Epidemiological characteristics of respiratory syncytial virus in hospitalized patients in Guangzhou from 2018 to 2022

Objective To analyze the epidemiological characteristics of respiratory syncytial virus（RSV） before and after the COVID-19 epidemic in Guangzhou in recent years. Methods Nasopharynx swabs from hospitalized patients with acute respiratory infection were collected from two sentinel hospitals in Guangzhou（Guangdong Maternal and Child Health Hospital and Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University） from 2018 to 2022. Luminex respiratory multi-pathogen detection technology was used to detect and type RSV in samples. Results A total of 1 243 nasopharyngeal swab samples were collected. The overall positive rate of RSV was 6. 11%（76/1 243）, including 39 RSV-A（51. 32%, 39/76） and 37 RSV-B（48. 68%, 37/76）. The highest detection rate of RSV in children under 3 years old was 8. 79%（66 cases）. Compared with 2018（8. 30%, 22/265） and 2020（14. 78%, 30/203）, the positive rate of RSV decreased significantly in 2019（3. 13%, 10/319）, 2021（4. 08%, 10/245） and 2022（1. 90%, 4/211）. Compared with 2018（8. 30%,22/265） and 2020（14. 78%,30/203）,the positive rate of RSV decreased significantly in 2019（3. 13%,10/319）, 2021（4. 08%,10/245） and 2022（1. 90%,4/211）. Type A prevailed in 2018（19/22） and 2022（4/4）, type B（25/30） prevailed in 2020, type A and type B coexisted in 2019 and 2021. The detection rate showed had no statistically significant seasonal difference except for 2020 [7. 14%（3/42）, 16. 39%（10/61）, 27. 12%（16/59）, 0（0/42）,χ~2= 16. 975,P＜0. 001]. Among all the 76 RSV positive samples, 17（22. 37%） showed multiple infections. Among them, human rhinovirus was the most common virus causing mixed infection, accounting for 58. 83%（10/17） of the mixed infection. Conclusion RSV is a common respiratory virus prevalent in Guangzhou, and children under 3 years old are the main population infected with RSV. RSV infection is prevalent every other year, with the characteristics of alternating epidemic of type A and type B, and the anti-seasonal epidemic appeared after the COVID-19. After the outbreak of COVID-19, the detection rate of RSV increased significantly in 2020. With the change of the national COVID-19 epidemic prevention and control policy, the detection rate of RSV declined significantly during 2021-2022.

Assessment of antibody responses against SARS-CoV-2 in unvaccinated individuals and vaccinees from Omicron-BA.2 infection in Zhaoqing, Guangdong Province, China.

Currently, the majority of the global population has been vaccinated with the COVID-19 vaccine, and characterization studies of antibodies in vivo from Omicron breakthrough infection and naive infection populations are urgently needed to provide pivotal clues about accurate diagnosis, treatment, and next-generation vaccine design against SARS-CoV-2 infection. We showed that after infection with Omicron-BA.2, the antibody levels of specific IgM against the Wuhan strain and specific IgG against Omicron were not significantly elevated within 27 days of onset. Interestingly, in this study, the levels of humoral immunity against Omicron-specific IgM were significantly increased after breakthrough infection, suggesting that the detection of Omicron-specific IgM antibodies can be used as a test criterion of Omicron breakthrough infection. In addition, we observed that serums from unvaccinated individuals and the majority of vaccinated infections possessed only low or no neutralizing activity against Omicron at the onset of Omicron breakthrough infections, and at the later stage of Omicron-BA.2 breakthrough infection, levels of neutralization antibody against the Wuhan and Omicron strains were elevated in infected individuals. The findings of this study provide important clues for the diagnosis of Omicron breakthrough infections, antibody characterization studies and vaccine design against COVID-19.

Low infectious risk of re-positive COVID-19 patients: a single-center study.

OBJECTIVE: The aim of this study was to investigate the infectiousness of re-positive coronavirus disease 2019 (COVID-19) patients. METHODS: All nucleic acid testing (NAT) was performed using throat swabs, nasopharyngeal swabs, and anal swabs, which were tested by Fluorescent quantitative realtime PCR. Re-positive cases were defined as a discharged patient who re-tested positive by NAT. Micro-neutralization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was performed based on the methods for severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) viruses. IgM and IgG against the N protein of SARS-CoV-2 were determined by ELISA. RESULTS: A total 255 (16.04%) of 1590 COVID-19 patients were re-positive. The re-positive cases were more likely to occur in patients in the 20-39 years age group and in patients with disease of moderate severity. Quantitative PCR showed that cycle threshold (Ct) values and viral loads were both far lower than in the hospitalized COVID-19 patients. The viral load in re-positive cases was very low. Viral culture of the samples from re-positive patients showed no cytopathic effect, and NAT of the culture medium of viral cultures all exhibited negative results. CONCLUSION: The viral load in re-positive cases was very low; patients were not infectious and the risk of human-to-human transmission was extremely low. Discharged COVID-19 patients should undergo home health management for 3 weeks.

Serosurvey in SARS-CoV-2 inactivated vaccine-elicited neutralizing antibodies against authentic SARS-CoV-2 and its viral variants.

Various variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been emerging and circulating in different parts of the world. Millions of vaccine doses have been administered globally, which reduces the morbidity and mortality of coronavirus disease-2019 efficiently. Here, we assess the immune responses of individuals after two shots of BBIBP-CorV or CoronaVac inactivated vaccine. We measured neutralizing antibody responses after the second vaccination by using authentic SARS-CoV-2 and its viral variants. All the serum samples efficiently neutralized SARS-CoV-2 wild-type lineage, in contrast, a part of serum samples failed to neutralize Alpha, Beta, Gamma, Delta, or Eta lineages, and only several serum samples were able to neutralize Omicron lineage virus strains (BA.1 and BA.2) with low neutralization titer. As compared with the neutralization of SARS-CoV-2 wild-type lineage, the neutralization of all other SARS-CoV-2 variant lineages was significantly lower. Considering that all the SARS-CoV-2 mutation viruses challenged the antibody neutralization induced by BBIBP-CorV and CoronaVac, it is necessary to carry out a third booster vaccination to increase the humoral immune response against the SARS-CoV-2 mutation viruses.

Numerical investigation of airborne transmission of respiratory infections on the subway platform

Underground subway platforms are among the world’s busiest public transportation systems, but the airborne transmission mechanism of respiratory infections on these platforms has been rarely studied. Here, computational fluid dynamics (CFD) modeling is used to investigate the airflow patterns and infection risks in an island platform under two common ventilation modes: Mode 1- both sides have air inlets and outlets;Mode 2- air inlets are present at the two sides and outlets are present in the middle. Under the investigated scenario, airflow structure is characterized by the ventilation jet and human thermal plumes. Their interaction with the infector’s breathing jet imposes the front passenger under the highest exposure risk by short-range airborne route, with intake fractions up to 2.57% (oral breathing) or 0.63% (nasal breathing) under Mode 1;oral breathing of the infector may impose higher risks for the front passenger compared with nasal breathing. Pathogen are efficiently diluted as they travel further, in particular to adjacent crowds. The maximum and median value of intake fractions of passengers in adjacent crowds are respectively 0.093% and 0.016% (oral breathing), and 0.073% and 0.014% (nasal breathing) under Mode 1. Compared with Mode 1, the 2nd mode minimizes the interaction of ventilation jet and breathing jet, where the maximum intake fraction is only 0.34%, and the median value in the same crowd and other crowds are reduced by 23-63%. Combining published quanta generation rate data of COVID-19 and influenza infectors, the predicted maximum and median infection risks for passengers in the same crowds are respectively 1.46%−40.23% and 0.038%−1.67% during the 3−10 min waiting period, which are more sensitive to ventilation rate and exposure time compared with return air. This study can provide practical guidance for the prevention of respiratory infections in subway platforms.

Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant.

The SARS-CoV-2 Delta variant has spread rapidly worldwide. To provide data on its virological profile, we here report the first local transmission of Delta in mainland China. All 167 infections could be traced back to the first index case. Daily sequential PCR testing of quarantined individuals indicated that the viral loads of Delta infections, when they first become PCR-positive, were on average ~1000 times greater compared to lineage A/B infections during the first epidemic wave in China in early 2020, suggesting potentially faster viral replication and greater infectiousness of Delta during early infection. The estimated transmission bottleneck size of the Delta variant was generally narrow, with 1-3 virions in 29 donor-recipient transmission pairs. However, the transmission of minor iSNVs resulted in at least 3 of the 34 substitutions that were identified in the outbreak, highlighting the contribution of intra-host variants to population-level viral diversity during rapid spread.

Genomic Evolution and Variation of SARS-CoV-2 in the Early Phase of COVID-19 Pandemic in Guangdong Province, China.

Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) with unknown origin spread rapidly to 222 countries, areas or territories. To investigate the genomic evolution and variation in the early phase of COVID-19 pandemic in Guangdong, 60 specimens of SARS-CoV-2 were used to perform whole genome sequencing, and genomics, amino acid variation and Spike protein structure modeling analyses. Phylogenetic analysis suggested that the early variation in the SARS-CoV-2 genome was still intra-species, with no evolution to other coronaviruses. There were one to seven nucleotide variations (SNVs) in each genome and all SNVs were distributed in various fragments of the genome. The Spike protein bound with human receptor, an amino acid salt bridge and a potential furin cleavage site were found in the SARS-CoV-2 using molecular modeling. Our study clarified the characteristics of SARS-CoV-2 genomic evolution, variation and Spike protein structure in the early phase of local cases in Guangdong, which provided reference for generating prevention and control strategies and tracing the source of new outbreaks.