ABSTRACT
Objective To analyze the epidemic trend of respiratory pathogens under non-pharmaceutical interventions during the COVID-19 pandemic in Guangzhou and to explore the causes. Methods Respiratory pathogens, namely influenza A virus (FluA), influenza B virus (FluB), respiratory syncytial virus (RSV), human parainfluenza virus (PIV), adenovirus (AdV), Mycoplasma pneumoniae (MP) and Chlamydia pneumoniae (Cpn), were selected from a total of 14549 patients from December 1, 2019 to November 30, 2022. The differences in the positive constituent ratios and detection rates of each pathogen were analyzed and compared among different years, ages, genders, and seasons. Results The detection rate of RSV (1.03%) was higher than that of FluA (0.42%), PIV (0.41%), MP (0.23%), AdV (0.10%), FluB (0.06%) and Cpn (0.01%), and the difference was statistically significant. There was a statistically significant difference between two comparisons of the detection rates of FluA in different years, with the lowest in 2021 (0%) and the highest in 2022 (1.32%). The detection rate of RSV in 2021 (0.80%) showed a decreasing trend compared to 2020 (1.43%). FluA replaced RSV in 2020 and 2021 as the dominant strain in 2022. The detection rates of RSV (5.21%), PIV (1.88%) and AdV (0.47%) in children were higher than those of 0.97%, 0.44% and 0.09% in young and middle-aged adults, respectively. They were also higher than 0.20%, 0.10% and 0.03% in the elderly, respectively, with statistically significant differences. The detection rate of FluA in children (0.89%) was higher than that in the elderly (0.36%), with a statistically significant difference. There was a statistically significant difference in the detection rates of RSV and PIV between young and middle-aged adults and the elderly. RSV was the predominant strain in both children and young and middle-aged adults, but it was replaced by FluA in the elderly. The detection rates of RSV (1.31%) and PIV (0.58%) were higher in female than in male (0.88% and 0.32%, respectively), and the differences were statistically significant. The predominant strain in both male and female was RSV. There were seasonal differences in the detection rates of FluA, RSV and PIV. The detection rate of FluA was highest in summer (1.34%), followed by winter (0.47%), spring and autumn were lowest, both were 0%. The detection rate of RSV was highest in autumn (2.19%), followed by summer (1.32%), spring and winter were lower (0.32% and 0.45%, respectively). The detection rate of PIV was highest in winter (1.01%), and 0.16%, 0.23%, and 0.21% in spring, summer, and autumn, respectively. The dominant strain was RSV in spring, summer and autumn, which was replaced by PIV in winter. Among the 13,270 patients who were screened for all seven of these pathogens simultaneously, the top four pathogen-positive composition ratios were RSV (41.54%), FluA (21.15%), PIV (18.46%) and MP (10.38%). Single pathogen infection was dominated by RSV infection, accounting for 0.81%, and two pathogen infections were dominated by FluA+PIV and RSV+ MP infection, with one case each. Conclusions RSV was more prevalent and Cpn was less common among respiratory pathogens infections in Guangzhou under non-pharmacological intervention during the New Coronavirus-19 pandemic. Annual differences existed in the detection rates of FluA and RSV. The detection rates of RSV and PIV were highest in children, followed by young and middle-aged adults, and the elderly. The detection rates of RSV and PIV were higher in females than in males. There were seasonal differences in the detection rates of FluA, RSV and PIV, with the highest detection rates of FluA in summer, RSV in autumn and PIV in winter. Infection patterns were more common with single pathogens. The predominant strain was mostly RSV, except in 2022 and in the elderly was replaced by FluA, and was replaced by PIV in winter.
Subject(s)
COVID-19 , Respiratory Syncytial Virus Infections , Chlamydia Infections , Pneumonia, MycoplasmaABSTRACT
Background: The recent outbreak of infections by the 2019 novel coronavirus (2019-nCoV), the third zoonotic CoV has raised great public health concern. The demand for rapid and accurate diagnosis of this novel pathogen brought significant clinical and technological challenges. Currently, metagenomic next-generation sequencing (mNGS) and reverse-transcription PCR (RT-PCR) are the most widely used molecular diagnostics. Methods: 2019-nCoV infections were confirmed in 52 specimens by mNGS. Genomic information was analyzed and used for the design and development of an isothermal, CRISPR-based diagnostic for this novel virus. The diagnostic performance of CRISPR-nCoV was assessed and compared across three technology platforms (mNGS, RT-PCR and CRISPR). Results: 2019-nCoVs sequenced in our study were conserved with the Wuhan strain, and shared certain genetic similarity with SARS-CoV. A high degree of variation in the level of viral RNA was observed in clinical specimens. CRISPR-nCoV demonstrated a near single-copy sensitivity and great clinical sensitivity with a shorter turn-around time than RT-PCR. Conclusion: CRISPR-nCoV presents as a promising diagnostic option for the emerging pathogen.