Prevalence and diversity of imported severe acute respiratory syndrome coronavirus 2 variants in China, 2021-2022.

The causative agent of coronavirus disease 2019 (COVID-19), known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread accumulatively to 240 countries and continues to evolve. To gain a comprehensive understanding of the epidemiological characteristics of imported variants in China and their correlation with global circulating variants, genomic surveillance data from 11 139 imported COVID-19 cases submitted by Chinese provincial CDC laboratories between 2021 and 2022 were analyzed. Consensus sequences underwent rigorous quality checks, followed by amino acid mutations analysis using Nextclade. Sequences with satisfactory quality control status were classified according to the Pango nomenclature. The results showed that the dominant variants in imported cases reflected the global epidemic trend. An increase in the number of imported SARS-CoV-2 lineages monitored in China in the second half of 2022, and the circulating Omicron subvariants changed from the ancestral lineages of BA.5 and BA.2 into the lineages containing key amino acid mutations of spike protein. There was significant variation in the detection of Omicron subvariants among continents (χ2 = 321.968, p < 0.001) in the second half of 2022, with four lineages (BA.2.3.7, BA.2.2, BA.5.2.7, and XBB.1.2) identified through imported surveillance mainly prevalent respectively in Taiwan, China, Hong Kong SAR, China, Russian Federation, and Singapore. These findings revealed the alterations in circulating imported variants from 2021 to 2022 in China, reflecting the higher diversity of lineages in the second half of 2022, and revealed the predominant lineages of countries or regions that are in close contacts to China, providing new insights into the global prevalence of SARS-CoV-2.

Genomic Surveillance for SARS-CoV-2 Variants: Dominance of XBB Replacement - China, January-June 2023.

Introduction: In the first half of 2023, a global shift was observed towards the predominance of XBB variants. China faced a significant epidemic between late 2022 and early 2023 due to Omicron subvariants BA.5.2 and BF.7. This study aims to depict the evolving variant distribution among provincial-level administrative divisions (PLADs) in China and explore the factors driving the predominance of XBB replacement. Methods: Sequences from local and imported coronavirus disease 2019 (COVID-19) cases recorded between January 1 and June 30, 2023, were included. The study analyzed the changing distribution of viral variants and assessed how the prior dominance of specific variants, XBB subvariants, and imported cases influenced the prevalence of the XBB replacement variant. Results: A total of 56,486 sequences were obtained from local cases, and 8,669 sequences were from imported cases. Starting in April, there was a shift in the prevalence of XBB from imported to local cases, with varying dominance among PLADs. In PLADs previously high in BF.7, the rise of XBB was delayed. A positive correlation was found between XBB proportions in imported cases from January to March and local cases in April. The distribution pattern of XBB subvariants differed between local and imported cases within the same PLAD. No significant differences were noted in the replacement rates of XBB subvariants. Conclusions: The timing of XBB dominance differed among various PLADs in China in the first half of 2023, correlating closely with the prevalence of XBB variants among imported cases.

Genotyping and traceability analysis of norovirus in Yantai between 2017 and 2019.

To investigate the diversity and evolution of noroviruses in Yantai in recent years, this study focused on the coat protein regions of norovirus-positive samples with nucleic acid detection (cycle threshold) values below 30 between 2017 and 2019. A total of 81 sequences were obtained for genotyping. Initially, a high-throughput sequencing approach was established to perform the whole-genome sequencing of multiple typical diarrheal strains. Using bioinformatics software such as BEAST, recombinant variant analysis was performed for each genotype of the norovirus strains, and genetic evolutionary analysis was conducted for the dominant strain GII.4, as well as the rare variant GII.21. The results showed that there were multiple genotypes such as GI.3, GI.6, GI.7, GII.1, GII.2, GII.3, GII.4, GII.6, GII.13, GII.17, GII.21, and GIX.1 in the positive samples of norovirus from 2017 to 2019. GII.4 is characterized by diverse genotypes, with new changes in antigenic epitopes occurring during the course of the epidemic. This may have led to the emergence of a new pandemic. This suggests a need to strengthen surveillance. The results of this study suggest that attention should be paid to the predominant genotypes prevalent in neighboring countries and regions, and the safety supervision of imported food should be strengthened to aid in the prevention and control of related viruses.

Genomic Surveillance for SARS-CoV-2 - China, September 26, 2022 to January 29, 2023.

Introduction: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has generated 2,431 variants over the course of its global transmission over the past 3 years. To better evaluate the genomic variation of SARS-CoV-2 before and after the optimization of coronavirus disease 2019 (COVID-19) prevention and control strategies, we analyzed the genetic evolution branch composition and genomic variation of SARS-CoV-2 in both domestic and imported cases in China (the data from Hong Kong and Macau Special Administrative Regions and Taiwan, China were not included) from September 26, 2022 to January 29, 2023. Methods: Analysis of the number of genome sequences, sampling time, dynamic changes of evolutionary branches, origin, and clinical typing of SARS-CoV-2 variants submitted by 31 provincial-level administrative divisions (PLADs) and Xinjiang Production and Construction Corps (XPCC) was conducted to assess the accuracy and timeliness of SARS-CoV-2 variant surveillance. Results: From September 26, 2022 to January 29, 2023, 20,013 valid genome sequences of domestic cases were reported in China, with 72 evolutionary branches. Additionally, 1,978 valid genome sequences of imported cases were reported, with 169 evolutionary branches. The prevalence of the Omicron variants of SARS-CoV-2 in both domestic and imported cases was consistent with that of international epidemic variants. Conclusions: This study provides an overview of the prevalence of Omicron variants of SARS-CoV-2 in China. After optimizing COVID-19 prevention and control strategies, no novel Omicron variants of SARS-CoV-2 with altered biological characteristics or public health significance have been identified since December 1, 2022.

Rotavirus Infection and Genotyping in Yantai, Shandong Province, 2017-2019.

PURPOSE: Rotavirus (RV) ranked first among infectious diarrhea-causing pathogens in Yantai from 2017 to 2019. This study investigated the seroserotypes of RV in Yantai, Shandong, from 2017 to 2019 to identify the dominant serotypes and explore the epidemic pattern, aiming to effectively reduce the infection rate, better guide vaccination, and help in epidemiological prevention and control. METHODS: A total of 2227 human diarrhea samples were collected from 2017 to 2019 in Yantai. The VP7 (G serotype) and VP4 (P serotype) genes of 467 RV-positive samples were amplified using two-round nested reverse transcription-polymerase chain reaction for G/P genotyping. RESULTS: The genotyping results of RV in Yantai from 2017 to 2019 revealed that G9 was the dominant serotype for all G serotypes, P[8] was the dominant serotype for all P serotypes, and G9P[8] was the dominant serotype for all G/P combinations. G9 serotype accounted for 60.84%, 95.65%, and 83.76% of the total RV samples collected in 2017, 2018, and 2019, respectively. P[8] accounted for 75.52%, 94.69%, and 88.89% of the RV-positive samples collected in 2017, 2018, and 2019, respectively. G9P[8] accounted for 60.84%, 94.69%, and 83.76% of the total RV samples collected in 2017, 2018, and 2019, respectively. Of the total 467 samples from 2017 to 2019, G2P[4] accounted for 3.64% (17/467), G3P[8] for 1.28% (6/467), and G1P[8] for 0.86% (4/467). CONCLUSION: This study revealed the epidemiological characteristics of RV infection and the development pattern of dominant serotypes in Yantai in recent years, guiding the selection of RV vaccines. The prioritization of vaccines containing G9 serotype for infants in Yantai in recent years is recommended.

Genomic Surveillance for SARS-CoV-2 Variants of Concern from Imported COVID-19 Cases - the Mainland of China, 2021.

Introduction: After the epidemic in Wuhan City was brought under control in 2020, local outbreaks of coronavirus disease 2019 (COVID-19) in the mainland of China were mainly due to imported COVID-19 cases. The ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to generate new variants. Some have been designated as variants of concern (VOCs) by the World Health Organization (WHO). To better assess the role of imported SARS-CoV-2 surveillance and the prevalence of VOCs in 2021, the genomic surveillance data of SARS-CoV-2 from imported COVID-19 cases of 2021 in the mainland of China were analyzed. Methods: The analyses included the number of sequence submissions, time of sequence deposition, and time of detection of the VOCs in order to determine the timeliness and sensitivity of the surveillance. The proportions of VOCs were analyzed and compared with data from the Global Initiative of Sharing All Influenza Data (GISAID). Results: A total of 3,355 sequences of imported cases were submitted from 29 provincial-level administrative divisions, with differences in the number of sequence submissions and median time of sequence deposition. A total of 2,388 sequences with more than 90% genomic coverage were used for lineage analysis. The epidemic trend from Alpha to Delta to Omicron in imported cases was consistent with that in the GISAID. In addition, VOCs from imported cases were usually identified after WHO designation and before causing local outbreaks. Conclusions: The global distribution of SARS-CoV-2 VOCs changed rapidly in 2021. Robust genomic surveillance of the imported SARS-CoV-2 in the mainland of China is of great significance.

Current status and capacity of pathogen laboratories in centers for disease control and prevention in China during the COVID-19 pandemic: A nationwide cross-sectional survey.

The pathogen laboratory (p-lab) is the core and primary department of centers for disease control and prevention (CDCs) in China to respond to infectious disease outbreaks such as COVID-19. To understand the current status and capacity of p-labs in Chinese CDCs during the COVID-19 pandemic, we conducted a nationwide cross-sectional survey among 399 respondents from 239 CDCs. Differences in the current status of p-labs in CDCs of provinces, cities, and counties mainly comprised laboratory equipment, IEIs, mastery of personal occupational skills, and maximum detection capacity. Most CDCs reported a lack of staff and funds for personnel, which should be a priority in China's upcoming public health reform. The development of sequencing technologies has received considerable attention in CDCs. These are mainly used to study respiratory viruses such as influenza and SARS-CoV-2. The COVID-19 pandemic has driven development of the CDCs in China, and personnel and funds are considered key factors in improving the detection capacity of CDC p-labs.

Detection and Genetic Correlation Analysis of Diarrhea Cases and Norovirus in Oysters in Yantai, China.

Background: This study aimed to assess the correlation between Norovirus (NoV), diarrhea, and raw oysters from the eastern coastal areas of Yantai, Shandong, China. Methods: Marine oysters were selected from the three aquatic markets in Laishan district, Yantai City, in March 2019. Meanwhile, 100 fecal samples were collected from patients with diarrhea from the same areas during the same period. Nucleic acids were extracted from these samples and detected by employing reverse transcription polymerase chain reaction (RT-PCR) for NoV GI/GII. The VP1 gene of the coat protein of NoV was amplified by semi-nested RT-PCR and sequenced. Sequence comparison of VP1 was performed with BioEdit software, and the evolutionary tree was constructed with Mega7.0 software. Results: Of the 151 oysters, 42 (27.8%) were positive for NoV. Among them, 32 (21.2%) were GII-positive, 10 (6.6%) were GI-positive, and one GI VP1 sequence was obtained in the oyster samples. Of 100 fecal samples from patients with diarrhea, 38 were GII-positive and 17 were GI-positive. Totally, 19 GII VP 1 sequences and eight GI VP 1 sequences were obtained. Two G1 VP 1 sequences in two fecal samples showed 98.7% nucleotide sequence identity and 99.1% amino acid sequence identity G1 VP 1 acquired in the oyster sample. Conclusions: The results suggest that oysters may be responsible for the spread of NoV in Yantai, Shandong province, China.

Analysis of the Transmission of SARS-CoV-2 Delta VOC in Yantai, China, August 2021.

Objective: Starting 31 July 2021, a SARS-CoV-2 outbreak occurred in Yantai, Shandong Province. The investigation showed that this outbreak was closely related to the epidemic at Nanjing Lukou Airport. In view of the fact that there were many people involved in this outbreak and these people had a complex activity area, the transmission route cannot be analyzed by simple epidemiological investigation. Here we combined the SARS-COV-2 whole-genome sequencing with epidemiology to determine the epidemic transmission route of Yantai. Methods: Thirteen samples of SARS-CoV-2 outbreak cases from 31 July to 4 August 2021 were collected and identified by fluorescence quantitative PCR, then whole-genome deep sequencing based on NGS was performed, and the data were analyzed and processed by biological software. Results: All sequences were over 29,000 bases in length and all belonged to B.1.617.2, which was the Delta strain. All sequences shared two amino acid deletions and 9 amino acid mutations in Spike protein compared with reference sequence NC_045512.2 (Wuhan virus strain). Compared with the sequence of Lukou Airport Delta strain, the homology was 99.99%. In order to confirm the transmission relationship between patients, we performed a phylogenetic tree analysis. The results showed that patient 1, patient 2, and patient 9 belong to an independent branch, and other patients have a close relationship. Combined with the epidemiological investigation, we speculated that the epidemic of Yantai was transmitted by two routes at the same time. Based on this information, our prevention and control work was carried out in two ways and effectively prevented the further spread of this epidemic.

SARS-CoV-2 cold-chain transmission: Characteristics, risks, and strategies.

Low temperature and certain humidity are conducive to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for long-time survival and long-distance spread during logistics and trades. Contaminated cold-chain or frozen products and outer packaging act as the carrier of SARS-CoV-2, that infects the high-risk population who works in the ports, cold storage or seafood market. Since the coronavirus disease 2019 (COVID-19) pandemic worldwide, multiple localized outbreaks caused by SARS-CoV-2 contaminated imported cold-chain products have been reported in China, which brought challenges to COVID-19 prevention and control. Here, we review the evidences of SARS-CoV-2 cold-chain transmission from six confirmed cold-chain related COVID-19 outbreaks in China, especially in terms of SARS-CoV-2 whole-genome sequencing and virus isolation. In addition, we summarize the characteristics and mode of SARS-CoV-2 cold-chain transmission from both six COVID-19 outbreaks in China and the outbreaks suspected cold-chain transmission in other countries. Finally, we analyze the underlying risks of SARS-CoV-2 cold-chain transmission and propose the preventive countermeasures.

Aetiological Characteristics of Infectious Diarrhea in Yantai City, Shandong Province, China in 2017.

This study aimed to analyse the pathogenic spectrum and epidemiological characteristics of infectious diarrhea in Yantai City, Shandong Province, China and provide a reference for its prevention and control. A total of 713 stool specimens collected within 3 days of diarrhea onset from January to December 2017 at secondary or higher hospitals in Yantai City were tested for 10 causative pathogens, using real-time polymerase chain reaction (RT-PCR). The top two rotaviruses and norovirus were analysed for typing and geographical distribution. The total positive rate was 46.56% (332/713), and 268 of 713 specimens contained at least one pathogen; 64 had at least two pathogens, accounting for 19.28% of the positive specimens (64/332). The positivity rates of rotavirus (RV), norovirus (NoVs) GI, norovirus (NoVs) GII, enterovirus universal (EV), enteric adenoviruses (EAdV), sapovirus (SaV), astrovirus (Astv), Salmonella (SE), Listeria monocytogenes (LiMo), and Vibrio parahaemolyticus (VP) were 20.06% (143/713), 1.82% (13/713), 12.84% (89/713), 10.66% (76/713), 4.07% (29/713), 0.42% (3/713), 2.38% (17/713), 1.54% (11/713), 1.82% (13/713), and 1.54% (11/713), respectively. Infectious diarrhea showed a high prevalence in young children aged 1-5 years, accounting for 48.6% of the total number of cases. Bacterial diarrhea was predominant in summer, and viral diarrhea was distributed throughout the year, without a significant seasonal pattern. Rotavirus is dominated by G9P, accounting for 81.82%, while norovirus is dominated by the GII type and has diverse characteristics. The aetiology of infectious diarrhea in Yantai is mainly viral, with RV, NoVs, EV, EAdV, and Astv being the most frequent pathogens. Continuous surveillance of infectious diarrhea diseases can help us understand its epidemiological and pathogenic characteristics, thereby taking targeted preventive and control measures in different seasons.

Surveillance and Analysis of SARS-CoV-2 Variant Importation - China, January-June 2022.

Introduction: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant is the dominant circulating strain worldwide. To assess the importation of SARS-CoV-2 variants in the mainland of China during the Omicron epidemic, the genomic surveillance data of SARS-CoV-2 from imported coronavirus disease 2019 (COVID-19) cases in the mainland of China during the first half of 2022 were analyzed. Methods: Sequences submitted from January to July 2022, with a collection date before June 30, 2022, were incorporated. The proportions of SARS-CoV-2 variants as well as the relationships between the origin and destination of each Omicron imported case were analyzed. Results: 4,946 sequences of imported cases were submitted from 27 provincial-level administrative divisions (PLADs), and the median submission interval was within 1 month after collection. In 3,851 Omicron sequences with good quality, 1 recombinant (XU) and 4 subvariants under monitoring (BA.4, BA.5, BA.2.12.1, and BA.2.13) were recorded, and 3 of them (BA.4, BA.5, and BA.2.12.1) caused local transmissions in the mainland of China later than that recorded in the surveillance. Omicron subvariants dominated in the first half of 2022 and shifted from BA.1 to BA.2 then to BA.4 and BA.5. The percentage of BA.2 in the imported SARS-CoV-2 surveillance data was far higher than that in the Global Initiative on Sharing All Influenza Data (GISAID). The imported cases from Hong Kong Special Administrative Region, China, accounted for 32.30% of Omicron cases sampled, and 98.71% of them were BA.2. Conclusions: The Omicron variant showed the intra-Omicron evolution in the first half of 2022, and all of the Omicron subvariants were introduced into the mainland of China multiple times from multiple different locations.

COVID-19 Outbreak Caused by Contaminated Packaging of Imported Cold-Chain Products - Liaoning Province, China, July 2020.

What is known about this topic? Few major outbreaks of coronavirus disease 2019 (COVID-19) have occurred in China after major non-pharmaceutical interventions and vaccines have been deployed and implemented. However, sporadic outbreaks that had high possibility to be linked to cold chain products were reported in several cities of China.. What is added by this report? In July 2020, a COVID-19 outbreak occurred in Dalian, China. The investigations of this outbreak strongly suggested that the infection source was from COVID-19 virus-contaminated packaging of frozen seafood during inbound unloading personnel contact. What are the implications for public health practice? Virus contaminated paper surfaces could maintain infectivity for at least 17-24 days at -25 ℃. Exposure to COVID-19 virus-contaminated surfaces is a potential route for introducing the virus to a susceptible population. Countries with no domestic transmission of COVID-19 should consider introducing prevention strategies for both inbound travellers and imported goods. Several measures to prevent the introduction of the virus via cold-chain goods can be implemented.

Mechanism of Microbial Metabolite Leupeptin in the Treatment of COVID-19 by Traditional Chinese Medicine Herbs.

Coronavirus disease 2019 (COVID-19) has caused huge deaths and economic losses worldwide in the current pandemic. The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is thought to be an ideal drug target for treating COVID-19. Leupeptin, a broad-spectrum covalent inhibitor of serine, cysteine, and threonine proteases, showed inhibitory activity against Mpro, with a 50% inhibitory concentration (IC50) value of 127.2 µM in vitro in our study here. In addition, leupeptin can also inhibit SARS-CoV-2 in Vero cells, with 50% effective concentration (EC50) values of 42.34 µM. More importantly, various strains of streptomyces that have a broad symbiotic relationship with medicinal plants can produce leupeptin and leupeptin analogs to regulate autogenous proteases. Fingerprinting and structure elucidation using high-performance liquid chromatography (HPLC) and high-resolution mass spectrometry (HRMS), respectively, further proved that the Qing-Fei-Pai-Du (QFPD) decoction, a traditional Chinese medicine (TCM) formula for the effective treatment of COVID-19 during the period of the Wuhan outbreak, contains leupeptin. All these results indicate that leupeptin at least contributes to the antiviral activity of the QFPD decoction against SARS-CoV-2. This also reminds us to pay attention to the microbiomes in TCM herbs as streptomyces in the soil might produce leupeptin that will later infiltrate the medicinal plant. We propose that plants, microbiome, and microbial metabolites form an ecosystem for the effective components of TCM herbs. IMPORTANCE A TCM formula has played an important role in the treatment of COVID-19 in China. However, the mechanism of TCM action is still unclear. In this study, we identified leupeptin, a metabolite produced by plant-symbiotic actinomyces (PSA), which showed antiviral activity in both cell culture and enzyme assays. Moreover, leupeptin found in the QFPD decoction was confirmed by both HPLC fingerprinting and HRMS. These results suggest that leupeptin likely contributes to the antiviral activity of the QFPD decoction against SARS-CoV-2. This result gives us important insight into further studies of the PSA metabolite and medicinal plant ecosystem for future TCM modernization research.

Orthogonal genome-wide screens of bat cells identify MTHFD1 as a target of broad antiviral therapy.

Bats are responsible for the zoonotic transmission of several major viral diseases, including those leading to the 2003 SARS outbreak and likely the ongoing COVID-19 pandemic. While comparative genomics studies have revealed characteristic adaptations of the bat innate immune system, functional genomic studies are urgently needed to provide a foundation for the molecular dissection of the viral tolerance in bats. Here we report the establishment of genome-wide RNA interference (RNAi) and CRISPR libraries for the screening of the model megabat, Pteropus alecto. We used the complementary RNAi and CRISPR libraries to interrogate P. alecto cells for infection with two different viruses: mumps virus and influenza A virus, respectively. Independent screening results converged on the endocytosis pathway and the protein secretory pathway as required for both viral infections. Additionally, we revealed a general dependence of the C1-tetrahydrofolate synthase gene, MTHFD1, for viral replication in bat cells and human cells. The MTHFD1 inhibitor, carolacton, potently blocked replication of several RNA viruses, including SARS-CoV-2. We also discovered that bats have lower expression levels of MTHFD1 than humans. Our studies provide a resource for systematic inquiry into the genetic underpinnings of bat biology and a potential target for developing broad-spectrum antiviral therapy.

A core-shell structured COVID-19 mRNA vaccine with favorable biodistribution pattern and promising immunity.

Although inoculation of COVID-19 vaccines has rolled out globally, there is still a critical need for safe and effective vaccines to ensure fair and equitable supply for all countries. Here, we report on the development of a highly efficacious mRNA vaccine, SW0123 that is composed of sequence-modified mRNA encoding the full-length SARS-CoV-2 Spike protein packaged in core-shell structured lipopolyplex (LPP) nanoparticles. SW0123 is easy to produce using a large-scale microfluidics-based apparatus. The unique core-shell structured nanoparticle facilitates vaccine uptake and demonstrates a high colloidal stability, and a desirable biodistribution pattern with low liver targeting effect upon intramuscular administration. Extensive evaluations in mice and nonhuman primates revealed strong immunogenicity of SW0123, represented by induction of Th1-polarized T cell responses and high levels of antibodies that were capable of neutralizing not only the wild-type SARS-CoV-2, but also a panel of variants including D614G and N501Y variants. In addition, SW0123 conferred effective protection in both mice and non-human primates upon SARS-CoV-2 challenge. Taken together, SW0123 is a promising vaccine candidate that holds prospects for further evaluation in humans.

Co-Immunization With CHIKV VLP and DNA Vaccines Induces a Promising Humoral Response in Mice.

Chikungunya fever is an acute infectious disease that is mediated by the mosquito-transmitted chikungunya virus (CHIKV), for which no licensed vaccines are currently available. Here, we explored several immunization protocols and investigated their immunity and protective effects in mice, with DNA- and virus-like particle (VLP)- vaccines, both alone and in combination. Both DNA and VLP vaccine candidates were developed and characterized, which express CHIKV structural genes (C-E3-E2-6K-E1). Mice were immunized twice, with different protocols, followed by immunological detection and CHIKV Ross challenge. The highest antigen-specific IgG and neutralizing activity were induced by DNA and VLP co-immunization, while the highest cellular immunity was induced by DNA vaccination alone. Although all vaccine groups could protect mice from lethal CHIKV challenge, demonstrated as reduced viral load in various tissues, without weight loss, mice co-immunized with DNA and VLP exhibited the mildest histopathological changes and lowest International Harmonization of Nomenclature and Diagnostic Criteria (INHAND) scores, in comparison to mice with either DNA or VLP vaccination alone. We concluded that co-immunization with DNA and VLP is a promising strategy to inducing better protective immunity against CHIKV infection.