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.

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.

Difference of Clinical Characteristics in Patients with Omicron and Delta Variants of SARS-CoV-2 in Beijing, China

Background Delta and Omicron are two main variants that have been prevalent since 2021. However, the Omicron variant of severe acute respiratory syndrome coronavirus 2 shows a less severe clinical presentation and high transmissibility. Therefore, we carried out this retrospective study to evaluate Omicron severity compared with the Delta variant and further comprehend the differences in clinical characteristics in patients with the Omicron variant. Methods We extracted clinical data and compared clinical severity, symptoms, vaccination status, laboratory parameters, viral shedding time, and computed tomography (CT) imaging between the two groups of patients, which included 109 COVID-19 cases with the Delta variant and 183 cases with the Omicron variant, from January 19 to April 1, 2022, in Beijing Ditan Hospital. In addition, the Beijing Center for Disease Prevention and Control conducted whole-genome sequencing. Results We obtained 94 strains of variants of concern/Delta and 110 strains of variants of concern/Omicron. For the 110 Omicron strains, three were assigned as BA.1.1, 53 as BA.2, and 54 as BA.2.2. Among patients with the Delta variant, 54% (59/109) were moderate, which was significantly higher than that of patients with the Omicron variant (7% (12/183), P < 0.001). The number of patients with mild symptoms in the Omicron group was significantly higher than in the Delta group (80% vs. 35%, P < 0.001). Compared with the Omicron group, patients with underlying diseases or obesity, 60 years or older, or unvaccinated in the Delta group had more severe disease, and there was a significant difference between the two groups. The viral shedding time in the Omicron group was shorter than in the Delta group ((11.9 ± 5.9) vs. (14.0 ± 5.8) days, P = 0.003). Among the 183 patients in the Omicron group, 104 (57%) had dry or sore throat symptoms, more than those in the Delta group (34% (37/109);P < 0.001). In the Delta group, patients in the moderate group had more fever and cough symptoms than those in the mild group. The remission time of CT imaging in the Omicron group was shorter than in the Delta group ((9.0 ± 5.2) vs. (13.2 ± 4.2) days, P = 0.018). Conclusions Patients with Delta variants are more likely to have pneumonia, mainly with fever and cough symptoms, while patients with the Omicron variant are mostly mild, with more prominent dry or sore throat symptoms. In addition, patients with the Omicron variant have a short viral shedding time and rapid absorption of pneumonia.

A Retrospective Modeling Study of the Targeted Non-Pharmaceutical Interventions During the Xinfadi Outbreak in the Early Stage of the COVID-19 Pandemic - Beijing, China, 2020.

What is already known about this topic?: China has repeatedly contained multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks through a comprehensive set of targeted non-pharmaceutical interventions (NPIs). However, the effectiveness of such NPIs has not been systematically assessed. What is added by this report?: A multilayer deployment of case isolation, contact tracing, targeted community lockdowns, and mobility restrictions could potentially contain outbreaks caused by the SARS-CoV-2 ancestral strain, without the requirement of city-wide lockdowns. Mass testing could further aid in the efficacy and speed of containment. What are the implications for public health practice?: Pursuing containment in a timely fashion at the beginning of the pandemic, before the virus had the opportunity to spread and undergo extensive adaptive evolution, could help in averting an overall pandemic disease burden and be socioeconomically cost-effective.

Association between COVID-19 and Male Fertility: Systematic Review and Meta-Analysis of Observational Studies.

PURPOSE: Whether COVID-19 reduces male fertility remains requires further investigation. This meta-analysis and systematic review evaluated the impact of COVID-19 on male fertility. MATERIALS AND METHODS: The literature in PubMed, Embase, MEDLINE, Web of Science, and Cochrane Library up to January 01, 2022 was systematically searched, and a meta-analysis was conducted to investigate the effect of COVID-19 on male fertility. Totally 17 studies with a total of 1,627 patients and 1,535 control subjects were included in our meta-analysis. RESULTS: Regarding sperm quality, COVID-19 decreased the total sperm count (p=0.012), sperm concentration (p=0.001), total motility (p=0.001), progressive sperm motility (p=0.048), and viability (p=0.031). Subgroup analyses showed that different control group populations did not change the results. It was found that during the illness stage of COVID-19, semen volume decreased, and during the recovery stage of COVID-19, sperm concentration and total motility decreased <90 days. We found that sperm concentration and total motility decreased during recovery for ≥90 days. Fever because of COVID-19 significantly reduced sperm concentration and progressive sperm motility, and COVID-19 without fever ≥90 days, the sperm total motility and progressive sperm motility decreased. Regarding disease severity, the moderate type of COVID-19 significantly reduced sperm total motility, but not the mild type. Regarding sex hormones, COVID-19 increased prolactin and estradiol. Subgroup analyses showed that during the illness stage, COVID-19 decreased testosterone (T) levels and increased luteinizing hormone levels. A potential publication bias may have existed in our meta-analysis. CONCLUSIONS: COVID-19 in men significantly reduced sperm quality and caused sex hormone disruption. COVID-19 had long-term effects on sperm quality, especially on sperm concentration and total motility. It is critical to conduct larger multicenter studies to determine the consequences of COVID-19 on male fertility.

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.

Interruption of Influenza Transmission under Public Health Emergency Response for COVID-19: a Study Based on Real-World Data from Beijing, China.

To estimate the effect of the corona virus disease 2019 (COVID-19) control measures taken to mitigate community transmission in many regions, we analyzed data from the influenza surveillance system in Beijing from week 27 of 2014 to week 26 of 2020. We collected weekly numbers of influenza-like illness (ILI) cases, weekly positive proportion of ILI cases, weekly ILI case proportion in outpatients, and the dates of implementation of COVID-19 measures. We compared the influenza activity indicators of the 2019/2020 season with the preceding five seasons and built two ARIMAX models to estimate the effectiveness of COVID-19 measures declared since January 24, 2020 by the emergency response. Based on the observed data, compared to the preceding five influenza seasons, ILIs, positive proportion of ILIs, and duration of the influenza epidemic period in 2019/2020 had increased from 13% to 54%; in particular, the number of weeks from the peak to the end of the influenza epidemic period had decreased from 12 to 1. According to ARIMAX model forecasting, after considering natural decline, weekly ILIs had decreased by 48.6%, weekly positive proportion had dropped by 15% in the second week after the emergency response was declared, and COVID-19 measures had reduced by 83%. We conclude that the public health emergency response can significantly interrupt the transmission of influenza.

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.

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.

An Updated Review on SARS-CoV-2 Infection in Animals.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has lasted for two years and caused millions of infections and deaths in humans. Although the origin of SARS-CoV-2 infection in humans remains unknown, infection in animals has been frequently reported in varieties of animals all over the world. Both experimental and natural infections of SARS-CoV-2 in different animal species provide useful information on viral host range and pathogenicity. As the pandemic continues to evolve, SARS-CoV-2 infection in animals will be expanding. In this review, we summarized SARS-CoV-2 testing and infection in animals as well as SARS-CoV-2 strains and transmission in animals. Current data showed that at least 18 different animal species tested positive for SARS-CoV-2. These 18 animal species belong to pet, captive, farmed, and wild animals. Fifteen of the eighteen animal species were known to be positive for the Delta variant and ten animal species were infected with two different types of variants. Human-to-animal, animal-to-animal, and animal-to-human transmission events were suggested in different outbreaks involved in animal infection with SARS-CoV-2. Continued testing, immunization, and surveillance are warranted.

Reconstruction of the Evolutionary Origin, Phylodynamics, and Phylogeography of the Porcine Circovirus Type 3.

Porcine circovirus type 3 (PCV3) is a newly identified virus associated with porcine dermatitis and nephropathy syndrome (PDNS) and multisystemic inflammatory responses in pigs. Recent studies suggests that PCV3 originated from bat circoviruses; however, the origin time, mode of spread, and geographic distribution of PCV3 remain unclear. In this study, the evolutionary origin, phylodynamics, and phylogeography of PCV3 were reconstructed based on the available complete genome sequences. PCV3 showed a closer relationship with bird circovirus than with bat circovirus, but their common ancestor was bat circovirus, indicating that birds may be intermediate hosts for the spread of circoviruses in pigs. Using the BEAST and phylogenetic analyses, three different clades of PCV3 (PCV3a, PCV3b, and PCV3c) were identified, with PCV3a being the most prevalent PCV3 clade. Further studies indicated that the earliest origin of PCV3 can be traced back to 1907.53-1923.44, with a substitution rate of 3.104 × 10-4 to 6.8524 × 10-4 substitution/site/year. A phylogeographic analysis highlighted Malaysia as the earliest location of the original PCV3, which migrated to Asia, America, and Europe. Overall, this study provides novel insights into the evolutionary origin, spread mode, and geographic distribution of PCV3, which will facilitate the prevention and control of PCV3 epidemics in the future.

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.

Factors Associated with SARS-CoV-2 Repeat Positivity - Beijing, China, June-September 2020.

INTRODUCTION: Repeat positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) following COVID-19 initial viral clearance (re-positivity) poses a public health management challenge. The objective was to determine factors associated with neutralizing antibody (Nab) level and re-positivity among patients infected with a single strain SARS-CoV-2. METHODS: During a single strain SARS-CoV-2 cluster in Beijing, China, longitudinal individual clinical, virological, and immunological data were collected from 368 infections from June 13 to September 22, 2020. Factors associated with Nab level and re-positivity were analyzed using generalized estimating equations. RESULTS: A total of 353 (96%) SARS-CoV-2 infections had demographic, clinical, and laboratory data available. Among the 353 infections, 55 (15.5%) were re-positive, and blood draws were taken from 346 individuals (98.0%) during hospitalization and/or during the follow-up period. Symptoms were milder for the second-time admission for the re-positives, although 36.4% of re-positives presented with radiographic appearance of pneumonia manifestation. Compared to non-re-positive patients, NAb titers were lower among re-positives; NAb was positively associated with clinical severity. Samples from the lower respiratory tract manifested higher viral load than that from the upper respiratory tract. Multivariable analysis showed re-positivity was positively associated with being female [odd ratio (OR)=1.7, 95% confidence interval (CI) 1.1-2.8] and being aged <18 years (OR=5.2, 95% CI 1.5-18.1); having initially asymptomatic infection (OR=13.7, 95% CI 1.6-116.3); and negatively associated with a higher NAb level (OR=0.9, 95% CI 0.5-1.7). CONCLUSIONS: NAb may be important for sustained viral clearance. Lower respiratory tract infection was associated with higher viral load among all infections when compared to upper respiratory tract infection. Continuous lower respiratory and intermittent upper respiratory viral shedding among COVID-19 infections may occur.

Genomic, immunological, and clinical analysis of COVID-19 vaccine breakthrough infections in Beijing, China.

As the coronavirus disease 2019 (COVID-19) pandemic is still ongoing and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are circulating worldwide, an increasing number of breakthrough infections are being detected despite the good efficacy of COVID-19 vaccines. Data on 88 COVID-19 breakthrough cases (breakthrough infections group) and 41 unvaccinated cases (unvaccinated group) from June 1 to August 22, 2021, were extracted from a cloud database established at Beijing Ditan Hospital to evaluate the clinical, immunological, and genomic characteristics of COVID-19 breakthrough infections. Among these 129 COVID-19 cases, 33 whole genomes were successfully sequenced, of which 23 were Delta variants, including 15 from the breakthrough infections group. Asymptomatic and mild cases predominated in both groups, but two patients developed severe disease in the unvaccinated group. The median time of viral shedding in the breakthrough infections group was significantly lower than that in the unvaccinated group (p = 0.003). In the breakthrough infections group, the IgG titers showed a significantly increasing trend (p = 0.007), and the CD4 + T lymphocyte count was significantly elevated (p = 0.018). For people infected with the Delta variant in the two groups, no significant difference was observed in either the quantitative reverse-transcription polymerase chain reaction results or viral shedding time. In conclusion, among vaccinated patients, the cases of COVID-19 vaccine breakthrough infections were mainly asymptomatic and mild, IgG titers were significantly increased and rose rapidly, and the viral shedding time was shorter.

Sustained Delivery of SARS-CoV-2 RBD Subunit Vaccine Using a High Affinity Injectable Hydrogel Scaffold.

The receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein that mediates viral entry into host cells is a good candidate immunogen for vaccine development against coronavirus disease 2019 (COVID-19). Because of its small size, most preclinical and early clinical efforts have focused on multimerizing RBD on various formats of nanoparticles to increase its immunogenicity. Using an easily administered injectable hydrogel scaffold that is rationally designed for enhanced retainment of RBD, an alternative and facile approach for boosting RBD immunogenicity in mice is demonstrated. Prolonged delivery of poly (I:C) adjuvanted RBD by the hydrogel scaffold results in sustained exposure to lymphoid tissues, which elicits serum IgG titers comparable to those induced by three bolus injections, but more long-lasting and polarized toward TH 1-mediated IgG2b. The hydrogel scaffold induces potent germinal center (GC) reactions, correlating with RBD-specific antibody generation and robust type 1 T cell responses. Besides being an enduring RBD reservoir, the hydrogel scaffold becomes a local inflammatory niche for innate immune cell activation. Collectively, the injectable hydrogel scaffold provides a simple, practical, and inexpensive means to enhance the efficacy of RBD-based subunit vaccines against COVID-19 and may be applicable to other circulating and emerging pathogens.