Characterisation of SARS-CoV-2 variants in Beijing during 2022: an epidemiological and phylogenetic analysis.

BACKGROUND: Due to the national dynamic zero-COVID strategy in China, there were no persistent local transmissions of SARS-CoV-2 in Beijing before December, 2022. However, imported cases have been frequently detected over the past 3 years. With soaring growth in the number of COVID-19 cases in China recently, there are concerns that there might be an emergence of novel SARS-CoV-2 variants. Routine surveillance of viral genomes has been carried out in Beijing over the last 3 years. Spatiotemporal analyses of recent viral genome sequences compared with that of global pooled and local data are crucial for the global response to the ongoing COVID-19 pandemic. METHODS: We routinely collected respiratory samples covering both imported and local cases in Beijing for the last 3 years (of which the present study pertains to samples collected between January and December, 2022), and then randomly selected samples for analysis. Next-generation sequencing was used to generate the SARS-CoV-2 genomes. Phylogenetic and population dynamic analyses were performed using high-quality complete sequences in this study. FINDINGS: We obtained a total of 2994 complete SARS-CoV-2 genome sequences in this study, among which 2881 were high quality and were used for further analysis. From Nov 14 to Dec 20, we sequenced 413 new samples, including 350 local cases and 63 imported cases. All of these genomes belong to the existing 123 Pango lineages, showing there are no persistently dominant variants or novel lineages. Nevertheless, BA.5.2 and BF.7 are currently dominant in Beijing, accounting for 90% of local cases since Nov 14 (315 of 350 local cases sequenced in this study). The effective population size for both BA.5.2 and BF.7 in Beijing increased after Nov 14, 2022. INTERPRETATION: The co-circulation of BF.7 and BA.5.2 has been present in the current outbreak since Nov 14, 2022 in Beijing, and there is no evidence that novel variants emerged. Although our data were only from Beijing, the results could be considered a snapshot of China, due to the frequent population exchange and the presence of circulating strains with high transmissibility. FUNDING: National Key Research and Development Program of China and Strategic Priority Research Program of the Chinese Academy of Sciences. TRANSLATION: For the Chinese translation of the abstract see Supplementary Materials section.

Major changes in prevalence and genotypes of rotavirus diarrhea in Beijing, China after RV5 rotavirus vaccine introduction.

To analyze the epidemiological characteristics of group A rotavirus (RVA) diarrhea in Beijing between 2019 and 2022 and evaluate the effectiveness of the RV5 vaccine. Stool specimens were collected from patients with acute diarrhea, and RVA was detected and genotyped. The whole genome of RVA was sequenced by fragment amplification and Sanger sequencing. Phylogenetic trees were constructed using Bayesian and maximum likelihood methods. Descriptive epidemiological methods were used to analyze the characteristics of RVA diarrhea. Test-negative design was used to evaluate the vaccine effectiveness (VE) of the RV5. Compared with 2011-2018, RVA-positive rates in patients with acute diarrhea under 5 years of age and adults decreased significantly between 2019 and 2022, to 9.45% (249/634) and 3.66% (220/6016), respectively. The predominant genotype of RVA had changed from G9-VIP[8]-III between 2019 and 2021 to G8-VP[8]-III in 2022, and P[8] sequences from G8-VP[8]-III strains formed a new branch called P[8]-IIIb. The complete genotype of G8-VP[8]-III was G8-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2. The VE of 3 doses of RV5 was 90.4% (95% CI: 28.8%-98.7%) against RVA diarrhea. The prevalence of RVA decreased in Beijing between 2019 and 2022, and the predominant genotype changed to G8P[8], which may be related to RV5 vaccination. Continuous surveillance is necessary to evaluate vaccine effectiveness and improve vaccine design.

Epidemiological features, genomic characteristics, and origin tracing of the COVID-19 outbreaks in Beijing from January to September 2022.

Different variants of severe acute respiratory syndrome coronavirus 2 have been discovered globally. At present, the Omicron variant has been extensively circulated worldwide. There have been several outbreaks of the Omicron variant in China. Here, we investigated the epidemiologic, genetic characteristics, and origin-tracing data of the outbreaks of COVID-19 in Beijing from January to September 2022. During this time, 19 outbreaks occurred in Beijing, with the infected cases ranging from 2 to 2230. Two concern variants were detected, with eight genotypes. Based on origin tracing analysis, two outbreaks were from the cold-chain transmission and three from items contaminated by humans. Imported cases have caused other outbreaks. Our study provided a detailed analysis of Beijing's outbreaks and valuable information to control the outbreak's spread.

Stability of SARS-CoV-2 and persistence of viral nucleic acids on common foods and widely used packaging material surfaces.

SARS-CoV-2 is still spreading globally. Studies have reported the stability of SARS-CoV-2 in aerosols and on surfaces under different conditions. However, studies on the stability of SARS-CoV-2 and viral nucleic acids on common food and packaging material surfaces are insufficient. The study evaluated the stability of SARS-CoV-2 using TCID50 assays and the persistence of SARS-CoV-2 nucleic acids using droplet digital polymerase chain reaction on various food and packaging material surfaces. Viral nucleic acids were stable on food and material surfaces under different conditions. The viability of SARS-CoV-2 varied among different surfaces. SARS-CoV-2 was inactivated on most food and packaging material surfaces within 1 day at room temperature but was more stable at lower temperatures. Viruses survived for at least 1 week on pork and plastic at 4°C, while no viable viruses were detected on hairtail, orange, or carton after 3 days. There were viable viruses and a slight titer decrease after 8 weeks on pork and plastic, but titers decreased rapidly on hairtail and carton at -20°C. These results highlight the need for targeted preventive and disinfection measures based on different types of foods, packaging materials, and environmental conditions, particularly in the cold-chain food trade, to combat the ongoing pandemic.

Phylogenetics and phylogeographic characteristics of coxsackievirus A16 in hand foot and mouth disease and herpangina cases collected in Beijing, China from 2019 to 2021.

Coxsackievirus A16 (CV-A16) is a significant pathogen responsible for causing hand foot and mouth disease (HFMD) and herpangina (HA). This study aimed to investigate the recent evolution and spread of CV-A16 by monitoring HFMD and HA cases in 29 hospitals across 16 districts in Beijing from 2019 to 2021. The first five cases of HFMD and the first five cases of HA each month in each hospital were included in the study. Real-time reverse transcription polymerase chain reaction was used to identify CV-A16, CV-A6, and EV-A71. From each district, two to four CV-A16 positive samples with a relatively long sampling time interval every month were selected for sequencing. A total of 3344 HFMD cases and 2704 HA cases were enrolled in this study, with 76.0% (2541/3344) of HFMD and 45.4% (1227/2704) of HA cases confirmed to be infected by enterovirus. Among the EV-positive samples, CV-A16 virus was detected in 33.61% (854/2541) of HFMD cases and 13.4% (165/1227) of HA cases, with the predominant cluster being B1a. Both B1a and B1b had a co-circulation of local and imported strains, with different origin time (1993 vs. 1995), different global distribution (14 countries vs. 10 countries), and different transmission centers but mainly distributed in the southern and eastern regions of Beijing. Strengthening surveillance of HFMD in southern and eastern regions will improve the prevention and control efficiency of enterovirus infections.

Stability of mpox virus on different commonly contacted surfaces.

Mpox is still spreading globally and is mostly reported to be transmitted by skin and mucosal contact. However, transmission through contact with fomites, contaminated objects, or surfaces has been reported in general population. Evaluation of the stability of mpox virus (MPXV) on different surfaces is important to minimize mpox transmission. In the study, the stability of MPXV on different kinds of commonly contacted surfaces was determined. MPXV was observed to have a surface-dependent stability pattern. Viable virus was detected on both glass and stainless steel for up to 5 days, and on plastic surfaces for up to 3 days. In contrast, no viable MPXV was detected on wooden board and cardboard, which are porous and water-absorbent surfaces, after 1 and 2 days of incubation, respectively. In addition, MPXV nucleic acids were more stable and showed better correlation with viral titers on stainless steel, plastic, and glass. The results indicate that fomite transmission of MPXV is plausible. Moreover, the stability of MPXV was highly surface-dependent and more stable on smooth surfaces, which could provide more information for minimizing the transmission of mpox and emphasize the significance of environmental disinfection in mpox prevention and control.

Transmissibility quantification of norovirus outbreaks in 2016-2021 in Beijing, China.

The transmissibility is a crucial feature for norovirus, yet its quantitative estimation has been limited. Our objective was to estimate the basic reproduction number (R0 ) of norovirus and investigate its variation characteristics. Norovirus outbreaks reported from September 2016 to August 2021 in Beijing were analyzed. The susceptible-infected-removed compartment model was established to estimate R0 . Linear regression models and logistic regression models were used to explore the factors affecting the transmissibility of norovirus. The overall median R0 of norovirus was estimated as 2.1 (interquartile range [IQR] 1.8-2.5), with 650 norovirus outbreaks. The transmissibility of norovirus varied by year, outbreak setting and genotype. The R0 of norovirus during September 2019 to August 2020 (median 2.1, IQR 1.8-2.4) and September 2020 to August 2021 (median 2.0, IQR 1.7-2.3) was lower than that of September 2016 to August 2017 (median 2.3, IQR 1.8-2.7) (ß = 0.94, p = 0.05; ß = 0.93, p = 0.008). The R0 of norovirus for all other settings was lower than that for kindergarten (median 2.4, IQR 2.0-2.9) (primary school: median 2.0, IQR 1.7-2.4, ß = 0.94, p = 0.001; secondary school: median 1.7, IQR 1.5-2.0, ß = 0.87, p < 0.001; college: median 1.7, IQR 1.5-1.8, ß = 0.89, p = 0.03; other closed settings: median 1.8, IQR 1.5-2.0, ß = 0.90, p = 0.004). GⅡ.2[P16] outbreaks had a median R0 of 2.2 (IQR 1.8-2.7), which was higher than that for GⅡ.6[P7] outbreaks (median 1.8, IQR: 1.8-2.0, odds ratio = 0.19, p = 0.03; GⅡ.2[P16] as reference) and mixed-genotype outbreaks (median 1.7, IQR: 1.5-1.8, ß = 0.92, p = 0.02; mixed-genotype as reference). In kindergartens and primary schools, norovirus shows increased transmissibility, emphasizing the vulnerable population and high-risk settings. Furthermore, the transmissibility of norovirus may change over time and with virus evolution, necessitating additional research to uncover the underlying mechanisms.

Clinical characteristics of abruptly increased paediatric patients with Omicron BF.7 or BA.5.2 in Beijing.

BACKGROUND: The coronavirus disease 2019 outbreak has hit Beijing since mid-Nov, 2022, with soaring growth of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among children. Therefore, it is vital to determine the clinical manifestations of epidemic SARS-CoV-2 strains in paediatric patients. METHODS: In this study, nucleic acid tests (NATs) for SARS-CoV-2 were performed in paediatric outpatients with symptoms of acute respiratory tract infection during 18 Nov-6 Dec, 2022. Half of the outpatients positive for SARS-CoV-2 were randomly selected to screen for other respiratory pathogens, whereas those with low cycle threshold values in SARS-CoV-2 NATs were amplified and sequenced to determine the SARS-CoV-2 variants. Finally, children positive for SARS-CoV-2 with clinical information in detail were enrolled in a follow-up study to identify potential factors significantly associated with long recovery. RESULTS: Among 9625 paediatric outpatients tested for nucleic acid of SARS-CoV-2, 733 (7.62%, 733/9625) were identified as SARS-CoV-2 NAT positive, with only three (0.82%, 3/366) co-infected with other pathogens among 366 randomly selected patients, and 71 (62.83%) determined as Omicron subvariant BF.7 and 42 (37.22%) as BA.5.2 among 113 successfully sequenced. Among the 681 patients with complete clinical information, fever was the most common symptom (96.8%). In a follow-up study of 592 patients, 46.96% became asymptomatic on the third day and 65.71% on the fifth day. Only 1.7% of infected children experienced febrile seizures. Combined with abnormal C-reactive protein, a higher percentage of antibiotics administration was observed. More co-living members and longer duration of first symptoms served as independent risk factors for long-term recovery, especially in children vaccinated for SARS-CoV-2. CONCLUSIONS: BF.7 and BA.5.2 were the dominate Omicron subvariants and caused milder infections during the SARS-CoV-2 outbreak in Beijing. The number of co-living members and duration of first symptoms were independent risk factors for long-term recovery.

Spatio-temporal distribution and influencing factors of norovirus outbreaks in Beijing, China from 2016 to 2020.

BACKGROUND: Noroviruses are a leading cause of acute gastroenteritis (AGE) worldwide. The geographical characteristics of norovirus outbreaks in Beijing and their influencing factors remain unknown. This study aimed to explore the spatial distributions, geographical characteristics, and influencing factors of norovirus outbreaks in Beijing, China. METHODS: Epidemiological data and specimens were collected through the AGE outbreak surveillance system in all 16 districts of Beijing. Data on spatial distribution, geographical characteristics, and influencing factors of norovirus outbreaks were analyzed using descriptive statistics methods. We measured spatial, geographical clustering of high- or low-value deviance from random distribution using Z-scores and P-values as statistical significance measures with Global Moran's I statistics and Getis-Ord Gi in ArcGIS. Linear regression and correlation methods were used to explore influencing factors. RESULTS: Between September 2016 and August 2020, 1,193 norovirus outbreaks were laboratory-confirmed. The number of outbreaks varied seasonally, typically peaking in spring (March to May) or winter (October to December). Outbreaks primarily occurred around central districts at the town level, and spatial autocorrelation was evident in both the entire study period and in individual years. Hotspots of norovirus outbreaks in Beijing were primarily found in contiguous areas between three central districts (Chaoyang, Haidian, Fengtai) and four suburban districts (Changping, Daxing, Fangshan, Tongzhou). The average population numbers, mean number of all schools, and mean number of kindergartens and primary schools for towns in central districts and hotspot areas were higher than those in suburban districts and non-hotspot areas respectively. Additionally, population numbers and densities of kindergartens and primary schools were influencing factors at the town level. CONCLUSIONS: Hotspots of norovirus outbreaks in Beijing were in contiguous areas between central and suburban districts with high populations, and high kindergarten and primary school densities were the likely driving forces. Outbreak surveillance needs to focus on contiguous areas between central and suburban districts with increased monitoring, medical resources, and health education.

The First Human Infection Case of Macacine Alphaherpesvirus 1 Virus in China.

BACKGROUND: Macacine alphaherpesvirus 1 (BV) was first reported in the 1930s and only about 60 cases have been diagnosed since then. METHODS: A 53-year-old male who worked as a veterinary surgeon, developed a fever with nausea and vomiting in April 2021 in Beijing, China. Real-time polymerase chain reaction (PCR) and metagenomics Next Generation Sequencing (mNGS) were used for diagnosis. RESULTS: BV DNA was confirmed by mNGS and PCR. The case died 51 days after onset, due to the damage to the brain and spinal cord caused by a viral infection and hypoxic-ischemic encephalopathy. The typical BV inclusion bodies in the brain were found for the first time. CONCLUSIONS: Here we reported the first human infection case of BV in China. This fatal case highlights the potential threat of BV to occupational workers and the essential role of surveillance.

Using an influenza surveillance system to estimate the number of SARS-CoV-2 infections in Beijing, China, weeks 2 to 6 2023.

With COVID-19 public health control measures downgraded in China in January 2023, reported COVID-19 case numbers may underestimate the true numbers after the SARS-CoV-2 Omicron wave. Using a multiplier model based on our influenza surveillance system, we estimated that the overall incidence of SARS-CoV-2 infections was 392/100,000 population in Beijing during the 5 weeks following policy adjustment. No notable change occurred after the Spring Festival in early February. The multiplier model provides an opportunity for assessing the actual COVID-19 situation.

Comparison of four commercial RT-PCR diagnostic kits for COVID-19 in China.

We compared the sensitivity and specificity of four commercial coronavirus disease (COVID-19) diagnostic kits using real-time reverse transcription-polymerase chain reaction (RT-PCR). Kits I-IV approved by the State Drug Administration of China were selected, and the detection targets were ORF1ab gene and N gene. Specificity was evaluated by detecting other respiratory viruses. The sensitivity and batch effect of each kit were evaluated by testing 10-fold dilutions of RNA. Clinical application was verified by testing nasopharyngeal swab and sputum specimens from COVID-19 patients. Among the 78 cases infected by other respiratory viruses, no amplification curve was observed using these four COVID-19 RT-PCR kits. The minimum detection limits of kits I-IV were 10-6 , 10-5 , 10-5 , and 10-6 dilutions, respectively, and concentrations were 10 copies/mL (10-5 dilution) and 1 copies/mL (10-6 dilution). The sensitivities of kits I-IV detected using 142 nasopharyngeal swab specimens from COVID-19 patients were 91.55%, 81.69%, 80.28%, and 90.85%, respectively, while they were 92.68%, 85.37%, 82.93%, and 93.90%, respectively, for the 82 sputum samples. The specificity of each kit was 100.00% (77/77). The total expected detection rate using sputum samples was 88.59% (691/780) higher than 86.15% (672/780) of nasopharyngeal swabs. Comparison of nasopharyngeal swab and sputum samples from the same COVID-19 patient led to the detection of ORF1ab and N genes in 16 (100%) sputum samples; only ORF1ab and N genes were detected in 12 (75%) and 14 (87.5%) nasopharyngeal swab specimens, respectively. In conclusion, comparison of commercial COVID-19 RT-PCR kits should be performed before using a new batch of such kits in routine diagnostics.

Potential False-Negative Nucleic Acid Testing Results for Severe Acute Respiratory Syndrome Coronavirus 2 from Thermal Inactivation of Samples with Low Viral Loads.

BACKGROUND: Coronavirus disease-2019 (COVID-19) has spread widely throughout the world since the end of 2019. Nucleic acid testing (NAT) has played an important role in patient diagnosis and management of COVID-19. In some circumstances, thermal inactivation at 56°C has been recommended to inactivate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) before NAT. However, this procedure could theoretically disrupt nucleic acid integrity of this single-stranded RNA virus and cause false negatives in real-time polymerase chain reaction (RT-PCR) tests. METHODS: We investigated whether thermal inactivation could affect the results of viral NAT. We examined the effects of thermal inactivation on the quantitative RT-PCR results of SARS-CoV-2, particularly with regard to the rates of false-negative results for specimens carrying low viral loads. We additionally investigated the effects of different specimen types, sample preservation times, and a chemical inactivation approach on NAT. RESULTS: Our study showed increased Ct values in specimens from diagnosed COVID-19 patients in RT-PCR tests after thermal incubation. Moreover, about half of the weak-positive samples (7 of 15 samples, 46.7%) were RT-PCR negative after heat inactivation in at least one parallel testing. The use of guanidinium-based lysis for preservation of these specimens had a smaller impact on RT-PCR results with fewer false negatives (2 of 15 samples, 13.3%) and significantly less increase in Ct values than heat inactivation. CONCLUSION: Thermal inactivation adversely affected the efficiency of RT-PCR for SARS-CoV-2 detection. Given the limited applicability associated with chemical inactivators, other approaches to ensure the overall protection of laboratory personnel need consideration.

Basic epidemiological parameter values from data of real-world in mega-cities: the characteristics of COVID-19 in Beijing, China.

BACKGROUND: With the spread of SARS-CoV-2 worldwide, understanding the basic epidemiological parameter values of COVID-19 from real-world data in mega-cities is essential for disease prevention and control. METHODS: To investigate the epidemiological parameters in SARS-CoV-2 infected cases in Beijing, we studied all confirmed cases and close contacts in Beijing from Jan 1st to Apr 3rd 2020. The epidemiological and virological characteristics of SARS-CoV-2 were analyzed. RESULTS: A total of 602 cases were positive for SARS-CoV-2, including 585 confirmed patients and 17 asymptomatic infections. The imported cases were mainly from Wuhan initially and then from abroad. Among 585 confirmed case-patients, the median age was 39 years old. The mean incubation period was 6.3 days. The secondary attack rate among households was higher than social contacts (15.6 vs 4.6%). The secondary attack rate of healthcare workers (HCWs) was higher than non-HCWs' (7.3 vs 4.2%). The basic reproduction number was 2.0, and the average serial interval was 7.6 days. No significant genetic variant was identified. CONCLUSIONS: The transmissibility of SARS-CoV-2 was relatively high, especially among households and from HCWs, which draws specific public health attention. So far, no evidence of widespread circulation of SARS-CoV-2 in communities in Beijing was found.

An outbreak of acute respiratory infection at a training base in Beijing, China due to human adenovirus type B55.

BACKGROUND: Twelve students experienced symptoms of acute respiratory infection (ARI) at a training base in Beijing from August 26 to August 30, 2015. We investigated the cause of this ARI outbreak. METHODS: In partnership with the local center for disease control, we collected a total of twelve pharyngeal swab specimens as well as demographic information for the affected patients. We used multiplex real-time PCR to screen for sixteen common respiratory viruses in these samples. To isolate HAdV, we inoculated Hep-2 cells with the human adenovirus (HAdV)-positive samples and then carried out sequencing and phylogenetic analysis of the hexon, fiber, and penton genes of the isolated adenoviruses. In addition, we analyzed the entire genome of one strain isolated from the index case to identify single-nucleotide substitutions. RESULTS: We identified ten HAdV-positive students using multiplex real-time PCR. None of the students were co-infected with other viruses. We successfully isolated seven HAdV strains from the pharyngeal swab specimens. The coding sequences of the hexon, fiber, and penton genes of these seven HAdV strains were identical, suggesting that they represented seven strains from a single virus clone. One HAdV isolate obtained from the index case, BJDX-01-2015, was selected for whole genome analysis. From this isolate, we obtained a 34,774-nucleotide sequence. The genome of BJDX-01-2015 clustered with HAdV-B55 in phylogenetic analyses and had 99.97% identity with human adenovirus 55 isolate HAdV-B/CHN/BJ01/2011/55 (GenBank accession no. JX491639). CONCLUSIONS: We identified HAdV-B55 as the strain associated with the August 2015 ARI outbreak at a training base in Beijing. This was the first reported outbreak in Beijing due to HAdV-B55. Continuous surveillance of respiratory adenoviruses is urgently needed to understand the epidemiological and evolutionary features of HAdV-B55, and an epidemiological modeling approach may provide further insights into this emerging public health threat. Furthermore, the clinical laboratory data from this outbreak provides important reference for the clinical diagnosis and may ultimately aid in informing the development of strategies to control and prevent respiratory tract infections caused by HAdV-B55.

Contamination by respiratory viruses on outer surface of medical masks used by hospital healthcare workers.

BACKGROUND: Medical masks are commonly used in health care settings to protect healthcare workers (HCWs) from respiratory and other infections. Airborne respiratory pathogens may settle on the surface of used masks layers, resulting in contamination. The main aim of this study was to study the presence of viruses on the surface of medical masks. METHODS: Two pilot studies in laboratory and clinical settings were carried out to determine the areas of masks likely to contain maximum viral particles. A laboratory study using a mannequin and fluorescent spray showed maximum particles concentrated on upper right, middle and left sections of the medical masks. These findings were confirmed through a small clinical study. The main study was then conducted in high-risk wards of three selected hospitals in Beijing China. Participants (n = 148) were asked to wear medical masks for a shift (6-8 h) or as long as they could tolerate. Used samples of medical masks were tested for presence of respiratory viruses in upper sections of the medical masks, in line with the pilot studies. RESULTS: Overall virus positivity rate was 10.1% (15/148). Commonly isolated viruses from masks samples were adenovirus (n = 7), bocavirus (n = 2), respiratory syncytial virus (n = 2) and influenza virus (n = 2). Virus positivity was significantly higher in masks samples worn for > 6 h (14.1%, 14/99 versus 1.2%, 1/49, OR 7.9, 95% CI 1.01-61.99) and in samples used by participants who examined > 25 patients per day (16.9%, 12/71 versus 3.9%, 3/77, OR 5.02, 95% CI 1.35-18.60). Most of the participants (83.8%, 124/148) reported at least one problem associated with mask use. Commonly reported problems were pressure on face (16.9%, 25/148), breathing difficulty (12.2%, 18/148), discomfort (9.5% 14/148), trouble communicating with the patient (7.4%, 11/148) and headache (6.1%, 9/148). CONCLUSION: Respiratory pathogens on the outer surface of the used medical masks may result in self-contamination. The risk is higher with longer duration of mask use (> 6 h) and with higher rates of clinical contact. Protocols on duration of mask use should specify a maximum time of continuous use, and should consider guidance in high contact settings. Viruses were isolated from the upper sections of around 10% samples, but other sections of masks may also be contaminated. HCWs should be aware of these risks in order to protect themselves and people around them.

Viral and bacterial upper respiratory tract infection in hospital health care workers over time and association with symptoms.

BACKGROUND: Bacterial colonisation of the respiratory tract is commonly described and usually thought to be of no clinical significance. The aim of this study was to examine the presence and significance of bacteria and viruses in the upper respiratory tract of healthcare workers (HCWs), and association with respiratory symptoms. METHODS: A prospective cohort study was conducted in China and 223 HCWs were recruited from fever clinics and respiratory, paediatric, emergency/Intensive medication wards. Participants were followed over 4 weeks (7th May 2015 to 4th June 2015) for development of clinical respiratory illness (CRI). Nasopharyngeal swabs were obtained at baseline and at the end of the study. The primary endpoints were laboratory-confirmed bacterial colonisation and viral respiratory infection. Rates of the following infections in symptomatic and asymptomatic participants were compared at the start or end of the study; 1) all bacterial/viral infections, 2) bacterial infection and bacterial-viral co-infections, excluding virus only infections, and 3) only bacterial infections. RESULTS: Bacterial colonisation was identified in 88% (196/223) of participants at the start or end of the study. Among these participants, 66% (148/223) had only bacterial colonisation while 22% (48/223) had co-infection with a virus. Bacteria were isolated from 170 (76.2%) participants at baseline and 127 (57%) participants at the end of the study. Laboratory confirmed viral infections were identified in 53 (23.8%) participants - 35 (15.7%) at the baseline and 20 (9.0%) at the end of the study. CRI symptoms were recorded in 12 participants (4.5%) and all had a positive bacterium isolation at baseline (n = 11) or end of the study (n = 1). Among asymptomatic participants, 187 (87%) had bacterial colonisation or bacterial/viral co-infection at baseline or end of the study. Viruses were also isolated from 5 (2.4%) asymptomatic cases. Rates of all infection outcomes were higher in symptomatic participants, however differences were not statistically significant. CONCLUSION: We isolated high rates of bacteria and viruses in the upper respiratory tract of hospital HCWs, which may reflect greater exposure to respiratory infections in the hospital. Although respiratory infections are mostly symptomatic, the association between bacterial colonization and symptomatic illness is not clear. In the healthcare setting, HCWs may acquire and transmit infection to patients and other HCWs around them. Larger studies are required to explore ongoing occupational risk of respiratory infection in hospitals HCWs.

Estimated burden of group a streptococcal pharyngitis among children in Beijing, China.

BACKGROUND: Burden of Group A streptococcus (GAS) pharyngitis is scarce in developing countries, still unknown in China. The objective of this study was to determine the incidence of clinical cases of pharyngitis and GAS culture-positive pharyngitis, and their outpatient visits among children aged 0-14 years in Beijing, the capital of China. METHODS: Multiplier model was used to estimate the numbers of pharyngitis cases, based on reported numbers of clinical cases and GAS culture-positive rates from GAS surveillances in Beijing, consultation rate, population coverage of GAS surveillances, sampling success rate, and test sensitivity of GAS culture from previous studies, surveys and surveillances. RESULTS: An average of 29804.6 (95 % CI: 28333.2-31276.0) clinical cases of pharyngitis per 100,000 person-years occurred among children aged 0-14 years, resulting in correspondingly 19519.0 (95 % CI: 18516.7-20521.2) outpatient visits per 100,000 person-years from 2012 to 2014 in Beijing. On average, there were 2685.1 (95 % CI: 2039.6-3330.6) GAS culture-positive cases of pharyngitis and 1652.7 (95 % CI: 1256.5-2049.0) outpatient visits per 100,000 person-years during the same period. The estimated burden of GAS pharyngitis was significantly higher than that of scarlet fever. Children aged 5-14 years had a higher burden of GAS pharyngitis than those aged 0-4 years. CONCLUSIONS: The present data suggests that GAS pharyngitis is very common in children in China. Further studies and surveillances are needed to monitor trends and the effectiveness of control measures.

Do corticosteroids reduce the mortality of influenza A (H1N1) infection? A meta-analysis.

INTRODUCTION: Corticosteroids are used empirically in influenza A (H1N1) treatment despite lack of clear evidence for effective treatment. This study aims to assess the efficacy of corticosteroids treatment for H1N1 infection. METHODS: Systematic review and meta-analysis were used to estimate the efficacy of corticosteroids for the prevention of mortality in H1N1 infection. Databases searched included MEDLINE, EMBASE, PubMed, Cochrane Central Register of Controlled Clinical Trials and so on, and bibliographies of retrieved articles, from April 2009 to October 2014. We included both cohort studies and case-control studies reported in English or Chinese that compared treatment effects between corticosteroids and non-corticosteroids therapy in inpatients with H1N1 virus infection. Cohort studies employed mortality as outcome, and case-control studies employed deaths as cases and survivors as controls; both were assessed in this meta-analysis. RESULTS: In total twenty-three eligible studies were included. Both cohort studies (nine studies, n = 1,405) and case-control studies (14 studies, n = 4,700) showed a similar trend toward increased mortality (cohort studies relative risk was 1.85 with 95% confidence interval (CI) 1.46 to 2.33; case-control studies odds ratio was 4.22 with 95% CI 3.10 to 5.76). The results from both subgroup analyses and sensitive analyses were consistent with each other, showing that steroid treatment is associated with mortality. However, considering the fact that corticosteroids were tend to be used in sickest case-patients and heterogeneity was observed between studies, we cannot make a solid conclusion. CONCLUSIONS: Available evidence did not support the use of corticosteroids as standard care for patients with severe influenza. We conclude that further research is required.

Genetic variation in the hemagglutinin of A(H1N1) 09pdm and A(H3N2) influenza viruses in the Beijing area from 2009 to 2014.

BACKGROUND: A(H1N1) 09pdm and A(H3N2) influenza viruses are the main cause of occasional influenza pandemics and seasonal influenza epidemics around the world. Unfortunately, the understanding of long-term genetic variation in these viruses remains limited. METHODS: In this study, hemagglutinin genes from 90 A(H1N1) 09pdm and 48 A(H3N2) influenza viruses in the Beijing area from 2009 to 2014 were sequenced and analyzed. RESULTS: The hemagglutinin genes in A(H1N1) 09pdm and A(H3N2) shared nucleotide similarity that ranged from 93.06% - 99.88% and 98.68% - 99.29%, respectively, compared with current vaccine strains. 10 and 7 amino acid mutations in antigenic sites were identified in these two strains, respectively. In addition, a new site 177 glycosylation, which did not exist in previous circulating strains, was identified in 3 A(H1N1) 09pdm isolates. CONCLUSIONS: This study demonstrated the continued evolution of seasonal influenza viruses in the Beijing area, indicating that an update of the vaccine is needed, especially for A(H1N1) 09pdm influenza virus.