A Tale of Two Cities: From Influenza HxNy to SARS-CoV-z

Respiratory Viruses and Mycoplasma Pneumoniae Surveillance Among Hospitalized Children with Acute Respiratory Infections - Wuhan City, Hubei Province, China, September-November 2023

What is already known about this topic?

Acute respiratory infections (ARIs) are a significant contributor to illness and death in children. There has been a notable rise in the occurrence of ARIs and the associated pathogens in China, which has garnered worldwide attention.

What is added by this report?

This study conducted a retrospective analysis of the clinical characteristics of children with ARIs in Wuhan City from September to November 2023. The study evaluated the epidemiological patterns of common respiratory viruses and Mycoplasma pneumoniae (MP), revealing a continued prevalence of MP and a growing trend of influenza. Our findings emphasize that the circulation of respiratory viruses and MP has not returned to pre-pandemic levels, underscoring the importance of enhancing surveillance for respiratory pathogens.

What are the implications for public health practice?

The epidemiology of ARIs and the pathogens involved need to be emphasized. This highlights the importance of developing policies to protect children from respiratory pathogens such as MP, influenza, and respiratory syncytial virus.

Seeing the T cell Immunity of SARS-CoV-2 and SARS-CoV: Believing the Epitope-Oriented Vaccines

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the end of 2019 stimulated vigorous research efforts in immunology and vaccinology. In addition to innate immune responses, both virus-specific humoral and cellular immune responses are of importance for viral clearance. T cell epitopes play a central role in T cell-based immune responses. Herein, we summarized the peptide/major histocompatibility complex (pMHC) structures of the SARS-CoV-2-derived T cell epitopes available in the Protein Data Bank (PDB) and proposed the challenge and opportunities for using of T cell epitopes in future vaccine development efforts. A total of 27 SARS-CoV-2 related pMHC structures and five complexes with T cell receptors were retrieved. The peptides are mainly distributed on spike (S), nucleocapsid (N), and ORF1ab proteins. Most peptides are conserved among variants of concerns (VOCs) for SARS-CoV-2, except for several mutated peptides located in the S protein. The structures of human leukocyte antigen (HLA) complexed with seven epitopes derived from SARS-CoV were also retrieved, which showed a potential cross T cell immunity with SARS-CoV-2. Structural studies of antigenic peptides from SARS-CoV-2 and SARS-CoV help to visualize the processes and the mechanisms of cross T cell immunity. T cell epitope-oriented vaccines are potential next-generation vaccines for SARS-CoV-2, which are worthy of further investigation.

Inactivated vaccine fueled adaptive immune responses to Omicron in 2-year COVID-19 convalescents

Over 3 years, humans have experienced multiple rounds of global transmission of SARS-CoV-2 and its variants. In addition, the widely used vaccines against SARS-CoV-2 involve multiple strategies of development and inoculation. Thus, the acquired immunity established among humans is complicated, and there is a lack of understanding within a panoramic vision. Here, we provided the special characteristics of the cellular and humoral responses in 2-year convalescents after inactivated vaccines, in parallel to vaccinated COVID-19 naïve persons and unvaccinated controls. The decreasing trends of the IgG, IgA, and NAb, but not IgM of the convalescents were reversed by the vaccination. Both cellular and humoral immunity in convalescents after vaccination were higher than the vaccinated COVID-19 naïve persons. Notably, inoculation with inactivated vaccine fueled the NAb to BA.1, BA.2, BA.4, and BA.5 in 2-year convalescents, much higher than the NAb during 6 months and 1 year after symptoms onset. And no obvious T cell escaping to the S protein was observed in 2-year convalescents after inoculation. The study provides insight into the complicated features of human acquired immunity to SARS-CoV-2 and variants in the real world, indicating that promoting vaccine inoculation is essential for achieving herd immunity against emerging variants, especially in convalescents.

A black goat-derived novel genotype of Aichi virus C blurs the boundary between caprine and porcine kobuviruses

Aichi virus C, a species in the genus Kobuvirus, causes diarrhea diseases in pigs and goats and pose health threat and economic loss for stock farming. A nearly complete genome sequence of caprine kobuvirus GCCDC14 was obtained from an anal swab of a black goat died from diarrhea collected in Hubei, China in 2019. Phylogenetic analyses suggested that GCCDC14 is a novel genotype of Aichi virus C, forming a sister branch to other caprine kobuviruses, with P1 and VP0 genes more closely related to porcine kobuviruses and VP3 in an independent branch. Compared to previous caprine kobuviruses, unique amino acid changes in the poly-l-proline type II helix structure of VP0 and VP1 were found, which may affect the cellular machinery of host and pathogenicity. This study indicates the presence of the kobuvirus with continuously evolving features and emphasizes the surveillance and genetic evolution investigation of kobuviruses for safety of husbandry.

Characterisation of SARS-CoV-2 variants in Beijing during 2022: an epidemiological and phylogenetic analysis

BACKGROUND

Due to the national dynamic zero-COVID strategy in China, there were no persistent local transmissions of SARS-CoV-2 in Beijing before December, 2022. However, imported cases have been frequently detected over the past 3 years. With soaring growth in the number of COVID-19 cases in China recently, there are concerns that there might be an emergence of novel SARS-CoV-2 variants. Routine surveillance of viral genomes has been carried out in Beijing over the last 3 years. Spatiotemporal analyses of recent viral genome sequences compared with that of global pooled and local data are crucial for the global response to the ongoing COVID-19 pandemic.

METHODS

We routinely collected respiratory samples covering both imported and local cases in Beijing for the last 3 years (of which the present study pertains to samples collected between January and December, 2022), and then randomly selected samples for analysis. Next-generation sequencing was used to generate the SARS-CoV-2 genomes. Phylogenetic and population dynamic analyses were performed using high-quality complete sequences in this study.

FINDINGS

We obtained a total of 2994 complete SARS-CoV-2 genome sequences in this study, among which 2881 were high quality and were used for further analysis. From Nov 14 to Dec 20, we sequenced 413 new samples, including 350 local cases and 63 imported cases. All of these genomes belong to the existing 123 Pango lineages, showing there are no persistently dominant variants or novel lineages. Nevertheless, BA.5.2 and BF.7 are currently dominant in Beijing, accounting for 90% of local cases since Nov 14 (315 of 350 local cases sequenced in this study). The effective population size for both BA.5.2 and BF.7 in Beijing increased after Nov 14, 2022.

INTERPRETATION

The co-circulation of BF.7 and BA.5.2 has been present in the current outbreak since Nov 14, 2022 in Beijing, and there is no evidence that novel variants emerged. Although our data were only from Beijing, the results could be considered a snapshot of China, due to the frequent population exchange and the presence of circulating strains with high transmissibility.

FUNDING

National Key Research and Development Program of China and Strategic Priority Research Program of the Chinese Academy of Sciences.

TRANSLATION

For the Chinese translation of the abstract see Supplementary Materials section.

Effects of the Enhanced Public Health Intervention during the COVID‐19 Epidemic on Respiratory and Gastrointestinal Infectious Diseases in China

The public health interventions to mitigate coronavirus disease 2019 (COVID‐19) could also potentially reduce the global activity of influenza. However, this strategy's impact on other common infectious diseases is unknown. We collected data of 10 respiratory infectious (RI) diseases, influenza‐like illnesses (ILIs), and seven gastrointestinal infectious (GI) diseases during 2015–2020 in China and applied two proportional tests to check the differences in the yearly incidence and mortality, and case‐fatality rates (CFRs) over the years 2015–2020. The results showed that the overall RI activity decreased by 7.47%, from 181.64 in 2015–2019 to 168.08 per 100 000 in 2020 (p < 0.001); however, the incidence of influenza was seen to have a 16.08% escalation (p < 0.001). In contrast, the average weekly ILI percentage and positive influenza virus rate decreased by 6.25% and 61.94%, respectively, in 2020 compared to the previous 5 years (all p < 0.001). The overall incidence of GI decreased by 45.28%, from 253.73 in 2015–2019 to 138.84 in 2020 per 100 000 (p < 0.001), and with the greatest decline seen in hand, foot, and mouth disease (HFMD) (64.66%; p < 0.001). The mortality and CFRs from RI increased by 128.49% and 146.95%, respectively, in 2020, compared to 2015–2019 (p < 0.001). However, the mortality rates and CFRs of seven GI decreased by 70.56% and 46.12%, respectively (p < 0.001). In conclusion, China's COVID‐19 elimination/containment strategy is very effective in reducing the incidence rates of RI and GI, and ILI activity, as well as the mortality and CFRs of GI diseases.

COVID‐19 elimination strategy in China decreased the activity of respiratory infectious diseases (RI) and influenza‐like illnesses.

A 16.08% escalation was seen in influenza in 2020 compared to 2015–2019.

The mortality of RI increased slightly in 2020 compared to 2015–2019.

COVID‐19 elimination strategy in China decreased dramatically the activity and mortality of gastrointestinal infectious diseases.