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1.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-315888

ABSTRACT

Background: The re-emerging outbreak of COVID-19 in Beijing China in summer of 2020 was originated from a contaminated super food wholesale market. The transmission mechanism was analyzed. Methods: We hypothesized that the Xinfadi outbreak was associated with activities of food-trade. Therefore, all the confirmed cases were divided into groups of sellers, buyer, seller transmitted and buyer transmitted. Data for each case were georeferenced and aggregated to the 500m-spaced hexagon grids using geodata and base maps, road networks, urban points of interest from OpenStreetMap. The Xinfadi-related trade activity data were derived using Python crawling scripts. The spatial association of the outbreak was studied with Moran’s I statistic method and a Susceptible-Infected-Recovered (SIR) coupled Agent-Based Model (ABM). Findings: Of 335 cases reported, 177 (45·3%) were sellers who worked for the Market, 83 (23·7%) were buyers who visited the Market, and 74 were transmitted by either of the infected buyers or sellers. The Market was the outbreak center, which were spreading along the urban rapid transit lines. The areas with a high incidence were concentrated across neighborhoods in the southwest of Beijing's Fifth Ring Road and the west section of the Fourth Ring of southwestern Beijing, and the west portion of Fuxing Road. The highest number of seller transmission hubs were located in Market neighborhood, however the buyer transmission hubs extended to cover more than three different districts. Our SIR-ABM model analysis suggested that the trade-distancing strategy effectively reduced the R0. The retail shops closure strategy reduced nearly half number of visitors to market. The Buy-local policy option reduced more than 70% infection in total. Interpretation: The Xinfadi outbreak was associated contaminated super food market by people's movements for food-trade, including their interactions in related activities. Therefore, the retails closures and buy-local policy could reduce size of the outbreak and prevent possible outbreak in future.Funding Statement: Ministry of Science and Technology China (Grant number 2018ZX10712001-017 and 2018ZX10712001-018), Chinese Academy of Medical Sciences (2018RU010), Chinese Academy (2020-XZ-37) and the National Natural Science Foundation of China (71603253 and 72074209).Declaration of Interests: All authors declare no competing interests.

2.
Front Nutr ; 8: 789242, 2021.
Article in English | MEDLINE | ID: covidwho-1639197

ABSTRACT

Boosting and prolonging SARS-CoV-2 vaccine-elicited immunity is paramount for containing the COVID-19 pandemic, which wanes substantially within months after vaccination. Here we demonstrate that the unique strain of probiotic Lactobacillus plantarum GUANKE (LPG) could promote SARS-CoV-2-specific immune responses in both effective and memory phases through enhancing interferon signaling and suppressing apoptotic and inflammatory pathways. Interestingly, oral LPG administration promoted SARS-CoV-2 neutralization antibodies even 6 months after immunization. Furthermore, when LPG was given immediately after SARS-CoV-2 vaccine inoculation, specific neutralization antibodies could be boosted >8-fold in bronchoalveolar lavage (BAL) and >2-fold in sera, T-cell responses were persistent and stable for a prolonged period both in BAL and the spleen. Transcriptional analyses showed that oral application of LPG mobilized immune responses in the mucosal and systemic compartments; in particular, gut-spleen and gut-lung immune axes were observed. These results suggest that LPG could be applied in combination with SARS-CoV-2 vaccines to boost and prolong both the effective and memory immune responses in mucosal and systemic compartments, thereby improving the efficacy of SARS-CoV-2 vaccination.

3.
Front Immunol ; 12: 791753, 2021.
Article in English | MEDLINE | ID: covidwho-1639168

ABSTRACT

Background: Infection of SARS-CoV-2 may cause acute respiratory syndrome. It has been reported that SARS-CoV-2 nucleocapsid protein (N-protein) presents early in body fluids during infection. The direct involvement of N-protein in lung injury is poorly understood. Methods: Recombinant N-protein was pretreated with polymyxin B, a lipopolysaccharide (LPS)-neutralizing agent. C57BL/6, C3H/HeJ (resistant to LPS), and C3H/HeN (control for C3H/HeJ) mice were exposed to N-protein via intratracheal administration to examine acute lung injury. In vitro, bone marrow-derived macrophages (BMDMs) were cultured with N-protein to study phosphorylation of nuclear factor kappa B (NF-ĸB) p65, macrophage polarization, and expression of proinflammatory cytokines. Results: N-protein produced acute lung injury in C57BL/6 mice, with elevated protein permeability, total cell count, neutrophil infiltration, and proinflammatory cytokines in the bronchioalveolar lavage. N-protein also induced lung injury in both C3H/HeJ and C3H/HeN mice, indicating that the effect could not be attributed to the LPS contamination. N-protein triggered phosphorylation of NF-ĸB p65 in vitro, which was abolished by both N-protein denaturation and treatment with an antibody for N-protein, demonstrating that the effect is N-protein specific. In addition, N-protein promoted M1 macrophage polarization and the expression of proinflammatory cytokines, which was also blocked by N-protein denaturation and antibody for N-protein. Furthermore, N-protein induced NF-ĸB p65 phosphorylation in the lung, while pyrrolidine dithiocarbamate, an NF-ĸB inhibitor, alleviated the effect of N-protein on acute lung injury. Conclusions: SARS-CoV-2 N-protein itself is toxic and induces acute lung injury in mice. Both N-protein and NF-ĸB pathway may be therapeutic targets for treating multi-organ injuries in Coronavirus disease 2019 (COVID-19).


Subject(s)
Acute Lung Injury/virology , COVID-19 , Coronavirus Nucleocapsid Proteins/toxicity , NF-kappa B/metabolism , Acute Lung Injury/metabolism , Animals , Mice , Mice, Inbred C3H , Mice, Inbred C57BL , Phosphoproteins/toxicity , SARS-CoV-2
4.
J Biosaf Biosecur ; 4(1): 33-37, 2022 Jun.
Article in English | MEDLINE | ID: covidwho-1587192

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved rapidly into new variants throughout the pandemic. The Omicron variant has more than 50 mutations when compared with the original wild-type strain and has been identified globally in numerous countries. In this report, we analyzed the mutational profiles of several variants, including the per-site mutation rate, to determine evolutionary relationships. The Omicron variant was found to have a unique mutation profile when compared with that of other SARS-CoV-2 variants, containing mutations that are rare in clinical samples. Moreover, the presence of five mouse-adapted mutation sites suggests that Omicron may have evolved in a mouse host. Mutations in the Omicron receptor-binding domain (RBD) region, in particular, have potential implications for the ongoing pandemic.

5.
J Biosaf Biosecur ; 4(1): 38-42, 2022 Jun.
Article in English | MEDLINE | ID: covidwho-1560781
6.
Biosens Bioelectron ; 197: 113771, 2022 Feb 01.
Article in English | MEDLINE | ID: covidwho-1536447

ABSTRACT

Due to the similar clinical symptoms of influenza (Flu) and coronavirus disease 2019 (COVID-19), there is a looming infection threat of concurrent Flu viruses and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this work, we introduce a customized isothermal amplification integrated lateral flow strip (LFS) that is capable performing duplex reverse transcription-recombinase polymerase amplification (RT-RPA) and colorimetric LFS in a sequential manner. With customized amplification primer sets targeted to SARS-CoV-2 (opening reading frame 1a/b and nucleoprotein genes) and Flu viruses (Flu A and Flu B), the platform allows the rapid and simultaneous visual screening of SARS-CoV-2 and Flu viruses (Flu A and Flu B) without cross reactivity, false positives, and false negatives. Moreover, it maximally eases the detection, reduces the detection time (1 h), and improves the assay performance to detect as low as 10 copies of the viral RNA. Its clinical application is powerfully demonstrated with 100% accuracy for evaluating 15 SARS-CoV-2-positive clinical samples, 10 Flu viruses-positive clinical samples, and 5 negative clinical samples, which were pre-confirmed by standard qRT-PCR. We envision this portable device can meet the increasing need of online monitoring the serious infectious diseases that substantially affects health care systems worldwide.


Subject(s)
Biosensing Techniques , COVID-19 , Influenza, Human , Humans , Influenza, Human/diagnosis , Nucleic Acid Amplification Techniques , SARS-CoV-2 , Sensitivity and Specificity
7.
Front Microbiol ; 12: 755599, 2021.
Article in English | MEDLINE | ID: covidwho-1482024

ABSTRACT

Although plateau pikas are the keystone species in the plateau ecosystem of the Qinghai Province of China, little is known about their role in the evolution and transmission of viral pathogens, especially coronaviruses. Here, we describe the characterization and evolution of a novel alphacoronavirus, termed plateau pika coronavirus (PPCoV) P83, which has a prevalence of 4.5% in plateau pika fecal samples. In addition to classical gene order, the complete viral genome contains a unique nonstructural protein (NS2), several variable transcription regulatory sequences and a highly divergent spike protein. Phylogenetic analysis indicates that the newly discovered PPCoV falls into the genus Alphacoronavirus and is most closely related to rodent alphacoronaviruses. The co-speciation analysis shows that the phylogenetic trees of the alphacoronaviruses and their hosts are not always matched, suggesting inter-species transmission is common in alphacoronaviruses. And, PPCoV origin was estimated by molecular clock based on membrane and RNA-dependent RNA polymerase encoding genes, respectively, which revealed an apparent discrepancy with that of co-speciation analysis. PPCoV was detected mainly in intestinal samples, indicating a potential enteric tropism for the virus. Overall, this study extends the host range of alphacoronaviruses to a new order (Lagomorpha), indicating that plateau pikas may be the natural reservoir of PPCoV and play an important and long-term role in alphacoronavirus evolution.

9.
Virol Sin ; 36(3): 402-411, 2021 Jun.
Article in English | MEDLINE | ID: covidwho-1372824

ABSTRACT

Outbreaks of severe virus infections with the potential to cause global pandemics are increasingly concerning. One type of those commonly emerging and re-emerging pathogens are coronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2). Wild animals are hosts of different coronaviruses with the potential risk of cross-species transmission. However, little is known about the reservoir and host of coronaviruses in wild animals in Qinghai Province, where has the greatest biodiversity among the world's high-altitude regions. Here, from the next-generation sequencing data, we obtained a known beta-coronavirus (beta-CoV) genome and a novel delta-coronavirus (delta-CoV) genome from faecal samples of 29 marmots, 50 rats and 25 birds in Yushu Tibetan Autonomous Prefecture, Qinghai Province, China in July 2019. According to the phylogenetic analysis, the beta-CoV shared high nucleotide identity with Coronavirus HKU24. Although the novel delta-CoV (MtCoV) was closely related to Sparrow deltacoronavirus ISU42824, the protein spike of the novel delta-CoV showed highest amino acid identity to Sparrow coronavirus HKU17 (73.1%). Interestingly, our results identified a novel host (Montifringilla taczanowskii) for the novel delta-CoV and the potential cross-species transmission. The most recent common ancestor (tMRCA) of MtCoVs along with other closest members of the species of Coronavirus HKU15 was estimated to be 289 years ago. Thus, this study increases our understanding of the genetic diversity of beta-CoVs and delta-CoVs, and also provides a new perspective of the coronavirus hosts.


Subject(s)
Animals, Wild/virology , Coronavirus/isolation & purification , Phylogeny , Animals , Birds/virology , China , Coronavirus/classification , Marmota/virology , Rats/virology , Tibet
10.
Journal of Biosafety and Biosecurity ; 3(2):67-71, 2021.
Article in English | ScienceDirect | ID: covidwho-1355671

ABSTRACT

China is one of the countries with the richest wildlife population. The large variety of widely distributed species act as natural or susceptible hosts for numerous infectious diseases. It is estimated that there are more than 1.2 million unknown virus species in China, and there might be 10,000–30,000 unknown bacteria in wild mammals on the Qinghai-Tibet Plateau alone. There are no less than 600,000 species of animal-borne parasites and approximately 2 million species of fungi worldwide. With rapid economic growth and globalization, humans and wildlife interact more frequently, which enhances the probability of wildlife-borne pathogens infecting humans. The occurrence of animal-borne infectious diseases will become the “new normal” we have to face in the future. Therefore, research should be carried out on wildlife-borne microorganisms and the prevention and control of emerging infectious diseases to establish an analytical framework and an evaluation technology system for risk assessment and early warning of potential animal-borne emerging infectious diseases. This will not only improve our understanding of wildlife-borne microbial communities but also enable in-depth analysis, discovery, early warning, and even prediction of major animal-borne emerging infectious diseases that might occur in the future. Furthermore, this research will reduce response times, minimize the social and economic impact and losses, enable interventions related to the emergence or spread of the disease as early as possible, and comprehensively improve our management of infectious disease outbreaks.

12.
J Biosaf Biosecur ; 3(1): 51-55, 2021 Jun.
Article in English | MEDLINE | ID: covidwho-1284239

ABSTRACT

The origin of SARS-CoV-2 is still an unresolved mystery. In this study, we systematically reviewed the main research progress of wild animals carrying virus highly homologous to SARS-CoV-2 and analyzed the natural foci characteristics of SARS-CoV-2. The complexity of SARS-CoV-2 origin in wild animals and the possibility of SARS-CoV-2 long-term existence in human populations are also discussed. The joint investigation of corona virus carried by wildlife, as well as the ecology and patho-ecology of bats and other wildlife, are key measures to further clarify the characteristics of natural foci of SARS-CoV-2 and actively defend against future outbreaks of emerging zoonotic diseases.

13.
J Biosaf Biosecur ; 3(1): 58-65, 2021 Jun.
Article in English | MEDLINE | ID: covidwho-1284238

ABSTRACT

The re-emerging outbreak of COVID-19 in Beijing, China, in the summer of 2020 originated from a SARS-CoV-2-infested wholesale food supermarket. We postulated that the Xinfadi market outbreak has links with food-trade activities. Our Susceptible to the disease, Infectious, and Recovered coupled Agent Based Modelling (SIR-ABM) analysis for studying the diffusion of SARS-CoV-2 particles suggested that the trade-distancing strategy effectively reduces the reproduction number (R0). The retail shop closure strategy reduced the number of visitors to the market by nearly half. In addition, the buy-local policy option reduced the infection by more than 70% in total. Therefore, retail closures and buy-local policies could serve as significantly effective strategies that have the potential to reduce the size of the outbreak and prevent probable outbreaks in the future.

14.
J Biosaf Biosecur ; 3(1): 35-40, 2021 Jun.
Article in English | MEDLINE | ID: covidwho-1240455

ABSTRACT

INTRODUCTION: The significance of asymptomatic or pre-asymptomatic individuals in driving the COVID-19 epidemic in China or other countries remains uncertain. METHOD: We collected and analyzed all the epidemiologic and virological diagnostic details of the infected individuals released by public health authorities and reiterated every episode of outbreak on a timeline. All individuals associated with the five outbreaks had tested positive for SARS-CoV-2 infection. RESULTS: In this study, all five COVID-19 outbreaks reported in China since October 2020 were analyzed. The Kashgar outbreak in Xinjiang province came into light for the first time on October 22, 2020. However, it was initiated before October 11, 2020, by a local asymptomatic import and export worker, who was infected at the working place. Subsequently, his wife caught the infection, which led to 430 more infections reported in the outbreak. The Beijing outbreak with 41 cases was noticed for the first time on December 22, 2020. However, our analysis revealed that it was initiated by an asymptomatic individual from Indonesia on December 10, 2020. The Shenyang outbreak, with 38 cases, noticed for the first time on December 23, 2020, was initiated by a pre-symptomatic individual from South Korea on December 13, 2020. CONCLUSION: The asymptomatic or pre-symptomatic individuals during the asymptomatic period were unsuspectingly infected by SARS-CoV-2, and unintentionally transmitted the virus to a large number of people. These findings suggest that early detection of asymptomatic or pre-symptomatic individuals is of critical importance in preventing future outbreaks or epidemics.

15.
Infect Dis Poverty ; 10(1): 56, 2021 Apr 26.
Article in English | MEDLINE | ID: covidwho-1204112

ABSTRACT

BACKGROUND: As one of the non-pharmacological interventions to control the transmission of COVID-19, determining the quarantine duration is mainly based on the accurate estimates of the incubation period. However, patients with coarse information of the exposure date, as well as infections other than the symptomatic, were not taken into account in previously published studies. Thus, by using the statistical method dealing with the interval-censored data, we assessed the quarantine duration for both common and uncommon infections. The latter type includes the presymptomatic, the asymptomatic and the recurrent test positive patients. METHODS: As of 10 December 2020, information on cases have been collected from the English and Chinese databases, including Pubmed, Google scholar, CNKI (China National Knowledge Infrastructure) and Wanfang. Official websites and medias were also searched as data sources. All data were transformed into doubly interval-censored and the accelerated failure time model was applied. By estimating the incubation period and the time-to-event distribution of worldwide COVID-19 patients, we obtain the large percentiles for determining and suggesting the quarantine policies. For symptomatic and presymptomatic COVID-19 patients, the incubation time is the duration from exposure to symptom onset. For the asymptomatic, we substitute the date of first positive result of nucleic acid testing for that of symptom onset. Furthermore, the time from hospital discharge or getting negative test result to the positive recurrence has been calculated for recurrent positive patients. RESULTS: A total of 1920 laboratory confirmed COVID-19 cases were included. Among all uncommon infections, 34.1% (n = 55) of them developed symptoms or were identified beyond fourteen days. Based on all collected cases, the 95th and 99th percentiles were estimated to be 16.2 days (95% CI 15.5-17.0) and 22.9 days (21.7‒24.3) respectively. Besides, we got similar estimates based on merely symptomatic and presymptomatic infections as 15.1 days (14.4‒15.7) and 21.1 days (20.0‒22.2). CONCLUSIONS: There are a certain number of infected people who require longer quarantine duration. Our findings well support the current practice of the extended active monitoring. To further prevent possible transmissions induced and facilitated by such infectious outliers after the 14-days quarantine, properly prolonging the quarantine duration could be prudent for high-risk scenarios and in regions with insufficient test resources.


Subject(s)
COVID-19/prevention & control , Quarantine/methods , SARS-CoV-2/physiology , Adolescent , Adult , Aged , Asymptomatic Diseases/epidemiology , Asymptomatic Infections/epidemiology , Carrier State/epidemiology , Child , Child, Preschool , Female , Humans , Infant , Infant, Newborn , Infectious Disease Incubation Period , Male , Middle Aged , Models, Statistical , Time Factors , Young Adult
16.
Disease Surveillance ; 36(1):23-28, 2021.
Article in Chinese | GIM | ID: covidwho-1190524

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has swept the world in 2020, resulting in unprecedented pandemic of coronavirus disease 2019 (COVID-19). The number of infected persons and deaths increase every day at a frightening speed, threatening the health and life of people in the world and causing heavy burden to the global public health system. So far, nucleic acid detection is the main diagnostic method and gold standard for COVID-19. Meanwhile, other techniques and methods are also in developing for the diagnosis of SARS-CoV-2 infection. Proteomics technique is one of them. Proteomics technique has been widely used in the research of disease-related mechanism, development of diagnostic methods and pathogen identification. Up to now, there are mainly two applications of proteomics in the diagnosis of SARS-CoV-2 infection. First, proteomics based on virus particles has great potential in early diagnosis. Second, proteomics based on body fluids can be used not only for early diagnosis, but also for good monitoring the progress of infection, predicting the trend of disease, and evaluating the prognoses. In this paper, the research and application of proteomics technique in the diagnosis of SARS-CoV-2 infection in the world are summarized and prospected.

17.
Disease Surveillance ; 36(1):29-36, 2021.
Article in Chinese | GIM | ID: covidwho-1190523

ABSTRACT

Serological detection of specific antibody is an important method in the diagnosis of SARS-CoV-2 infection. However, numerous antibody detection kits for SARS-CoV-2 have been available within a short period, their accuracy and effectiveness are uncertain. This paper summarizes the current status of antibody detection kits for SARS-CoV-2 at home and abroad to provide reference on their uses by staffs in hospitals and CDCs.

18.
Disease Surveillance ; 36(1):16-22, 2021.
Article in Chinese | CAB Abstracts | ID: covidwho-1190522

ABSTRACT

Coronavirus disease 2019 (COVID-19) spreads rapidly and widely in the world, which is mainly transmitted through respiratory droplets and contact with contaminated media. In this study, SARS-CoV-2 was found to have a similar stability to severe acute respiratory syndrome coronavirus (SARS-CoV) by analyzing its survival time on different subject surfaces and main influencing factors in related research. SARS-CoV-2 can survive for several days at various subject surfaces or media at room temperature (stainless steel: 2 days, plastic: 3 days, glass: 4 days, etc.), and SARS-CoV-2 can persist for longer time at low temperature and low relative humidity, which has caused severe threat to public health and has posed severe challenges to the prevention and control of COVID-19. According to available data, SARS-CoV-2 has the characteristics of high infectiousness and high covertness, similar to influenza A virus. By understanding the survival potential and infectiousness of SARS-CoV-2 in environment, targeted disinfection and effective protection can be implemented to reduce the incidence of COVID-19.

19.
Disease Surveillance ; 35(12):1068-1072, 2020.
Article in Chinese | GIM | ID: covidwho-1190519

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a natural emerging virus, with rapid virus replication, wide cell tropism, and strong survival ability. Its epidemic characteristics are similar to those of influenza virus. Asymptomatic infections are widespread in a covert way, and the virus has adapted to human population, making it difficult to control the transmission. The global epidemic in 2020/2021 may further deteriorate before the SARS-CoV-2 vaccines are widely applied and show protective effectiveness, and China will still face the risk of continuous overseas multi-channel import and local outbreaks or recurrence of the epidemic. Therefore, it is necessary to carry out further surveillance about the prevalence and infection of SARS-CoV-2 in the population and the corresponding environment of the high-risk areas in China, and establish a national super mobile SARS-CoV-2 detection network laboratory for performing ultra-large-scale testing tasks;implement differentiated vaccination strategies and closely follow up and monitor the effectiveness and efficiency of vaccination;and continue to strengthen effective public health measures such as wearing masks, washing hands frequently, keeping social distances, opening windows frequently, and reducing gatherings. The coronavirus disease 2019 (COVID-19) epidemic warns us once again that the continuous emergence of new infectious diseases caused by unknown pathogens of wild animal origin has become the new normal status. It is necessary to systematically carry out unknown microbial discovery and reverse pathogenic etiology research in a prospective manner, and actively defend against emerging infectious diseases in the future.

20.
J Infect Dis ; 223(8): 1313-1321, 2021 04 23.
Article in English | MEDLINE | ID: covidwho-1091239

ABSTRACT

Domestic cats, an important companion animal, can be infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). This has aroused concern regarding the ability of domestic cats to spread the virus that causes coronavirus disease 2019. We systematically demonstrated the pathogenesis and transmissibility of SARS-CoV-2 in cats. Serial passaging of the virus between cats dramatically attenuated the viral transmissibility, likely owing to variations of the amino acids in the receptor-binding domain sites of angiotensin-converting enzyme 2 between humans and cats. These findings provide insight into the transmissibility of SARS-CoV-2 in cats and information for protecting the health of humans and cats.


Subject(s)
COVID-19/transmission , COVID-19/veterinary , SARS-CoV-2/pathogenicity , Amino Acids/metabolism , Angiotensin-Converting Enzyme 2/metabolism , Animals , COVID-19/metabolism , Cats , Cell Line , Chlorocebus aethiops , Female , Humans , Male , Vero Cells
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