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A total of 445 nasopharyngeal swab specimens from FRS patients with available clinical information were analyzed. Overall, 265 (59.55%) of the patients were male and 180 (40.45%) were female. The median age was 16 years [interquartile range (IQR)3-61]. The patients were divided into six age groups: (0-1)-year-old, (1-5)-year-old, (5-18)-year-old, (18-40)-year-old, (40-65)-year-old, and ≥ 65-year-old. The number of people in each age group was 77, 70, 80, 60, 68, and 90, respectively.
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No pathogens were detected in 220 (49%) samples, while 147 (38%) of the specimens showed single infections, 53 (12%) showed viral-viral co-infections, and 25 (6%) of the specimens were viral-bacterial co-infections (Figure 1A). The positive detection rate in females was 53.33% (96/180), while it was 48.68% (129/265) in males, which did not differ significantly (P= 0.3346). Similarly, the positive detection rate in different age groups was diverse, but these differences were not statistically significant (P= 0.2124) (Table 1).
Figure 1. The etiology characteristics of acute febrile respiratory syndrome in Qinghai. (A) Detection rate of single infection or co-infections in 445 respiratory samples. The color pie chart represents the rate of any pathogen detection, and the gray part represents the rate of no-pathogen detection. (B) The numbers of single infection and co-infections for individual respiratory pathogen. (C) Distribution of the AFRS cases from January to December.
Table 1. Distribution of Virus in Different Groups
Virus Gender* Age-group* (y) Totol (N = 445) F (n = 180) M (n = 265) 0-1 (n = 77) 1-5 (n = 70) 5-18 (n = 80) 18-40 (n = 60) 40-65 (n = 68) > 65 (n = 90) IFV 68 (42.50) 55 (39.86) 25 (47.17) 7 (21.21) 17 (34.69) 25 (42.37) 23 (47.92) 26 (46.43) 123 (41.28) HCoVs 17 (10.63) 19 (13.77) 4 (7.55) 1 (3.03) 2 (4.08) 12 (20.34) 8 (16.67) 9 (16.07) 36 (12.08) PIVs 13 (8.13) 15 (10.87) 7 (13.21) 10 (30.30) 2 (4.08) 3 (5.08) 2 (4.17) 4 (7.14) 28 (9.40) RSV 4 (2.50) 6 (4.35) 2 (3.77) 1 (3.03) 2 (4.08) 3 (5.08) 1 (2.08) 1 (1.79) 10 (3.36) hMPV 2 (1.25) 0 (0.00) 0 (0.00) 0 (0.00) 0 (0.00) 0 (0.00) 0 (0.00) 2 (3.57) 2 (0.67) AdV 32 (20.00) 24 (17.39) 10 (18.87) 5 (15.15) 18 (36.73) 9 (15.25) 10 (20.83) 4 (7.14) 56 (18.79) EV/RV 17 (10.63) 16 (11.59) 2 (3.77) 4 (12.12) 7 (14.29) 7 (11.86) 4 (8.33) 9 (16.07) 33 (11.07) HBoV 7 (4.38) 3 (2.17) 3 (5.66) 5 (15.15) 1 (2.04) 0 (0.00) 0 (0.00) 1 (1.79) 10 (3.36) totol 160 (100) 138 (100) 53 (100) 33 (100) 49 (100) 59 (100) 48 (100) 56 (100) 298 (100) Fisher's 1.52 × 106 3.52 × 10-33 Exact values 0.7008 0.0001 Note.*: Values are shown as No.(%). IFV: influenza; HCoV: human coronavirus; PIV: parainfluenza virus; RSV: respiratory syncytial virus; hMPV: human metapneumovirus; AdV: adenovirus; EV/RV: enterovirus/rhinovirus; HBoV: human bocavirus. Overall, 329 pathogens were detected, among which 298 (90.58%) were viruses and 31 (9%) were bacteria. Among the viruses, influenza virus (IFV) was most commonly detected, with a proportion of 41.28% (123/298), followed by AdV with a proportion of 18.79% (56/298) (Figure 1B, Table 1). Among IFV infections, the most commonly detected virus was IFV-A (118/123), followed by IFV-B (3/123) and IFV-A (H1N1) pdm09 (2/123). Among the bacteria, 28 were identified as M. pneu, 2 were B. pert, 1 was L. pneu, and C. pneu was not detected. Among all of the pathogens, IFV, AdV, HCoVs, RV/EV, PIVs, and M. pneu were in the top of five, with detection rates of 37.38% (123/329), 17.02% (56/329), 10.94% (36/329), 10.03% (33/329), 8.51% (28/329), and 8.51% (28/329), respectively.
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The distribution of respiratory viruses among groups is shown in Table 2. The proportion of viruses differed between males and females, but the difference was not statistically significant (P= 0.7008). The most commonly detected viruses in males and females were IFV, AdV, HCoVs, and EV/RV, while two positive hMPV infections were detected in the male group.
Table 2. Distribution of Co-infection
Group Virus NO.* Virus NO.* Dual Infections (n = 62) Inter- AdV + RV/EV 1 (1.61) RV/EV + M. pneu 1 (1.61) AdV + IFV 14 (22.58) PIV + IFV 2 (3.23) AdV + PIV 1 (1.61) PIV + AdV 1 (1.61) HBoV + B. pert 1 (1.61) IFV + M. pneu 14 (22.58) HBoV + M. pneu 1 (1.61) PIV + B. pert 1 (1.61) HCoV + IFV 6 (9.68) PIV + RV/EV 1 (1.61) HCoV + AdV 2 (3.23) RSV + AdV 3 (4.84) HCoV + RV/EV 1 (1.61) RSV + HBoV 1 (1.61) hMPV + RV/EV 1 (1.61) RSV + IFV 1 (1.61) RV/EV + IFV 1 (1.61) Intra- IFV-A + IFV-H1N1pdm09 1 (1.61) HCoV-OC43 + HCoV-HKU1 5 (8.06) IFV-A + IFV-B 1 (1.61) PIV-1 + PIV-3 1 (1.61) Triple and above Infections (n = 16) Inter- AdV + RV/EV + IFV 2 (12.5) RSV + AdV + IFV 1 (6.25) AdV + IFV + M. pneu 2 (12.5) AdV + RV/EV + IFV + M. pneu 2 (12.5) HCoV + RV/EV + IFV 1 (6.25) PIV + RSV + AdV + IFV 3 (18.75) RV/EV + IFV + M. pneu 2 (12.5) PIV + AdV + IFV + M.pneu 1 (6.25) PIV + AdV + IFV 2 (12.5) Note. *: Values are shown as No.(%). AdV: adenovirus; EV/RV: enterovirus/rhinovirus; IFV: influenza; PIV: parainfluenza virus; HBoV: human bocavirus; B. pert: Bordetella pertussis; M. pneu: Mycoplasma pneumoniae; HCoV: human coronavirus; IFV: influenza; hMPV: human metapneumovirus. Conversely, the proportion of respiratory viruses differed significantly among different age groups (P= 0.0001). Among (0-1)-year-old, (1-5)-year-old, and (5-18)-year-old, the top three detected viruses were similar, consisting of IFV, AdV and PIVs, while the three most common viruses among (18-40)-year-old and (40-65)-year-old were IFV, HCoVs, and AdV. In the over 65-year-old age group, the top three respiratory viruses were IFV, HCoVs, and EV/RV. The most common respiratory viruses in the (0-1)-year-old, (1-5)-year-old, (5-18)-year-old, (18-40)-year-old, (40-65)-year-old, and over 65-year-old age groups were IFV (n = 25), PIVs (n = 10), AdV (n = 18), IFV (n = 25), IFV (n = 23), and IFV (n = 26).
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All of the pathogens were analyzed according to the monthly distribution, and the most common viruses were mapped in Figure 1C. Overall, the total number of respiratory pathogens was found to be highest in September (n = 46) and November (n = 44). Only IFV and AdV were screened throughout the year. For IFV, four peak months were identified, July (n = 18), September (n = 24), October (n = 15) and November (n = 15). AdV peaked in January (n = 8) and December (n = 10). HCoVs and RV/EV peaked in July, with 11 and 7 cases, respectively. Although the monthly trend of the pathogens was not obvious, they were more likely to be found in July, September, and November.
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Co-infection was detected in 78 specimens, with a detection rate of 17.53% (78/445) being observed for all of the specimens and 34.67% (78/225) for positive specimens. Co-infection was significantly (χ2 = 4.6074, P = 0.0312) less common in male patients (38/265, 14.34%) than in female patients (40/180, 22.22%). The co-infection rate varied significantly among age groups (χ2 = 12.8745, P= 0.0246). The distribution of co-infections is shown in Table 2. Dual infections were the most frequently detected co-infection mode, and IFV/AdV (n = 14) and IFV/PIV (n = 14) were the most common co-infection combinations. Intra-species co-infections were seen in IFV, HCoV, and PIV.
Among the respiratory viruses, IFV (64/123, 52.03%), RV/EV (20/33, 60.61%), and HBoV (7/10, 70.00%) were more commonly detected as single pathogens, with a proportion over 50%, whereas HCoVs (20/36, 55.56%), PIVs (17/28, 60.71%), RSV (9/10, 90.00%), and AdV (36/56, 64.28%) were primarily detected in co-infections. One of two hMPV-positive cases was a co-infection. Among bacteria, 22 M. pneu (22/28, 78.57%) and 2 B. pert (2/2, 100%) were detected in co-infections, while 1 L. pneu (1/1, 100%) was observed as a single infection (Figure 1B).
All of the experimental results were validated using single or multiple PCR assays established in our laboratory (data not shown).
doi: 10.3967/bes2019.058
Viral and Bacterial Etiology of Acute Febrile Respiratory Syndrome among Patients in Qinghai, China
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Abstract:
Objective This study was conducted to investigate the viral and bacterial etiology and epidemiology of patients with acute febrile respiratory syndrome (AFRS) in Qinghai using a commercial routine multiplex-ligation-nucleic acid amplification test (NAT)-based assay. Methods A total of 445 nasopharyngeal swabs specimens from patients with AFRS were analyzed using the RespiFinderSmart22kit (PathoFinder BV, Netherlands) and the LightCycler 480 real-time PCR system. Results Among the 225 (225/445, 51%) positive specimens, 329 positive pathogens were detected, including 298 (90.58%) viruses and 31 (9%) bacteria. The most commonly detected pathogens were infiuenza virus (IFV; 37.39%; 123/329), adenovirus (AdV; 17.02%; 56/329), human coronaviruses (HCoVs; 10.94%; 36/329), rhinovirus/enterovirus (RV/EV; 10.03%; 33/329), parainfiuenza viruses (PIVs; 8.51%; 28/329), and Mycoplasma pneumoniae (M. pneu; 8.51%; 28/329), respectively. Among the co-infected cases (17.53%; 78/445), IFV/AdV and IFV/M. pneu were the most common co-infections. Most of the respiratory viruses were detected in summer and fall. Conclusion In our study, IFV-A was the most common respiratory pathogen among 22 detected pathogens, followed by AdV, HCoV, RV/EV, PIV, and M. pneu. Bacteria appeared less frequently than viruses, and co-infection was the most common phenomenon among viral pathogens. Pathogens were distributed among different age groups and respiratory viruses were generally active in July, September, and November. Enhanced surveillance and early detection can be useful in the diagnosis, treatment, and prevention of AFRS, as well as for guiding the development of appropriate public health strategies. -
Figure 1. The etiology characteristics of acute febrile respiratory syndrome in Qinghai. (A) Detection rate of single infection or co-infections in 445 respiratory samples. The color pie chart represents the rate of any pathogen detection, and the gray part represents the rate of no-pathogen detection. (B) The numbers of single infection and co-infections for individual respiratory pathogen. (C) Distribution of the AFRS cases from January to December.
Table 1. Distribution of Virus in Different Groups
Virus Gender* Age-group* (y) Totol (N = 445) F (n = 180) M (n = 265) 0-1 (n = 77) 1-5 (n = 70) 5-18 (n = 80) 18-40 (n = 60) 40-65 (n = 68) > 65 (n = 90) IFV 68 (42.50) 55 (39.86) 25 (47.17) 7 (21.21) 17 (34.69) 25 (42.37) 23 (47.92) 26 (46.43) 123 (41.28) HCoVs 17 (10.63) 19 (13.77) 4 (7.55) 1 (3.03) 2 (4.08) 12 (20.34) 8 (16.67) 9 (16.07) 36 (12.08) PIVs 13 (8.13) 15 (10.87) 7 (13.21) 10 (30.30) 2 (4.08) 3 (5.08) 2 (4.17) 4 (7.14) 28 (9.40) RSV 4 (2.50) 6 (4.35) 2 (3.77) 1 (3.03) 2 (4.08) 3 (5.08) 1 (2.08) 1 (1.79) 10 (3.36) hMPV 2 (1.25) 0 (0.00) 0 (0.00) 0 (0.00) 0 (0.00) 0 (0.00) 0 (0.00) 2 (3.57) 2 (0.67) AdV 32 (20.00) 24 (17.39) 10 (18.87) 5 (15.15) 18 (36.73) 9 (15.25) 10 (20.83) 4 (7.14) 56 (18.79) EV/RV 17 (10.63) 16 (11.59) 2 (3.77) 4 (12.12) 7 (14.29) 7 (11.86) 4 (8.33) 9 (16.07) 33 (11.07) HBoV 7 (4.38) 3 (2.17) 3 (5.66) 5 (15.15) 1 (2.04) 0 (0.00) 0 (0.00) 1 (1.79) 10 (3.36) totol 160 (100) 138 (100) 53 (100) 33 (100) 49 (100) 59 (100) 48 (100) 56 (100) 298 (100) Fisher's 1.52 × 106 3.52 × 10-33 Exact values 0.7008 0.0001 Note.*: Values are shown as No.(%). IFV: influenza; HCoV: human coronavirus; PIV: parainfluenza virus; RSV: respiratory syncytial virus; hMPV: human metapneumovirus; AdV: adenovirus; EV/RV: enterovirus/rhinovirus; HBoV: human bocavirus. Table 2. Distribution of Co-infection
Group Virus NO.* Virus NO.* Dual Infections (n = 62) Inter- AdV + RV/EV 1 (1.61) RV/EV + M. pneu 1 (1.61) AdV + IFV 14 (22.58) PIV + IFV 2 (3.23) AdV + PIV 1 (1.61) PIV + AdV 1 (1.61) HBoV + B. pert 1 (1.61) IFV + M. pneu 14 (22.58) HBoV + M. pneu 1 (1.61) PIV + B. pert 1 (1.61) HCoV + IFV 6 (9.68) PIV + RV/EV 1 (1.61) HCoV + AdV 2 (3.23) RSV + AdV 3 (4.84) HCoV + RV/EV 1 (1.61) RSV + HBoV 1 (1.61) hMPV + RV/EV 1 (1.61) RSV + IFV 1 (1.61) RV/EV + IFV 1 (1.61) Intra- IFV-A + IFV-H1N1pdm09 1 (1.61) HCoV-OC43 + HCoV-HKU1 5 (8.06) IFV-A + IFV-B 1 (1.61) PIV-1 + PIV-3 1 (1.61) Triple and above Infections (n = 16) Inter- AdV + RV/EV + IFV 2 (12.5) RSV + AdV + IFV 1 (6.25) AdV + IFV + M. pneu 2 (12.5) AdV + RV/EV + IFV + M. pneu 2 (12.5) HCoV + RV/EV + IFV 1 (6.25) PIV + RSV + AdV + IFV 3 (18.75) RV/EV + IFV + M. pneu 2 (12.5) PIV + AdV + IFV + M.pneu 1 (6.25) PIV + AdV + IFV 2 (12.5) Note. *: Values are shown as No.(%). AdV: adenovirus; EV/RV: enterovirus/rhinovirus; IFV: influenza; PIV: parainfluenza virus; HBoV: human bocavirus; B. pert: Bordetella pertussis; M. pneu: Mycoplasma pneumoniae; HCoV: human coronavirus; IFV: influenza; hMPV: human metapneumovirus. -
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