Prevalence and molecular characteristics of respiratory syncytial virus in hospitalized children in Shenzhen during the COVID-19 pandemic: a retrospective study

Introduction

As a negative-sense single-stranded RNA virus, respiratory syncytial virus (RSV) is a member of the Paramyxoviridae family’s genus Pneumovirus (1). It is the leading cause of admission in children under the age of 5 years (2). A global meta-analysis estimated that RSV-related acute lower respiratory tract infections (ALRTI) resulted in approximately 33 million cases, 3.6 million hospitalizations, and 26,300 deaths during hospitalization among children younger than 5 years of age (3). RSV causes 118,200 fatalities per year, most of which occur in low- and middle-income countries, making it a leading cause of respiratory illness in children worldwide (4).

Clinical manifestation of ALRTI in pediatric patients is disease-specific but essentially involves fever, cough, wheezing, tachypnea, dyspnea, nasal flaring, chest retractions, and cyanosis (5). Those with severe diseases can develop further into hypoxemia, respiratory distress, continuing high fever, and even failure of the lungs, necessitating hospitalization (6,7).

RSV is further classified into two broad subtypes, A and B, based on the antigenic features of its surface glycoprotein G (8). Further genetic investigations have identified at least 15 genotypes for RSV-A and 30 genotypes for RSV-B (9). New genotypes, like ON1 (RSV-A) and BA (RSV-B), have also been associated with increased transmission and potential variation in clinical severity, but evidence is conflicting between studies (10-12). Some studies suggest that RSV-A strains may be linked to more severe disease, and RSV-B infection is milder, though there is not robust evidence (12). However, whether severity of illness is influenced by various RSV subtypes and genotypes remains unknown.

Reduced early-life RSV exposure during the coronavirus disease 2019 (COVID-19) pandemic may have made children susceptible to severe infection post-pandemic (2,13). In addition, monoclonal antibodies such as palivizumab and nirsevimab have proved useful in RSV prevention in infants (14). New RSV vaccines have been approved for maternal and elderly populations, while pediatric vaccines remain in clinical trials with a high cost and limited supply. This situation has constrained widespread application of RSV vaccine among children in China (15).

In a bid to enhance understanding of RSV epidemiology in China, the current study was undertaken to investigate the prevalence, molecular profile, and clinical presentation of RSV among hospitalized children in Shenzhen during the COVID-19 period. We present this article in accordance with the STROBE reporting checklist (available at https://tp.amegroups.com/article/view/10.21037/tp-2025-aw-776/rc).

Methods

Patients and sample collection

This study retrospectively collected hospitalized children with ALRTI in the Pediatric Intensive Care Unit (PICU), Shenzhen Maternity and Child Healthcare Hospital between June and September 2021. The study was conducted in accordance with the Declaration of Helsinki and its subsequent amendments. The study was approved by the Institutional Ethics Committee of Shenzhen Maternity and Child Healthcare Hospital (No. SFYLS[2023]001). The requirement of written informed consent was waived by the Ethics Committee because this study was a retrospective study.

• Inclusion criteria: acutely ill hospitalized children with respiratory illness who tested positive for RSV by a seven-common-virus multiplex antigen detection assay were included in the study.
• Exclusion criteria: excluded were children with chronic lung disease (e.g., bronchopulmonary dysplasia, asthma), congenital heart disease, immunodeficiency, metabolic disease, or neuromuscular disease, because these diseases may speed up the infection and severity of the RSV. Those cases with COVID-19 antigen tests positive were also excluded, along with those involving mixed infections.

Nasopharyngeal swabs were also collected from included children within 24 hours of admission and archived at −80 ℃ for eventual molecular testing. Clinical data including demographic data, laboratory data, imaging data, oxygen supplementation requirement, and admissions to PICU were abstracted from medical records. Severity of illness was quantified as mild, moderate and severe using a validated Clinical Disease Severity Score (16).

Nucleic acid extraction and reverse transcription

Viral ribonucleic acid (RNA) was extracted using a commercial RNA extraction kit (Trizol extraction kit: B511321, Sangon Biotech, Shanghai, China) according to the manufacturer’s instruction. Complementary deoxyribonucleic acid (cDNA) was synthesized using the reverse transcription in the condition of 70 ℃ for 5 min, 42 ℃ for 60 min, and 72 ℃ for 10 min. The reaction mixture (10.0 µL total) was 5 µL total RNA, 1 µL random primer, 1 µL double distilled water, 2.0 µL 5× First-Strand Buffer, 0.5 µL 10 mM deoxyribonucleoside triphosphates, 0.25 µL ribonuclease inhibitor, and 0.25 µL reverse transcriptase. Two sets of primers were used for nested polymerase chain reaction (PCR). For first-round PCR, G-F (5'-GTTATGACACTGGTATACCAACC-3') and G-R (5'-GGGGCAAATGCAACCATGTCC-3') were employed. The second-round PCR included the universal primer P1 (5'-TGGGACACTCTTAATCAT-3'), RSV-A-specific primer P2 (5'-TGATTCCAAGCTGAGGAT-3'), and RSV-B-specific primer P3 (5'-GTTGTATGGTGTGTTTC-3'). The conditions for PCR were an initial denaturation of 94 ℃ for 3 min, with 33 cycles of denaturation (94 ℃, 30 s), annealing (58 ℃, 30 s), and extension (72 ℃, 90 s), and a final extension of 72 ℃ for 20 s. The PCR products were purified by a 1% agarose gel and sequenced by Sangon Biotech Co., Ltd. (Shanghai, China).

Phylogenetic analysis

Basic Local Alignment Search Tool [National Center for Biotechnology Information (NCBI) BLAST] was used to verify the sequence (https://blast.ncbi.nlm.nih.gov/). Using CLUSTALW in MEGA X software, multiple sequence alignment and phylogenetic analysis of the second hypervariable region of the RSV-G gene were carried out. Strains retrieved from GenBank (https://www.ncbi.nlm.nih.gov/) were compared to the genotyping. Using the Neighbor-Joining approach, phylogenetic trees were built, and confidence levels were determined using bootstrap values (1,000 repetitions).

Statistical analysis

SPSS software (IBM SPSS Statistics for Windows, version 26.0., IBM Corp., Armonk, NY, USA) was used for all statistical analyses. Continuous normally distributed data were subjected to the Student’s t-test, while non-normally distributed data were subjected to the Mann-Whitney U test. Fisher’s exact or Chi-squared test, as appropriate, was used to compare the range of variables. Statistical significance was defined as a P value of less than 0.05.

Results

Epidemio-demographic characteristics of RSV-positive cases

Three hundred and eighty children were screened based on the inclusion and exclusion criteria at the hospital for ALRTI during the study period. Among them, 217 (57.11%) were RSV positive. Among the RSV-positive samples, 130 (34.21%) were males and 87 (22.89%) were females, and there was no statistically significant gender difference in detection (χ²=0.841, P=0.36). The age distribution in RSV-positive cases was: 110 (28.95%) were in the age range of ≤6 months, 26 (6.84%) in the age group of >6–12 months, 62 (16.32%) in the age range of >1–≤3 years, 15 (3.95%) in the age range of >3–≤6 years, and 4 (1.05%) in the age range of >6–14 years.

The detection rates of RSV were significantly greater in the age groups ≤6 months and >1–≤3 years compared to other age groups. There was no statistically significant variation between these two groups (χ²=0.851, P=0.36). Statistically significant variations in RSV detection rates between the ≤6 months and >3–≤6 years groups (χ²=23.563, P<0.001) and the ≤6 months and >6–14 years groups (χ²=9.306, P=0.002) were observed. In addition, significant differences were found between the >6–12 months and >3–≤6 years groups (χ²=8.683, P=0.003), the >3–≤6 years and >6–14 years groups (χ²=25.375, P<0.001), and the >1–≤3 years and >6–14 years groups (χ²=11.587, P=0.001). The differences in RSV detection rates among the other age groups were not statistically significant (Table 1).

Phylogenetic analysis of subtype and genotype

During the study, 217 out of 380 RSV-positive samples were successfully classified into RSV-A and RSV-B using specific primers. Among these, 27 samples were identified as RSV-A, and 24 samples were identified as RSV-B. The indexed RSV-A and RSV-B strains were used to make an evolutionary tree to further examine and describe the genotype. For clustering using sequences in the NCBI database, 19 specific RSV-A and 20 representative RSV-B sequences were used.

Phylogenetic analysis was performed using the second hypervariable region of the G gene for both RSV-A and RSV-B. The sequenced RSV-A samples were categorised into the ON1 genotype (Figure 1). For RSV-B, after comparing 24 sequenced RSV-B samples and 20 typical sequences, all 24 RSV-B samples were categorised as the BA9 genotype (Figure 2). The identification of RSV genotypes, such as ON1 and BA9, helps in understanding the genetic diversity and evolution of RSV strains. These findings are significant for monitoring the circulating strains in the population, as genetic variation in RSV can influence the virus’s transmissibility, virulence, and immunity evasion. By constructing phylogenetic trees, this study provides valuable insights into the ongoing genetic changes in RSV, which may impact future diagnostic, therapeutic, and vaccine development strategies.

Figure 1 Phylogenetic analysis of RSV-A strains based on the G gene. Phylogenetic trees of RSV-A strains isolated in this study were created by the maximum likelihood method with 1,000 bootstrap replicates, based on the second hypervariable region (HRV2) of the G gene. Reference sequences for different genotypes were downloaded from GenBank for alignment. In addition, 27 RSV-A strains isolated in this study are included in the analysis and are indicated by red stars for identification. Tree structure is informative on the evolutionary relationship and genetic variation of RSV-A strains in study over time. RSV, respiratory syncytial virus.

Figure 2 Phylogenetic analysis of RSV-B strains based on the G gene. Phylogenetic trees of the RSV-B strains isolated in this study were inferred by maximum likelihood with 1,000 bootstrap replicates from the second hypervariable region (HRV2) of the G gene. Reference sequences corresponding to various genotypes were downloaded from GenBank for reference. 24 RSV-A strains isolated in this study and marked by green circles are also included in the analysis. Tree topology assists in the comprehension of genetic variation and evolutionary relationship between RSV-B strains infecting patients within the observation period. RSV, respiratory syncytial virus.

Association between RSV molecular characteristics and clinical manifestation

Stratified analysis was used to compare clinical and demographic differences between children infected with the RSV-A ON1 genotype and those infected with the RSV-B BA9 genotype. Gender, age, birth weight, distribution method and postpartum nutrition were no different (Table 2). However, RSV-A ON1 infected children had a longer duration of hospitalization, median 6 days (interquartile range, 5–7 days), compared to RSV-B BA9 infected children, who had a median of 4.5 days (interquartile range, 4–6 days) (P=0.04). Further, a significantly higher proportion of RSV-A ON1-infected children were PICU-admitted (70.0%, 21/30), compared with RSV-B BA9-infected children (30.0%, 10/30) (P=0.008). Although the difference between the two groups in cough severity was significant, with 19.6% of the RSV-B children presenting severe cough and 11.1% of the RSV-A children, it was not statistically significant (P=0.06). No other significant differences were noted in fever patterns, respiratory symptoms, laboratory results, or treatment between the two groups.

Laboratory and imaging results also showed no noteworthy differences between groups, in white blood cell count, neutrophil count, lymphocyte count, platelet count, hemoglobin, C-reactive protein, procalcitonin, liver function tests (glutamic-pyruvic transaminase, glutamate aminotransferase), creatine kinase, and creatine kinase-MB form or Chest X-ray positive findings (diagnosed of lower respiratory tract infection, including bronchiolitis and pneumonia), between RSV-A (ON1) and RSV-B (BA9) groups.

As for treatment plans, there were no statistically significant differences between the two groups regarding administration of nebulizing medications, immunoglobulin, methylprednisolone, pectoral suction frequency, days of methylprednisolone treatment, types of ventilation support, or oxygen use days. Additionally, there were no differences between the prognosis and the costs of hospitalization in children with infections of the RSV-A ON1 genotype and those with infections of the RSV-B BA9 genotype.

Discussion

In this research, no significant disparity was noted in the demographic profile of patients such as age, gender, birth weight, and postnatal feeding, and also in clinical presentation, severity scores of diseases, laboratory findings, imaging results, and treatment plans among children who were infected with various RSV subtypes and genotypes. Nevertheless, we noted that patients who carried the RSV-A ON1 genotype had increased rates of admission into the PICU and prolonged duration of hospital stay compared to individuals with the RSV-B BA9 genotype. This would suggest that certain RSV genotypes and subtypes are capable of influencing the overall disease severity. It is therefore important to consider such outcomes when assessing the clinical course of RSV infection, particularly where RSV-A ON1 dominates. Previous studies have determinant of the seasonal pattern of RSV, which is highest during fall and spring in China (17). Not unexpectedly, in our observation, there was an unprecedented increase in the admission of kids to the pediatric respiratory and critical care unit due to RSV infection during summer 2021. This shift in the seasonality of epidemics has been explained due to the absence of RSV during winter 2020–2021, a scenario leading to an unexpected peak in cases during summer, as compared to other epidemic years (18).

RSV was identified through overall community positivity of 57.11% which is much higher by a considerable margin than in previous reports (19). Global molecular epidemiology studies done in 2017 and 2018 found that human RSV infection is most prevalent in infants under 12 months of age (20), and a study in Xiamen, China found that infants under 6 months of age were particularly vulnerable to RSV infection (21). In our study, high RSV detection rates in younger groups, especially in infants between 0–6 months and 1–3 years of age, can be attributed to their immature immune systems and limited prior risk to RSV, motivated to increase sensitivity to infection (22). Additionally, passive maternal antibodies only provide partial protection, which works within the first few months of life, which weakens infants (23). A lack of a significant difference between the age groups of 0–6 months and 1–3 years suggests that there is more sensitivity in childhood due to continuous immune system development and continuous risk in domestic home settings (22). Older children may also show partial immunity from previous RSV infections (24). Significant differences between young and old age groups strengthened need for targeted prevention strategies, especially for infants and children (25).

Earlier studies have mentioned that the incidence of RSV subtypes A and B cycles every year, with mixed infections involving both subtypes reported in some cases (26,27). In this study, a greater number of detections of subtype A were found, indicating that RSV-A could have been the prevailing subtype present in Shenzhen, Guangdong province, China, in 2021. Our study confirmed that the ON1 genotype was the prevailing genotype for RSV-A, while the BA9 genotype was the dominant strain for RSV-B, which is in accordance with global developments (21,28), as the ON1 genotype of RSV-A has emerged as the prevalent strain globally since its initial detection in Canada in 2010 (29,30). While we saw no significant difference in demographic characteristics, clinical presentation, or severity scores between children infected with different RSV subtypes and genotypes, we observed that PICU admission was higher and longer stay was observed among children with infection by the RSV-A ON1 genotype compared with the RSV-B BA9 genotype. This outcome suggests that RSV-A, particularly the ON1 genotype, may be associated with greater clinical severity. Perhaps the ON1 genotype possesses greater viral load or divergent immunoevasion capacity and the outcome is the greater severity. Besides, ON1 genotype would cause an increased level of inflammation and thus might be the cause of more severe clinical outcomes. Such potential mechanisms need to be kept in mind in future studies and might provide valuable contribution to personalized treatments of RSV infections (31,32).

Moreover, this finding suggests changing epidemiology of RSV during the impact of public health campaigns and viral evolution, which might be closely examined in order to direct prevention and treatment strategies in the future. Additional studies examining the genetic heterogeneity and epidemiological trends of RSV in different populations and nations will be essential to unraveling the underlying mechanisms and designing specific interventions. Significant research has probed the association between the molecular characteristics of RSV and clinical presentation, and findings have been inconclusive. Smith et al. (33) document that RSV subtype B infection exposes children to the risk of hospitalization and serious ALRTI. Other studies, however, argue that there is no distinctive difference in the clinical presentation among RSV subtypes. Additionally, some evidence suggests that some genotypes of RSV infection might have divergent clinical outcomes. Those cases with COVID-19 antigen tests positive in this study were excluded, along with those involving mixed infections. Excluding these cases aimed to eliminate the influence of the COVID-19 pandemic on the results.

Because our cohort was from a single center, there are a number of limitations, some of which include the small sample size and short follow-up interval. More profound conclusions on the molecular determinants of the clinical progression of RSV infection will have to arise from larger, multi-center cohorts with longer follow-up periods. In addition, although our research was aimed at acute clinical outcomes, more studies are required to investigate the long-term effects of infection with various RSV genotypes. It is important to determine whether children Infected with RSV-A ON1 have an increased risk of chronic respiratory complications, like asthma or bronchiolitis obliterans, in subsequent years. Knowledge of the long-term effect of RSV infections by genotype may guide improved long-term management strategies (34,35).

Conclusions

We found no relevant differences in demographic characteristics, clinical presentation, or severity scores for disease between children infected with different RSV subtypes and genotypes. Increased PICU admission rates and hospitalization times compared to children infected with the RSV-B BA9 genotype, however, were seen in those infected with the RSV-A ON1 genotype, suggesting that RSV-A may be associated with more serious clinical outcomes.

Acknowledgments

None.

Footnote

Reporting Checklist: The authors have completed the STROBE reporting checklist. Available at https://tp.amegroups.com/article/view/10.21037/tp-2025-aw-776/rc

Data Sharing Statement: Available at https://tp.amegroups.com/article/view/10.21037/tp-2025-aw-776/dss

Peer Review File: Available at https://tp.amegroups.com/article/view/10.21037/tp-2025-aw-776/prf

Funding: This study was supported by Sanming Project of Medicine in Shenzhen (No. SZSM202311021).

Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://tp.amegroups.com/article/view/10.21037/tp-2025-aw-776/coif). The authors have no conflicts of interest to declare.

Ethical Statement: The authors are accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. The study was conducted in accordance with the Declaration of Helsinki and its subsequent amendments. The study was approved by the Institutional Ethics Committee of Shenzhen Maternity and Child Healthcare Hospital (No. SFYLS[2023]001). The requirement of written informed consent was waived by the Ethics Committee because this study was a retrospective study.

Open Access Statement: This is an Open Access article distributed in accordance with the Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License (CC BY-NC-ND 4.0), which permits the non-commercial replication and distribution of the article with the strict proviso that no changes or edits are made and the original work is properly cited (including links to both the formal publication through the relevant DOI and the license). See: https://creativecommons.org/licenses/by-nc-nd/4.0/.

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