Comparison of 11 Respiratory Pathogens Among Hospitalized Children Before and After the COVID-19 Epidemic in Shenzhen, China

doi:10.21203/rs.3.rs-724494/v1

Background: The effect of SARS-CoV-2 on existing respiratory pathogens in circulation remains uncertain. This study aimed to assess the impact of SARS-CoV-2 on the prevalence of respiratory pathogens among hospitalized children.

Methods: This study enrolled hospitalized children with acute respiratory infections in Shenzhen Children’s Hospital from September to December 2019 (before the COVID-19 epidemic) and those from September to December 2020 (after the COVID-19 epidemic). Nasopharyngeal swabs were collected, and respiratory pathogens were detected using multiplex PCR. The absolute case number and detection rates of 11 pathogens were collected and analyzed.

Results: A total of 5696 children with respiratory tract infection received multiplex PCR examination for respiratory pathogens: 2298 from September to December 2019 and 3398 from September to December 2020. At least one pathogen was detected in 1850 (80.5%) patients in 2019, and in 2380 (70.0%) patients in 2020; the detection rate in 2020 was significantly lower than that in 2019. The detection rates reflected changes in these pathogens when the COVID-19 epidemic was well controlled. The Influenza A (InfA) detection rate was 5.6% in 2019, but 0% in 2020. The detection rates of Mycoplasma pneumoniae, Human adenovirus, and Human rhinovirus also decreased from 20% (460), 8.9% (206), and 41.8% (961) in 2019 to 1.0% (37), 2.1% (77), and 25.6% (873) in 2020, respectively. In contrast, the detection rates of Human respiratory syncytial virus, Human parainfluenza virus, and Human metapneumovirus increased from 6.6% (153), 9.9% (229), and 0.5% (12) in 2019 to 25.6% (873), 15.5% (530), and 7.2% (247) in 2020, respectively (p < 0.0001).

Conclusions: The emergence of SARS-CoV-2 was associated with the substantial reduction in the circulation of respiratory pathogens including influenza virus, rhinovirus, adenovirus, and Mycoplasma pneumoniae, as well as with the increase in respiratory syncytial virus, parainfluenza, and human metapneumovirus in Shenzhen. The reasons for this phenomenon require further studies.

Virology

SARS-CoV-2

respiratory pathogens

prevalence

children

Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a substantial health burden worldwide. A massive roll out of population-level nonpharmaceutical interventions have been conducted to curb transmission, including stay-at-home orders, the closure of schools and retail spaces, mandated face masks in public, and encouragement of social distancing and hand hygiene. Studies from France, Japan, Singapore, Mexico, and Zhejiang province of China have shown that these measures also coincided with a decline in the number of cases of influenza over the same time period, as compared with previous seasons[1–5]. However, few studies of how seasonal respiratory pathogens changed during the epidemic are well-controlled. Shenzhen is a large migratory city in China with high population density and population mobility; as of April 30, 2020, a total of 462 imported cases with COVID-19 were confirmed in Shenzhen. Starting in May 2020, students in Shenzhen went back to school, and the society resumed work and production. However, wearing masks, social distancing, and avoidance of activities associated with population gatherings were still required. To assess changes in seasonal respiratory viruses after the outbreak of COVID-19 in Shenzhen, hospitalized children with respiratory infections were recruited in Shenzhen Children’s Hospital. We compared the absolute case number and detection rates of 11 pathogens in the period from September to December 2019 with those from September to December 2020.

Patients

Patients with acute respiratory infections (ARIs) between September to December 2019 and September to December 2020 admitted to the pediatric wards were enrolled in Shenzhen Children’s Hospital. The inclusion criteria were as follows: age below 14 years and one or more respiratory symptoms (cough, sore throat, body temperature above 37.5°C, and dyspnea/tachypnoea). The study protocol was approved by the Ethical Committee of Shenzhen Children’s Hospital (number: 201601304). Written informed consent was obtained from the participants’ guardians. Clinical and demographic data, as well as samples for testing pathogens, were collected by trained nurses in line with a standardized protocol.

Specimens and detection of pathogens

Nasopharyngeal swabs were obtained by trained personnel following standard operating procedures within 24 h after admission. The specimens were transported immediately to the laboratory in sterile viral transport media. The total nucleic acids of each specimen were extracted using EasyPure Viral DNA/RNA Kit (TransGen Biotech, Beijing, China) in accordance with the manufacturer's instructions. Eleven common respiratory pathogens, including Influenza A (InfA), Influenza B (InfB), Human parainfluenza virus (HPIV), Human respiratory syncytial virus (RSV), adenoviruses (AdV), Human metapneumovirus (HMPV), Human rhinovirus (HRV), Human bocavirus (HBoV), Human coronavirus (HCoV), Chlamydia (Ch), and Mycoplasma pneumoniae (MP), were detected using a GeXP-based multiplex reverse transcription polymerase chain reaction (PCR) assay (Ningbo).

Statistical analysis

Statistical analyses were conducted using SPSS 23 (SPSS Inc. Chicago, IL, USA). For comparison of categorical data, chi-square or Fisher’s exact test was used. P-value < 0.05 was considered statistically significant.

Patient characteristics

A total of 5696 children with respiratory tract infection were enrolled in this study, 2298 in the period from September to December 2019 and 3398 in the period from September to December 2020. The age ranged from 1 month to 14 years, and the median age was 27.5 months in 2019 and 24 months in 2020. We divided the patients according to age into four groups, as follows: (i) infant group (1 month–1 year old), 713 cases in 2019 and 1071 cases in 2020; (ii) toddler group (1–3 years old), 641 cases in 2019 and 1036 cases in 2020; (iii) pre-school group (3–6 years old), 647 cases in 2019 and 932 cases in 2020; (iv) school children group (6–14 years old), 297 cases in 2019 and 359 cases in 2020. The subjects included 1389 boys (60.5%) and 909 girls (39.5%) (sex ratio, 1.53:1) in 2019, and 2023 boys (59.5%) and 1375 girls (40.5%) (sex ratio, 1.48:1) in 2020. There was no significant difference in sex ratio between 2019 and 2020 (X² = 0.4714, P = 0.4913).

Overall detection percentage of the 11 pathogens

In 2019, of 2298 specimens, 1850 (80.5%) tested positive for at least one of the 11 pathogens; in 1295 (70.0%) of these positive patients, single pathogen was detected, whereas in 555 (30.0%) patients, more than two pathogens were detected. In 2020, of 3398 specimens, 2380 (70.0%) tested positive for at least one of the 11 pathogens; in 2034 (85.5%) of these positive specimens, single pathogen was detected, and in 346 (14.5%) of patients, there were more than two pathogens. The detection rate in 2020 was significantly lower than that in 2019 (X² = 78.5290, P = 0.000).

Changes of specific pathogens between 2019 and 2020

The top three pathogens were HRV, MP, and HPIV in 2019, whereas HRV, RSV, and HPIV were dominant in 2020. Five pathogens (InfA, HRV, MP, AdV, and Ch) had a lower detection rate in 2020 than in 2019. The detection rate of InfA was 5.6% in 2019, but none in 2020. In contrast, the detection rates of RSV, HPIV, and HMPV in 2020 increased compared with those in 2019, where the detection rate of RSV showed the most significant increase, from 6.6–20.1%. Other pathogens, such as HBoV, InfB, and HCoV, showed similar detection rates between 2019 and 2020 (Table 1).

Table 1

Comparison of positive rates of 11 respiratory pathogens in 2019 and 2020
Pathogens	2019 N = 2298	2020 N = 3398	X²	P
Human rhinovirus (HRV)	961 (41.8%)	873 (25.6%)	163.3277	0.000
Mycoplasma pneumoniae (MP)	460 (20%)	37 (1.0%)	616.7384	0.000
Human parainfluenza virus (HPIV)	229 (9.9%)	530 (15.5%)	37.6529	0.000
Human adenovirus (AdV)	206 (8.9%)	77 (2.2%)	130.2703	0.000
Human respiratory syncytial virus (RSV)	152(6.6%)	683 (20.1%)	199.2841	0.000
Influenza A virus (InfA)	130 (5.6%)	0	196.7177	0.000
Human bocavirus (HBoV)	87 (3.7%)	152 (4.4%)	1.6111	0.2040
Human coronavirus (HCoV)	66 (2.8%)	123 (3.6%)	2.3891	0.1222
Chlamydia (Ch)	29 (1.2%)	22 (0.6%)	5.8343	0.0157
Human metapneumovirus (HMPV)	12 (0.5%)	247 (7.2%)	143.7734	0.000
Influenza B virus (InfB)	3 (0.1%)	1 (< 0.1%)	0.8164	0.3662

the detection rate of InfA was 5.6% in 2019, but none in 2020. In contrast, the detection rates of RSV, HPIV, and HMPV in 2020 increased compared with those in 2019, other pathogens, such as HBoV, InfB, and HCoV, showed similar detection rates between 2019 and 2020

Changes in specific pathogens based on month and age

The detection rate of pathogens in school children in 2020 was lower than that in 2019, but no significant differences between the two years were found in other age groups (Fig. 1). There was no difference in monthly trend of the detection rate between 2019 and 2020; in both years, the detection rate decreased from September to December (Fig. 2).

We also found some epidemic patterns of the viral infections from September to December, especially in 2020 after the epidemic. RSV was the most prevalent pathogen between September and October, and its occurrence sharply declined in November. In contrast, HPIV increased significantly in November 2020, while HMPV increased significantly in December 2020 (Fig. 2).

In this study, we retrospectively evaluated the overall prevalence of the most frequent respiratory pathogens among hospitalized children with ARIs before and after COVID-19 epidemic. The total positive rates of pathogens were 80.5% in 2019 and 70% in 2020, similar to those reported in other studies (from 62.4–85.2%)[6–8]. More specimens were tested in 2020 than in 2019, but the overall pathogens positive rate was significantly lower. The detection rates of InfA, MP, HRV, and AdV decreased significantly.

Droplet and contract transmission are believed to be the major transmission route of COVID-19[9, 10]; influenza has the similar route of transmission like COVID-19. Thus, many studies have shown that nonpharmaceutical interventions associated with reduced transmission of COVID-19 have also likely substantially reduced influenza[11, 12]. Indeed, the 2019–2020 influenza season was marked by decreased influenza transmission during the COVID-19 pandemic[13]. Shenzhen is located in southern China; it has a typical subtropical monsoon climate, where influenza is mostly detected in autumn and winter[14]. Despite the school year, resumed work, and the seasonal prevalence, the influenza detection rate remained low in 2020. The potential impact of the COVID-19 pandemic on influenza is not fully known, but the reason for the observed decrease may be multifactorial. First, the COVID-19 pandemic has altered health seeking behaviors and has increased attention to nonpharmaceutical interventions that reduce the risk of transmission of influenza[13]. Other factors, such as virus competition, may have contributed as well. Namely, Lubna Pinky showed that blocking one virus infection by the presence of another can be explained simply through resource competition[15]. It has been suggested that other mechanisms, such as the immune response or interference through viral proteins, are also responsible for the growth interference between two viruses [16]. Successful containment of seasonal influenza as a result of COVID-19 control measures has provided some useful insights into controlling emerging influenza epidemics in the future.

We found that several pathogens, including RSV, PIV, and HMPV, showed increased detection rates after the epidemic. RSV showed the most prominent increase, from 6.6–20.1%, what was different from other studies[17, 18]. RSV is detected primarily during the spring and summer in Shenzhen and is the most prevalent virus in infants[14]; in our study, the detection rate of RSV gradually decreased from September to December in both years (Fig. 2). RSV disease occurs across all ages, but it disproportionately affects children under the age of 2 years[19]; since wearing mask is difficult for children under 2 years of age, an epidemiological interference between RSV and influenza virus infections has been reported: the RSV epidemic is interrupted by an epidemic of influenza virus infection[20]. According to Takeuchi’s report, the admission number of patients with RSV infection decreased during the influenza epidemic period, suggesting the presence of an epidemiological interference between RSV and influenza virus infections[21]. No cases of InfA virus were detected in 2020, which might be the reason why RSV increased in 2020. In the 2019 and 2020 two years, we found that the detection rate of RSV decreased gradually from September to November, while the detection rate of HPIV increased gradually, and both decreased in December. It may be due to a phenomenon called viral interference where one virus blocks the growth of another virus[22]. In December 2020, the detection rate of HMPV increased significantly, while the detection rate of most pathogens decreased, and it seems that COVID-19 has no impact on the prevalence of HMPV. Mandy Jongbloed et al. has showed that HMPV and SARS-CoV-2 are probably co-circulating independently[23]. Continued monitoring of viral epidemic trends and further research are needed.

This study is limited in that it was performed in a single center in a restricted geographical area, in a short period instead of a whole year or longer period, and there was a preselection bias stemming from the fact that all of the patients were hospitalized. Moreover, we did not observe changes in bacteria that cause respiratory infections, which limits our observation range; thus, additional data are required to validate our conclusions on a larger scale.

Nonpharmaceutical interventions focusing on the reduction of the spread of SARS-CoV-2 seem to have diminished the transmission of influenza virus and also changed the prevalence of other respiratory pathogens. Further studies are needed to better understand the entire impact of COVID-19 on other pathogens.

Influenza A: InfA; Influenza B: InfB; Human parainfluenza virus: HPIV; Human respiratory syncytial virus: RSV; adenoviruses: AdV; Human metapneumovirus: HMPV; Human rhinovirus: HRV; Human bocavirus: HBoV; Human coronavirus: HCoV; Chlamydia: Ch; Mycoplasma pneumoniae: MP; polymerase chain reaction: PCR.

Acknowledgment

Not applicable.

Authors’ contributions

Li Li and Heping Wang have contributed equally to this work.

LL and HPW designed this study; ALL, RJW collected data; LL, HPW and TTZ performed the statistical analyses and outcome assessments, and wrote the paper. YJZ, YMB, YSC and WJW also contributed to the statistical analyses and the outcome assessments. All authors read and approved the final manuscript.

Funding

This work was supported by grants from the Shenzhen Fund for Guangdong Provincial High-level Clinical Key Specialties (SZGSP012) and Shenzhen Key Medical Discipline Construction Fund (SZXK032) to Wenjian Wang, which had a role in the data collection and analysis and the manuscript writing, reviewing, and editing.

Availability of data and materials

The key information and data generated and/or analyzed during this study were included in this article.

Ethics approval and consent to participate

Ethical approval for this study was obtained from the Ethical Committee of Shenzhen Children’s Hospital (Shenzhen, Guangdong Province, China) under registration number 2016013. All experiments were performed under the relevant guidelines and regulations. Guardians of all children included in this study provided written informed consent to participate.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Boelle PY, Souty C, Launay T, Guerrisi C, Turbelin C, Behillil S, et al. Excess cases of influenza-like illnesses synchronous with coronavirus disease (COVID-19) epidemic, France, March 2020. Euro Surveill. 2020;25(14).
H S, M I, P U. Seasonal Influenza Activity During the SARS-CoV-2 Outbreak in Japan. JAMA. 2020;323(19):1969-71.
Soo. RJJ, Calvin J C, Stefan Ma RP, Lee. V. Decreased Influenza Incidence under COVID-19 Control Measures, Singapore. JAMA. 2020;26(14):1406-7.
Murillo-Zamora E, Guzman-Esquivel J, Sanchez-Pina RA, Cedeno-Laurent G, Delgado-Enciso I, Mendoza-Cano O. Physical distancing reduced the incidence of influenza and supports a favorable impact on SARS-CoV-2 spread in Mexico. J Infect Dev Ctries. 2020;14(9):953-6.
Cheng W, Yu Z, Liu S, Sun W, Ling F, Pan J, et al. Successful interruption of seasonal influenza transmission under the COVID-19 rapid response in Zhejiang Province, China. Public Health. 2020;189:123-5.
Cantais A, Mory O, Pillet S, Verhoeven PO, Bonneau J, Patural H, et al. Epidemiology and microbiological investigations of community-acquired pneumonia in children admitted at the emergency department of a university hospital. Journal of clinical virology. 2014;60(4):402-7.
Akturk H, Sutcu M, Badur S, Torun SH, Citak A, Erol OB, et al. Evaluation of epidemiological and clinical features of influenza and other respiratory viruses. Turk Pediatri Ars. 2015;50(4):217-25.
Zhong P, Zhang H, Chen X, Lv F. Clinical characteristics of the lower respiratory tract infection caused by a single infection or coinfection of the human parainfluenza virus in children. J Med Virol. 2019;91(9):1625-32.
Mendez-Brito A, Bcheraoui CE, Pozo-Martin F. Systematic review of empirical studies comparing the effectiveness of non-pharmaceutical interventions against COVID-19. J Infect. 2021.
Leung NHL. Transmissibility and transmission of respiratory viruses. Nat Rev Microbiol. 2021.
Cowling BJ, Ali ST, Ng TWY, Tsang TK, Li JCM, Min Whui Fong, et al. Impact assessment of non-pharmaceutical interventions against coronavirus disease 2019 and influenza in Hong Kong: an observational study. Lancet Public Health. 2020;5(e279-288).
Chiu NC, Chi H, Tai YL, Peng CC, Tseng CY, Chen CC, et al. Impact of Wearing Masks, Hand Hygiene, and Social Distancing on Influenza, Enterovirus, and All-Cause Pneumonia During the Coronavirus Pandemic: Retrospective National Epidemiological Surveillance Study. J Med Internet Res. 2020;22(8):e21257.
de St Maurice A, Martin-Blais R, Halasa N. Preparing for the 2020-2021 influenza season. Pediatr Transplant. 2021:e14025.
Wang H, Zheng Y, Deng J, Wang W, Liu P, Yang F, et al. Prevalence of respiratory viruses among children hospitalized from respiratory infections in Shenzhen, China. Virology Journal. 2016;13(1).
Pinky L, Dobrovolny HM. Coinfections of the Respiratory Tract: Viral Competition for Resources. PLoS One. 2016;11(5):e0155589.
Dobrescu I, Levast B, Lai K, Delgado-Ortega M, Walker S, Banman S, et al. In vitro and ex vivo analyses of co-infections with swine influenza and porcine reproductive and respiratory syndrome viruses. Vet Microbiol. 2014;169(1-2):18-32.
Nolen LD, Seeman S, Bruden D, Klejka J, Desnoyers C, James, et al. Impact of Social Distancing and Travel Restrictions on nonCOVID-19 Respiratory Hospital Admissions in Young Children in Rural Alaska. Clin Infect Dis. 2021;72(12).
Varela FH, Scotta MC, Polese-Bonatto M, Sartor ITS, Ferreira CF, Fernandes IR, et al. Absence of detection of RSV and influenza during the COVID-19 pandemic in a Brazilian cohort: Likely role of lower transmission in the community. J Glob Health. 2021;11:05007.
Hirve S, Crawford N, Palekar R, Zhang W. Clinical characteristics, predictors, and performance of case definition-Interim results from the WHO global respiratory syncytial virus surveillance pilot. Influenza Other Respir Viruses. 2020;14(6):647-57.
Nozomi N, Hisahide N, Jin LM, Kanjiro U. The clinical features of respiratory syncytial virus: Lower respiratory tract infection after upper respiratory tract infection due to influenza virus. Pediatrics International. 2005;47:412–6.
Takeuchi YJApJOe. Epidemiological and clinical features of influenza and respiratory syncytial virus infections among children in Japan. 1988;30(3):231-9.
Latorre-Margalef N, Brown JD, Fojtik A, Poulson RL, Carter D, Franca M, et al. Competition between influenza A virus subtypes through heterosubtypic immunity modulates re-infection and antibody dynamics in the mallard duck. PLoS Pathog. 2017;13(6):e1006419.
Jongbloed M, Leijte WT, Linssen CFM, van den Hoogen BG, van Gorp ECM, de Kruif MD. Clinical impact of human metapneumovirus infections before and during the COVID-19 pandemic. Infect Dis (Lond). 2021;53(7):488-97.

Comparison of 11 Respiratory Pathogens Among Hospitalized Children Before and After the COVID-19 Epidemic in Shenzhen, China

Status:

Version 1

Abstract

Figures

Background

Methods

Patients

Specimens and detection of pathogens

Statistical analysis

Results

Discussion

Conclusions

Abbreviations

Declarations

References

Status:

Version 1