Pathogen Profile of Children Hospitalised with Severe Acute Respiratory Infections during COVID-19 Pandemic in the Free State Province, South Africa

Abstract

Severe acute respiratory infections (SARI) contribute to mortality in children ≤5 years. Their microbiological aetiologies are often unknown and may be exacerbated in light of coronavirus disease 19 (COVID-19). This study reports on respiratory pathogens in children ≤5 years (n = 84) admitted with SARI during and between the second and third waves of COVID-19 infection in South Africa. Nasopharyngeal/oropharyngeal swabs collected were subjected to viral detection using QIAstat-Dx® Respiratory SARS-CoV-2 Panel. The results revealed viral positivity and negativity detection rates of 88% (74/84) and 12% (10/84), respectively. Of the 21 targeted pathogens, human rhinovirus/enterovirus (30%), respiratory syncytial virus (RSV; 26%), and severe acute respiratory syndrome coronavirus 2 (24%) were mostly detected, with other viruses being 20% and a co-infection rate of 64.2% (54/84). Generally, RSV-positive samples had lower Ct values, and fewer viruses were detected during the third wave. Changes in the circulation patterns of respiratory viruses with total absence of influenza virus could be attributed to measures against COVID-19 transmission, which may result in waned immunity, thereby increasing susceptibility to severe infections in the following season. High viral co-infection rate, as detected, may complicate diagnosis. Nonetheless, accurate identification of the pathogens may guide treatment decisions and infection control.

Metagenomics characterization of respiratory viral RNA pathogens in children under five years with severe acute respiratory infection in the Free State, South Africa

“…However, both studies highlighted the several advantages of mNGS over the mRT-PCR and suggested that lower abundance of the viruses detected by RT-PCR could have resulted in a lower detection rate by mNGS. Furthermore, corresponding with the previously reported data from the mRT-PCR assay in the same patients, 25 RSV and HRV were the most predominant viral pathogens detected in the respiratory samples by the mNGS-based approach. This observation agrees with others who showed that RSV and HRV are the most prevalent viruses in children with SARI.…”

“…Furthermore, corresponding with the previously reported data from the mRT‐PCR assay in the same patients, 25 RSV and HRV were the most predominant viral pathogens detected in the respiratory samples by the mNGS‐based approach. This observation agrees with others who showed that RSV and HRV are the most prevalent viruses in children with SARI 4,8,45,46 .…”

“…Recently, mNGS reports have been benchmarked against traditional methods such as mRT‐PCR or culture to further establish the utility of mNGS in clinical diagnostics. Compared with the 97.6% detectability rate in this study by mNGS, mRT‐PCR results in the same participants yielded 88% positivity detection rate 25 . Besides, mNGS identified more viral pathogens (179 vs. 154) than the mRT‐PCR.…”

“…The detailed demographic and clinical characteristics of the participants enrolled in this study are as previously described 25 . Demographically, 34 (40.4%) were females, while 50 (59.6%) were males.…”

Immediate and long-term changes in the epidemiology, infection spectrum, and clinical characteristics of viral and bacterial respiratory infections in Western China after the COVID-19 outbreak: a modeling study

“…This is due to the overall decrease in bacterial respiratory infections due to NPIs. The positive rate of viral infection in ARI patients aged <5 years increased after COVID-19, as was also seen in South Africa, where NPIs during COVID-19 changed the infection spectrum, making children more likely to be infected with other respiratory viruses [27]. The proportion of ARI patients with clinical symptoms decreased after COVID-19, which may be related to the decreased positive rates of viral and bacterial infections after COVID-19.…”