. Once the viral infection has triggered a cytokine storm due to the high viral load, the inflammatory response causes severe pathological injury or even death. In this case, receiving an immunomodulator alone cannot help animal to survive [25] .
This likely explains why immunomodulator treatment prior to viral infection results in a better survival rate [26, 30] . In our study, treatment of EAP shortly after infection or 24 h postinfection did not provide a survival advantage (data not show).
The antiinfluenza properties of IL-6, TNF-, and IFNhave been discussed in many studies, despite their participation in cytokine storms triggered by influenza infection. IL-6 plays an important role in protecting against influenza A virus as it is required for viral clearance and essential for animal survival [31] . TNF-has been reported to exert a defensive effect against influenza infection in vitro [32] . IFN-treatment in the early stages of influenza infection improves the survival rate in mouse models [33] . In addition, high levels of IFN-secretion stimulated by ginseng polysaccharides provide an antiinfluenza effect in vivo [12] . In this report, intranasal administration of EAP before H5N1 challenge elevates expression of IL-6, TNF-, and IFNcompared with mice receiving PBS. The high levels of these mediators contribute to the viral clearance and antiviral response. Pulmonary viral titers following EAP treatment were lower at day 3 postinfection. In contrast, IL-6 and IFN-mRNA
levels were slightly lower, while TNF-production was significantly lower than that of PBS group. Regarding the excessive inflammation induced by H5N1 virus, massive secretion of mediators contributes to lung injury rather than an antiviral response. Therefore, the timing of EAP treatment as a prophylactic agent is very important.
The immunomodulatory activities of botanical polysaccharides are thought to be mediated by several PRRs [11] . In this study, we examined the mRNA levels of TLR2, TLR4, Dectin-1, and MR after EAP treatment. EAP was found to upregulate Dectin-1 and MR mRNA expressions significantly both in vivo and in vitro. Our hypothesis is that the innate immune recognition of EAP is driven mainly via a Dectin-1 and MR dependent pathway. Binding to these receptors, EAP may activate complex intracellular signaling pathways, and increase cytokine production, leading to an antiviral response. Thus, the protection against H5N1 by EAP treatment is less likely to cause drug resistance, and may represent a broad-spectrum antiinfluenza effect.
In conclusion, our study demonstrates that EAP leaf extract is a prophylactic and immune enhancement agent against H5N1 influenza virus infection. Treatment with EAP effectively inhibits H5N1 viral replication and improves animal survival. This approach offers an alternative strategy for antiinfluenza immunomodulatory agent development, and benefits the utilization of E. adenophorum products.
A 3-year prospective study of the epidemiology of acute respiratory viral infections in hospitalized children in Shenzhen, China

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4181804/

SHA: ef5fe7296ec8baf90d974cf5737af0da3ed403ea

Authors: He, Ying; Lin, Guang-Yu; Wang, Qiong; Cai, Xiao-Ying; Zhang, Yin-Hui; Lin, Chuang-Xing; Lu, Chang-Dong; Lu, Xue-Dong
Date: 2014-05-14
DOI: 10.1111/irv.12257
License: cc-by
Abstract: BACKGROUND: The epidemiology of local viral etiologies is essential for the management of viral respiratory tract infections. Limited data are available in China to describe the epidemiology of viral respiratory infections, especially in small–medium cities and rural areas. OBJECTIVES: To determine the viral etiology and seasonality of acute respiratory infections in hospitalized children, a 3-year study was conducted in Shenzhen, China. METHODS: Nasopharyngeal aspirates from eligible children were collected. Influenza and other respiratory viruses were tested by molecular assays simultaneously. Data were analyzed to describe the frequency and seasonality. RESULTS: Of the 2025 children enrolled in the study, 971 (48·0%) were positive for at least one viral pathogen, in which 890 (91·7%) were <4 years of age. The three most prevalent viruses were influenza A (IAV; 35·8%), respiratory syncytial virus (RSV; 30·5%) and human rhinovirus (HRV; 21·5%). Co-infections were found in
302 cases (31·1%), and dual viral infection was dominant. RSV, HRV and IAV were the most frequent viral agents involved in co-infection. On the whole, the obvious seasonal peaks mainly from March to May were observed with peak strength varying from 1 year to another. CONCLUSIONS: This study provides a basic profile of the epidemiology of acute respiratory viral infection in hospitalized children in Shenzhen. The spectrum of viruses in the study site is similar to that in other places, but the seasonality is closely related to geographic position, different from that in big cities in northern China and neighboring Hong Kong.
Text: Acute respiratory tract infections (ARTIs) are a persistent and pervasive public health problem in both developed and developing countries. They cause a great burden of disease worldwide. Especially in developing countries including China, ARTIs, mainly pneumonia, are the leading cause of death among children under the age of 5 years. 1,2 A great variety of pathogens can cause ARTIs, and viruses have been considered as the predominant pathogens in this children population. 3, 4 The most frequently reported viruses include respiratory syncytial virus (RSV), influenza viruses A and B (IAV, IBV), parainfluenza viruses (PIVs), human rhinovirus (HRV) and adenovirus (ADV), which are responsible for most episodes of ARTIs in children. 1 In the past decade, several new viruses associated with ARTIs such as human metapneumovirus (HMPV), novel strains of coronaviruses (SARS-CoV, HCoV-NL63 and HKUI), human bocavirus (BOV), WU polyomavirus (WUPoyV) and KI polyomavirus (KIPoyV) have been
discovered in human respiratory tract specimens. Among them, some have been identified to be causative pathogens of ARTIs. 1, 4, 5 Currently, there are no approved vaccines or medications available for most of the respiratory viruses. 1 A better understanding of the epidemiology of viral respiratory tract infections in children plays a key role for the prevention, control and treatment of ARTIs. Studies showed that many viral respiratory infections exhibited predictable seasonal variations. However, the epidemiological profiles of viral respiratory infections from different climate zones or different countries in the same climate zone may be varied. [6] [7] [8] [9] [10] [11] [12] China is a large country crossing three climate zones, and great differences in climate are found from region to region. A better understanding of the epidemiology of ARTIs in different regions could be helpful to develop effective surveillance, prevention and treatment strategies. Although some studies on
the epidemiology of ARTIs have recently been reported in big cities such as Beijing, Shanghai and Hong Kong, [13] [14] [15] [16] the epidemic characteristics of viruses in ARTIs are still not well established all around China, especially in other cities and rural areas.
Shenzhen is the largest migratory city of China with high population density and population mobility. It is located in southern China at 22°27 0 -22°52 0 N and 113°46 0 -114°37 0 E, immediately north of Hong Kong, with a typical subtropical monsoon climate. The annual average temperature and relative humidity of Shenzhen are about 23°C (12-33°C) and 77%, respectively. The purpose of this study is to investigate the prevalence, seasonality and clinical characteristics of acute viral respiratory infections in hospitalized children in Shenzhen and to provide insights into etiologies of ARTIs in local infants and children.
A consecutive 3-year prospective study from July 2007 to June 2010 was conducted in Shenzhen, a coastal city neighboring Hong Kong. Four hospitals including a children's hospital were chosen for the study. Selected patients with ARTIs admitted to the pediatric wards were enrolled. The inclusion criteria were as follows: less than 14 years old, acute fever (T ≥ 38°C), with any one of respiratory symptoms (such as sore throat, cough, wheezing and dyspnoea/ tachypnoea), normal or low leukocyte count, the onset of illness within 3 days before hospitalization. The diagnosis of pneumonia was based on the guideline of the management of childhood community acquired pneumonia (CAP) issued by the Chinese Medical Association in 2006. 17 In the guideline, the clinical symptoms and signs for the diagnosis of childhood CAP include fever, cough, tachypnoea (defined according to different age), difficulty breathing and/or lower chest wall indrawing. X-ray evaluation has been carried out when
necessary. The study protocol was approved by the medical ethical committees of the hospitals. Written informed consent was obtained from the parents or legal guardians of the children.
Nasopharyngeal aspirates (NPA) were obtained by trained personnel following standard operating procedures within 24 hour after admission. The specimens were transported immediately to the laboratory by sterile viral transport media, then divided into aliquots and immediately frozen at À80°C until further processing.

Total viral nucleic acids (DNA and RNA) were extracted from 200 ll of NPA specimen using the AxyPrep Body Fluid DNA/RNA Miniprep Kit (Axygen, Union City, CA, USA), according to the manufacturer's instructions. Purified DNA and RNA were stored at À80°C in aliquots for further PCR analysis.
For each specimen, assays for ten common and newly identified viruses were performed. Briefly, WUPoyV and BOV were tested using monoplex PCRs described previously. 18, 19 Other viruses were tested using the Luminex platform and multiplex xTAG TM respiratory viral panel assay (RVP Assay) according to the manufacturer's instructions. 20 All multiple infection samples were retested. If there was discordance between two tests, the sample was confirmed by monoplex PCR.

Statistical Package for the Social Sciences (SPSS) for Windows version 11.0 (SPSS Inc. Chicago, IL, USA) was used. For comparison of categorical data, chi-square or Fisher's exact test was used. All tests were two-tailed, and a P value below 0Á05 was considered statistically significant.
A total of 2025 specimens were obtained from 2025 eligible patients ranging from 15 days to 14 years old with a median age of 12 months, in which 89Á6% of patients were < 4 years old. There were 964 (47Á6%) females and 1061 (52Á4%) males included. Of all hospitalized children enrolled in this study, 84Á0% involved lower respiratory infection and 16Á0% had upper respiratory tract infection (Table 1) . Among 971 positive cases, 572 (58Á9%) were diagnosed as pneumonia.
About 971 of the 2025 cases (48Á0%) were positive for at least one viral pathogen. Among them, IAV, RSV, HRV and PIVs were detected in 348 (35Á8%), 296 (30Á5%), 209 (21Á5%) and 169 (17Á4%) cases, respectively. Single infection was observed in 669 (68Á9%) cases, and multiple infection was found in 302 (31Á1%). Our results also showed that RSV, IAV and HRV were the main pathogens in single viral infection cases ( Table 1) . The monthly positive rates varied from 32Á5% to 75Á0% with a mean of 45Á1% ( Figure 1 ). In the year 2009, when influenza A (H1N1) was pandemic worldwide, the positive rate started to increase in March and the highest positive rate 75Á0% was observed in May.

Among the 971 positive cases, a total of 1335 viral pathogens were detected. The most frequently detected pathogen was IAV (26Á1%, 348/1335), followed by RSV (22Á2%, 296/1335), HRV (15Á7%, 209/1335), PIV1 and PIV3 (12Á7%, 169/1335) (
About 302 co-infection cases were identified, accounting for 14Á9% of all 2025 hospitalized children. During the H1N1 outbreak from March to August 2009, co-infection cases and co-infection rate increased significantly ( Figure 2 ). 143 of 302 (47Á4%) co-infection cases were detected during that time. Among them, 121 cases were involved in IAV infection, including 90 dual infection cases. Of all co-infection cases, 247 (81Á8%), 49 (16Á2%) and 5 (1Á7%) were infected with two, three and four potential viral pathogens, respectively. One multiple infection with five viruses was detected in a RSV  IAV  HRV  BOV  PIV3  ADV  HMPV  WUPoyV  PIV1  IBV  Total   A  Total cases  163  172  85  55  51  49  37  26  24  7  669  Bronchitis  12  19  7  7  5  2  2  3  5  0  62  Bronchiolitis  45  19  20  7  13  9  8  2  5  0  128  Pneumonia  93  97  55  28  24  28  25  18  14  5  387  URTI  13  37  3  13  9  10  2  3  0  2 *Case number and percentage in all enrolled children. **Incidence rate in this age
group significantly higher than the other age groups.
***No significant difference between these three age groups. †No significant differences between these two age groups, but significantly lower than the other age groups. 6-month-old infant. IAV, RSV and HRV were the three most frequently found viruses in co-infection and detected in 176, 133 and 124 cases with co-infection rates of 50Á6%, 44Á9% and 59Á3%, respectively ( Table 2) . Various multiple infection patterns were observed in the study. A total of 152 (50Á3%) co-infection cases involved at least two viruses of RSV, HRV and IAV. Co-infection rate of each individual virus detected varied significantly. The lowest and highest co-infection rates were observed in WUPoyV (33Á3%) and IBV (66Á7%), respectively. 91Á4% (276/302) of co-infection cases were tested in the age group of 4 years old or younger ( Table 2) , but among all age groups, no statistical difference in co-infection rate was found (v 2 = 1Á83, P = 0Á8721). Gender-specific difference in co-infection rate was not observed
(v 2 = 2Á17, P = 0Á1404). There was no significant difference in co-infection rates between PICU and non-PICU cases. Similarly, no significant difference in clinical symptoms was observed between co-infection and single cases (data not shown).
In general, respiratory viruses were detected more often in the period of March to May than in other months (55Á4% and 40Á6%, respectively, v 2 = 28Á06, P = 0Á0000), and obvious seasonal peaks were observed during those months with peak strength varying from 1 year to another. A weaker seasonal peak could also be distinguished in some winter months in different years ( Figure 1) .
The seasonality profile of each individual virus detected was diversified. A seasonal distribution of IAV can be observed from late spring to summer (mainly March to May) and sometimes in fall (October, November or December). A wide seasonal peak of IAV infection was detected from March to August 2009 ( Figure 3A ). Although RSV was tested almost a whole year, two yearly peaks were identified. One was found in November and/or December and the other stronger one was found in March to May of the year. The peak duration in 2009 was longer than those in other years. The seasonal trends of HRV and PIVs were similar to that of RSV, but the peaks of these three viruses fluctuated and shifted mildly ( Figure 3B ). Although IBV and ADV had a low detection rate in the study, similar seasonality was observed and their infection peaks were mainly in midwinter. Peaks in spring and summer were also observed in some years ( Figure 3C ).
Our investigation did not find regular seasonality in BOV infections. A sudden increase in BOV infection was recorded in April and May 2010. Although the positive rate of HMPV infection was only 4Á8%, regular seasonality was observed from March to May of each year. Of 39 patients with WUPoyV infection, 36 were detected after July 2008. Our data implied that peak months of WUPoyV infection were from March to May ( Figure 3D ).

The positive rates of viral infections in male and female were 52Á5% and 47Á5%, respectively. No significant gender difference was revealed (v 2 = 0Á012, P = 0Á9118). The distribution of viral agents and infection patterns in different age groups are shown in Table 2 .
Of all 971 positive children, 890 (91Á7%) were 4 years old or younger. The positive rate in this age group was significantly higher than that in children more than 4 years old (v 2 = 8Á26, P = 0Á0041). Children under 6 months were the most susceptible to respiratory viral pathogens with a positive rate of 14Á8% (Table 2) .

Very few long-term prospective studies were performed for viral etiologies of ARTIs among hospitalized children. In this present study, the infection frequency, seasonality, co-infection pattern and clinical features of viral respiratory infections were investigated based on prospective analysis of three consecutive year's data from hospitalized children with ARTIs. Our results provided a distinctive epidemiological profile of viral respiratory infections in hospitalized children with ARTIs in the study areas, which was different from those in the big cities in northern China such as Beijing and Shanghai and also different from that in adjacent Hong Kong.