Clinical characteristics and host immunity responses of SARS-CoV-2 Omicron variant BA.2 with deletion of ORF7a, ORF7b and ORF8.

BACKGROUND: The pathogenicity and virulence of the Omicron strain have weakened significantly pathogenesis of Omicron variants. Accumulating data indicated accessory proteins play crucial roles in host immune evasion and virus pathogenesis of SARS-CoV-2. Therefore, the impact of simultaneous deletion of accessory protein ORF7a, ORF7b and ORF8 on the clinical characteristics and specific immunity in Omicron breakthrough infected patients (BIPs) need to be verified. METHODS: Herein, plasma cytokines were identified using a commercial Multi-cytokine detection kit. Enzyme-linked immunosorbent assay and pseudovirus neutralization assays were utilized to determine the titers of SARS-CoV-2 specific binding antibodies and neutralizing antibodies, respectively. In addition, an enzyme-linked immunospot assay was used to quantify SARS-CoV-2 specific T cells and memory B cells. RESULTS: A local COVID-19 outbreak was caused by the Omicron BA.2 variant, which featured a deletion of 871 base pairs (∆871 BA.2), resulting in the removal of ORF7a, ORF7b, and ORF8. We found that hospitalized patients with ∆871 BA.2 had significantly shorter hospital stays than those with wild-type (WT) BA.2. Plasma cytokine levels in both ∆871 BA.2 and WT BA.2 patients were within the normal range of reference, and there was no notable difference in the titers of SARS-CoV-2 ancestor or Omicron-specific binding IgG antibodies, neutralizing antibody titers, effector T cells, and memory B cells frequencies between ∆871 BA.2 and WT BA.2 infected adult patients. However, antibody titers in ∆871 BA.2 infected adolescents were higher than in adults. CONCLUSIONS: The simultaneous deletion of ORF7a, ORF7b, and ORF8 facilitates the rapid clearance of the BA.2 variant, without impacting cytokine levels or affecting SARS-CoV-2 specific humoral and cellular immunity in Omicron-infected individuals.

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.

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.

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.

Adenovirus infection in children hospitalized with pneumonia in Guangzhou, China.

BACKGROUND: HAdV infection can cause a variety of diseases. Although infections with HAdVs often are mild, life-threatening respiratory disease can occur. Pneumonia is one of the more serious types of HAdV-induced respiratory disease in children. In this study, we determined the prevalence and genotype of HAdVs among children hospitalized with pneumonia in Guangzhou, China. METHODS: Nasopharyngeal swabs (NPSs) were collected from children hospitalized with pneumonia in Guangzhou, China, from January 2013 to June 2019. HAdVs were detected by real-time polymerase chain reaction assay, and hexon, fiber, and penton gene were amplified and used for phylogenetic analysis. Epidemiological data were analyzed using SPSS16.0 software. RESULTS AND CONCLUSIONS: A total of 1778 children hospitalized with pneumonia were enrolled. The overall HAdV detection rate was 3.26%. And the yearly detection rate varied from around 2.5% in 2013-2017 to around 6% in 2018-2019. Children >5 years had the highest HAdV infection rate. 92.86% of HAdV sequences obtained in this study were belonged to species B, and no recombination was observed. HAdV-B7 and HAdV-B3 were the common types detected in the study period, with the predominant HAdV genotype shifted from HAdV-B3 in 2015-2016 to HAdV-B7 in 2017-2018. The discrepancies in HAdV detection rates in different study period and changes of HAdV predominant types over time highlighted the importance of continued surveillance.

ERG-Associated lncRNA (ERGAL) Promotes the Stability and Integrity of Vascular Endothelial Barrier During Dengue Viral Infection via Interaction With miR-183-5p.

Dengue virus (DENV) continues to be a major public health problem. DENV infection will cause mild dengue and severe dengue. Severe dengue is clinically manifested as serious complications, including dengue hemorrhagic fever and/or dengue shock syndrome (DHF/DSS), which is mainly characterized by vascular leakage. Currently, the pathogenesis of severe dengue is not elucidated thoroughly, and there are no known therapeutic targets for controlling the disease effectively. This study aimed to further reveal the potential molecular mechanism of severe dengue. In this study, the long non-coding RNA, ERG-associated lncRNA (lncRNA-ERGAL), was activated and significantly up-regulated in DENV-infected vascular endothelial cells. After knockdown of lncRNA-ERGAL, the expression of ERG, VE-cadherin, and claudin-5 was repressed; besides, cell apoptosis was enhanced, and cytoskeletal remodeling was disordered, leading to instability and increased permeability of vascular endothelial barrier during DENV infection. Fluorescence in situ hybridization (FISH) assay showed lncRNA-ERGAL to be mainly expressed in the cytoplasm. Moreover, the expression of miR-183-5p was found to increase during DENV infection and revealed to regulate ERG, junction-associated proteins, and the cytoskeletal structure after overexpression and knockdown. Then, ERGAL was confirmed to interact with miR-183-5p by luciferase reporter assay. Collectively, ERGAL acted as a miRNA sponge that can promote stability and integrity of vascular endothelial barrier during DENV infection via binding to miR-183-5p, thus revealing the potential molecular mechanism of severe dengue and providing a foundation for a promising clinical target in the future.

Avian Influenza Virus Detection Rates in Poultry and Environment at Live Poultry Markets, Guangdong, China.

We report the use of environmental samples to assess avian influenza virus activity in chickens at live poultry markets in China. Results of environmental and chicken samples correlate moderately well. However, collection of multiple environmental samples from holding, processing, and selling areas is recommended to detect viruses expected to have low prevalence.

Epidemiology, evolution and transmission of human metapneumovirus in Guangzhou China, 2013-2017.

Human metapneumovirus (hMPV), first identified in 2001, is a major viral respiratory pathogen that worldwide reported. Fundamental questions concerning the dynamics of viral evolution and transmission at both regional and global scales remain unanswered. In this study, we obtained 32 G gene and 51 F gene sequences of hMPV in Guangzhou, China in 2013-2017. Temporal and spatial phylogenetic analyses were undertaken by incorporating publicly available hMPV G gene (978) and F gene (767) sequences. The phylogenetic results show different global distribution patterns of hMPV before 1990, 1990-2005, and 2006-2017. A sharply increasing hMPV positive rate (11%) was detected in Guangzhou 2017, mainly caused by the B1 lineage of hMPV. A close phylogenetic relation was observed between hMPV strains from China and Japan, suggesting frequent hMPV transmissions between these regions. These results provide new insights into hMPV evolution, transmission, and spatial distribution and highlight Asia as a new epicenter for viral transmission and novel variant seeding after the year 2005. Conducting molecular surveillance of hMPV in Asian countries is critical for understanding the global circulation of hMPV and future vaccine design.