First detection of multiple cases related to CV-A16 strain of B1c clade in Beijing in 2022.

Coxsackievirus A16 (CV-A16) is a significant etiologic agent of hand, foot, and mouth disease (HFMD) and herpangina (HA), with the capacity to progress to severe complications, including encephalitis, aseptic meningitis, acute flaccid paralysis, myocarditis, and other critical conditions. Beijing's epidemiological surveillance system, established in 2008, encompasses 29 hospitals and 16 district disease control centers. From 2019 to 2021, the circulation of CV-A16 was characterized by the co-circulation of B1a and B1b clades. Multiple cases of HFMD linked to clade B1c has not been reported in Beijing until 2022. This study enrolled 400 HFMD and 493 HA cases. Employing real-time RT-PCR, 368 enterovirus-positive cases were identified, with 180 selected for sequencing. CV-A16 was detected in 18.89% (34/180) of the cases, second only to CV-A6, identified in 63.33% (114/180). Full-length VP1 gene sequences were successfully amplified and sequenced in 22 cases, revealing the presence of clades B1a, B1b, and B1c in 14, 3, and 5 cases, respectively. A cluster of five B1c clade cases occurred between June 29 and July 17, 2022, within a 7-km diameter region in Shunyi District. Phylogenetic analysis of five complete VP1 gene sequences and two full-genome sequences revealed close clustering with the 2018 Indian strain (GenBank accession: MH780757.1) within the B1c India branch, with NCBI BLAST results showing over 98% similarity. Comparative sequence analysis identified three unique amino acid variations (P3S, V25A, and I235V). The 2022 Shunyi District HFMD cases represent the first instances of spatiotemporally correlated CV-A16 B1c clade infections in Beijing, underscoring the necessity for heightened surveillance of B1c clade CV-A16 in HFMD and HA in this region.

Severe pigeon paramyxovirus 1 infection in a human case with probable post-COVID-19 condition.

Pigeon paramyxovirus 1 (PPMV-1) is an antigenic host variant of avian paramyxovirus 1. Sporadic outbreaks of PPMV-1 infection have occurred in pigeons in China; however, few cases of human PPMV-1 infection have been reported. The purpose of this article is to report a case of severe human PPMV-1 infection in an individual with probable post-COVID-19 syndrome (long COVID) who presented with rapidly progressing pulmonary infection. The patient was a 66-year-old man who was admitted to the intensive care unit 11 days after onset of pneumonia and recovered 64 days after onset. PPMV-1 was isolated from the patient's sputum and in cloacal smear samples from domesticated pigeons belonging to the patient's neighbour. Residual severe acute respiratory syndrome coronavirus 2 was detected in respiratory and anal swab samples from the patient. Sequencing analyses revealed that the PPMV-1 genome belonged to genotype VI.2.1.1.2.2 and had the 112RRQKRF117 motif in the cleavage site of the fusion protein, which is indicative of high virulence. This case of cross-species transmission of PPMV-1 from a pigeon to a human highlights the risk of severe PPMV-1 infection in immunocompromised patients, especially those with long COVID. Enhanced surveillance for increased risk of severe viral infection is warranted in this population.

A Comparison of Clinical Characteristics of Infections with SARS-CoV-2 Omicron Subvariants BF.7.14 and BA.5.2.48 - China, October-December 2022.

What is already known about this topic?: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve, the clinical manifestations resulting from different SARS-CoV-2 variants may demonstrate significant variation. What is added by this report?: We conducted a comparative analysis of the clinical features associated with SARS-CoV-2 Omicron subvariants BF.7.14 and BA.5.2.48 infections. The results of our study indicate that there are no substantial differences in clinical manifestations, duration of illness, healthcare-seeking behaviors, or treatment between these two subvariants. What are the implications for public health practice?: Timely identification of alterations in the clinical spectrum is crucial for researchers and healthcare practitioners in order to enhance their comprehension of clinical manifestations, as well as the progression of SARS-CoV-2. Furthermore, this information is beneficial for policymakers in the process of revising and implementing appropriate countermeasures.

Stability of SARS-CoV-2 and persistence of viral nucleic acids on common foods and widely used packaging material surfaces.

SARS-CoV-2 is still spreading globally. Studies have reported the stability of SARS-CoV-2 in aerosols and on surfaces under different conditions. However, studies on the stability of SARS-CoV-2 and viral nucleic acids on common food and packaging material surfaces are insufficient. The study evaluated the stability of SARS-CoV-2 using TCID50 assays and the persistence of SARS-CoV-2 nucleic acids using droplet digital polymerase chain reaction on various food and packaging material surfaces. Viral nucleic acids were stable on food and material surfaces under different conditions. The viability of SARS-CoV-2 varied among different surfaces. SARS-CoV-2 was inactivated on most food and packaging material surfaces within 1 day at room temperature but was more stable at lower temperatures. Viruses survived for at least 1 week on pork and plastic at 4°C, while no viable viruses were detected on hairtail, orange, or carton after 3 days. There were viable viruses and a slight titer decrease after 8 weeks on pork and plastic, but titers decreased rapidly on hairtail and carton at -20°C. These results highlight the need for targeted preventive and disinfection measures based on different types of foods, packaging materials, and environmental conditions, particularly in the cold-chain food trade, to combat the ongoing pandemic.

Dynamic Changes of ORF1ab and N Gene Ct Values in COVID-19 Omicron Inpatients of Different Age Groups - Beijing Municipality, China, November-December 2022.

Introduction: In November 2021, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant was identified as the variant of concern and has since spread globally, replacing other cocirculating variants. To better understand the dynamic changes in viral load over time and the natural history of the virus infection, we analyzed the expression of the open reading frames 1ab (ORF1ab) and nucleocapsid (N) genes in patients infected with Omicron. Methods: We included patients initially admitted to the hospital for SARS-CoV-2 infection between November 5 and December 25, 2022. We collected daily oropharyngeal swabs for quantitative reverse transcriptase-polymerase chain reaction tests using commercial kits. We depicted the cycle threshold (Ct) values for amplification of ORF1ab and N genes from individual patients in age-specific groups in a time series. Results: A total of 480 inpatients were included in the study, with a median age of 59 years (interquartile range, 42 to 78; range, 16 to 106). In the <45-year-old age group, the Ct values for ORF1ab and N gene amplification remained below 35 for 9.0 and 11.5 days, respectively. In the ≥80-year-old age group, the Ct values for ORF1ab and N genes stayed below 35 for 11.5 and 15.0 days, respectively, which was the longest among all age groups. The Ct values for N gene amplification took longer to rise above 35 than those for ORF1ab gene amplification. Conclusion: The time to test negative varied among different age groups, with viral nucleic acid shedding taking longer in older age groups compared to younger age groups. As a result, the time to resolution of Omicron infection increased with increasing age.

Epidemiological features, genomic characteristics, and origin tracing of the COVID-19 outbreaks in Beijing from January to September 2022.

Different variants of severe acute respiratory syndrome coronavirus 2 have been discovered globally. At present, the Omicron variant has been extensively circulated worldwide. There have been several outbreaks of the Omicron variant in China. Here, we investigated the epidemiologic, genetic characteristics, and origin-tracing data of the outbreaks of COVID-19 in Beijing from January to September 2022. During this time, 19 outbreaks occurred in Beijing, with the infected cases ranging from 2 to 2230. Two concern variants were detected, with eight genotypes. Based on origin tracing analysis, two outbreaks were from the cold-chain transmission and three from items contaminated by humans. Imported cases have caused other outbreaks. Our study provided a detailed analysis of Beijing's outbreaks and valuable information to control the outbreak's spread.

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.

Screening and Analysis of Serum Protein Biomarkers Infected by Coronavirus Disease 2019 (COVID-19).

Coronavirus disease 2019 (COVID-19) has spread widely around the world, and in-depth research on COVID-19 is necessary for biomarkers and target drug discovery. This analysis collected serum from six COVID-19-infected patients and six healthy people. The protein changes in the infected and healthy control serum samples were evaluated by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and high-performance liquid chromatography (HPLC). The differential protein signature in both groups was retrieved and analyzed by the Kyoto Encyclopedia of Gene and Genomes (KEGG), Gene ontology, COG/KOG, protein-protein interaction, and protein domain interactions tools. We shortlisted 24 differentially expressed proteins between both groups. Ten genes were significantly up-regulated in the infection group, and fourteen genes were significantly down-regulated. The GO and KEGG pathway enrichment analysis suggested that the chromosomal part and chromosome were the most enriched items. The oxytocin signaling pathway was the most enriched item of KEGG analysis. The netrin module (non-TIMP type) was the most enriched protein domain in this study. Functional analysis of S100A9, PIGR, C4B, IL-6R, IGLV3-19, IGLV3-1, and IGLV5-45 revealed that SARS-CoV-2 was closely related to immune response.

Assessing the feasibility of sustaining SARS-CoV-2 local containment in China in the era of highly transmissible variants.

BACKGROUND: The SARS-CoV-2 containment strategy has been successful in mainland China prior to the emergence of Omicron. However, in the era of highly transmissible variants, whether it is possible for China to sustain a local containment policy and under what conditions China could transition away from it are of paramount importance at the current stage of the pandemic. METHODS: We developed a spatially structured, fully stochastic, individual-based SARS-CoV-2 transmission model to evaluate the feasibility of sustaining SARS-CoV-2 local containment in mainland China considering the Omicron variants, China's current immunization level, and nonpharmaceutical interventions (NPIs). We also built a statistical model to estimate the overall disease burden under various hypothetical mitigation scenarios. RESULTS: We found that due to high transmissibility, neither Omicron BA.1 nor BA.2 could be contained by China's pre-Omicron NPI strategies which were successful prior to the emergence of the Omicron variants. However, increased intervention intensity, such as enhanced population mobility restrictions and multi-round mass testing, could lead to containment success. We estimated that an acute Omicron epidemic wave in mainland China would result in significant number of deaths if China were to reopen under current vaccine coverage with no antiviral uptake, while increasing vaccination coverage and antiviral uptake could substantially reduce the disease burden. CONCLUSIONS: As China's current vaccination has yet to reach high coverage in older populations, NPIs remain essential tools to maintain low levels of infection while building up protective population immunity, ensuring a smooth transition out of the pandemic phase while minimizing the overall disease burden.

Mass screening is a key component to fight against SARS-CoV-2 and return to normalcy.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had highly transmissible and pathogenic, which caused serious economic loss and hazard to public health. Different countries have developed strategies to deal with the COVID-19 pandemic that fit their epidemiological situations, capacities, and values. Mass screening combined with control measures rapidly reduced the transmission of the SARS-CoV-2 infection. The COVID-19 pandemic has dramatically highlighted the essential role of diagnostics capacity in the control of communicable diseases. Mass screening has been increasingly used to detect suspected COVID-19 cases and their close contacts, asymptomatic case, patients attending fever clinics, high-risk populations, employees, even all population to identify infectious individuals. Mass screening is a key component to fight against SARS-CoV-2 and return to normalcy. Here we describe the history of mass screening, define the scope of mass screening, describe its application scenarios, and discuss the impact and challenges of using this approach to control COVID-19. We conclude that through a comprehension screening program and strong testing capabilities, mass screening could help us return to normalcy more quickly.

Assessing the feasibility of sustaining SARS-CoV-2 local containment in China in the era of highly transmissible variants.

We developed a spatially structured, fully stochastic, individual-based SARS-CoV-2 transmission model to evaluate the feasibility of sustaining SARS-CoV-2 local containment in mainland China considering currently dominant Omicron variants, China's current immunization level, and non-pharmaceutical interventions (NPIs). We also built a statistical model to estimate the overall disease burden under various hypothetical mitigation scenarios. We found that due to high transmissibility, neither Omicron BA.1 or BA.2 could be contained by China's pre-Omicron NPI strategies which were successful prior to the emergence of the Omicron variants. However, increased intervention intensity, such as enhanced population mobility restrictions and multi-round mass testing, could lead to containment success. We estimated that an acute Omicron epidemic wave in mainland China would result in significant number of deaths if China were to reopen under current vaccine coverage with no antiviral uptake, while increasing vaccination coverage and antiviral uptake could substantially reduce the disease burden. As China's current vaccination has yet to reach high coverage in older populations, NPIs remain essential tools to maintain low levels of infection while building up protective population immunity, ensuring a smooth transition out of the pandemic phase while minimizing the overall disease burden.

Genomic characteristics of SARS-CoV-2 in Beijing, China, 2021.

At present, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread worldwide, which has emerged multiple variants and brought a threat to global public health. To analyze the genomic characteristics and variations of SARS-CoV-2 imported into Beijing, we collected the respiratory tract specimens of 112 cases of coronavirus disease 2019 (COVID-19) from January to September 2021 in Beijing, China, including 40 local cases and 72 imported cases. The whole-genome sequences of the viruses were sequenced by the next-generation sequencing method. Variant markers and phylogenic features of SARS-CoV-2 were analyzed. Our results showed that in all 112 sequences, the mutations were concentrated in spike protein. D614G was found in all sequences, and mutations including L452R, T478K, P681R/H, and D950N in some cases. Furthermore, 112 sequences belonged to 23 lineages by phylogenetic analysis. B.1.1.7 (Alpha) and B.1.617.2 (Delta) lineages were dominant. Our study drew a variation image of SARS-CoV-2 and could help evaluate the potential risk of COVID-19 for pandemic preparedness and response.

Importation of SARS-CoV-2 Omicron variant in Beijing, China.

Omicron (B.1.1.529), the fifth variant of concern (VOC) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was firstly identified in November 2021 in South Africa. Omicron contains far more genome mutations than any other VOCs ever found, raising significant concerns about its increased transmissibility and immune evasion. Here, we report the importation of the Omicron variant into Beijing, China, in December 2021. Full-length genome sequences of five imported strains were obtained, with their genetic features characterized. Each strain contained 57 to 61 nucleotide substitutions, 39 deletions, and 9 insertions in the genome. Thirty to thirty-two amino acid changes were found in the spike proteins of the five strains. The phylogenetic tree constructed by the maximum likelihood method showed that all five imported genomes belonged to Omicron (BA.1) (alias of B.1.1.529.1), which is leading to the current surge of coronavirus disease 2019 (COVID-19) cases worldwide. The globally increased COVID-19 cases driven by the Omicron variant pose a significant challenge to disease prevention and control in China. Continuous viral genetic surveillance and increased testing among international travellers are required to contain this highly contagious variant.

Substitution of I222L-E119V in neuraminidase from highly pathogenic avian influenza H7N9 virus exhibited synergistic resistance effect to oseltamivir in mice.

That the high frequency and good replication capacity of strains with reduced susceptibility to neuraminidase inhibitors (NAIs) in highly pathogenic avian influenza H7N9 (HPAI H7N9) virus made it a significance to further study its drug resistance. HPAI H7N9 viruses bearing NA I222L or E119V substitution and two mutations of I222L-E119V as well as their NAIs-sensitive counterpart were generated by reverse genetics for NA inhibition test and replication capability evaluation in vitro. The attenuated H7N9/PR8 recombinant viruses were developed to study the pathogenicity and drug resistance brought by the above substitutions to mice. The IC50 fold change of oseltamivir to HPAI H7N9 with NA222L-119V is 306.34 times than that of its susceptible strain, and 3.5 times than the E119V mutant virus. HPAI H7N9 bearing NA222L-119V had good replication ability with peak value of more than 6log10 TCID50/ml in MDCK cells. H7N9/PR8 virus bearing NA222L-119V substitutions leaded to diffuse pneumonia, significant weight loss and fatality in mice. NA E119V made H7N9/PR8 virus resistant to oseltamivir, and I222L-E119V had synergistic resistance to oseltamivir in mice. Due to the good fitness of drug resistant strains of HPAI H7N9 virus, it is necessary to strengthen drug resistance surveillance and new drug research.

Retrospective study of clinical characteristics and viral etiologies of patients with viral pneumonia in Beijing.

AIMS: The virus is common in patients with viral pneumonia. However, the viral etiology and clinical features of patients with viral pneumonia in China remain unclear. The main purpose of this study was to analyze the viral causes and epidemiology of patients with viral pneumonia in Beijing, which can significantly improve the pertinence and accuracy of clinical treatment of the disease. METHODS: Firstly, 1539 respiratory specimens of pneumonia (oropharyngeal swabs, nasopharyngeal swabs, saliva samples and bronchoalveolar lavage fluid) were collected from 19 hospitals in Beijing from September 2015 to August 2018. Then, TaqMan low-density microfluidic chip technology was used to detect viral pneumonia specimens in 1539 respiratory tract specimens of pneumonia and determine the types of viral bacteria in them. Lastly, the analysis of demographic, clinical and etiological data of patients with viral pneumonia was performed. RESULTS: The results showed that among the 1539 respiratory tract specimens with pneumonia, 760 were detected as viral pneumonia specimens, with a positive rate of 49.4%. Among which, 467 were infected with mono-viral and 293 were infected with multi-viral. Influenza A virus (Flu A), mycoplasma pneumoniae (MPn), Ebola virus (EBV) and herpes simplex virus type 1 (HSV-1) were the major viral components in the samples of these patients. Furthermore, these viral species were significantly associated with sample sources, onset season and certain clinical characteristics. DISCUSSION: Our findings may provide corresponding treatment strategies for viral pneumonia patients infected with specific viruses.

Epidemiology and Genotypic Diversity of Eurasian Avian-Like H1N1 Swine Influenza Viruses in China.

Eurasian avian-like H1N1 (EA H1N1) swine influenza virus (SIV) outside European countries was first detected in Hong Kong Special Administrative Region (Hong Kong, SAR) of China in 2001. Afterwards, EA H1N1 SIVs have become predominant in pig population in this country. However, the epidemiology and genotypic diversity of EA H1N1 SIVs in China are still unknown. Here, we collected the EA H1N1 SIVs sequences from China between 2001 and 2018 and analyzed the epidemic and phylogenic features, and key molecular markers of these EA H1N1 SIVs. Our results showed that EA H1N1 SIVs distributed in nineteen provinces/municipalities of China. After a long-time evolution and transmission, EA H1N1 SIVs were continuously reassorted with other co-circulated influenza viruses, including 2009 pandemic H1N1 (A(H1N1)pdm09), and triple reassortment H1N2 (TR H1N2) influenza viruses, generated 11 genotypes. Genotype 3 and 5, both of which were the reassortments among EA H1N1, A(H1N1)pdm09 and TR H1N2 viruses with different origins of M genes, have become predominant in pig population. Furthermore, key molecular signatures were identified in EA H1N1 SIVs. Our study has drawn a genotypic diversity image of EA H1N1 viruses, and could help to evaluate the potential risk of EA H1N1 for pandemic preparedness and response.

A single N342D substitution in Influenza B Virus NA protein determines viral pathogenicity in mice.

Influenza B virus (IBV) is one of the most important human respiratory viruses: it causes approximately one-third of the global influenza-related disease burden each year. However, compared with the several pathogenicity-related molecular markers that have been identified for influenza A virus (IAV), little is known about potential IBV pathogenicity-related markers. Here, although the IBV strain B/Anhui-Tunxi/1528/2014 (AH1528/14) exhibited a more efficient replication ability in vitro and higher pathogenicity in vivo compared with IBV strain B/Anhui-Baohe/127/2015 (AH127/15), only three amino acids differences (HAA390E, NAN342D and PB1V212I) were observed among their full genomes. The contributions of each amino acid difference to the virus pathogenicity were further investigated. Compared with the wild type IBV virus rAH127, the recombinant virus harbouring a single substitution of HAA390E had a similar phenotype, whereas the recombinant virus harbouring PB1V212I replicated to a moderately higher titre in both MDCK cells and in mice. Notably, the virus harbouring NAN342D showed significantly better growth properties in MDCK cells and higher fatality rates in mice. In addition, the presence of NAN342D dramatically enhanced the viral neuraminidase activity. In conclusion, our study identified a novel IBV molecular marker, NAN342D, that could significantly increase the virulence of IBV in mice.