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1.
Nat Commun ; 15(1): 7033, 2024 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-39147778

RESUMO

The SARS-CoV-2 Omicron variant sparked the largest wave of infections worldwide. Mainland China eased its strict COVID-19 measures in late 2022 and experienced two nationwide Omicron waves in 2023. Here, we investigated lineage distribution and virus evolution in Guangdong, China, 2022-2023 by comparing 5813 local viral genomes with the datasets from other regions of China and worldwide. Additionally, we conducted three large-scale serological surveys involving 1696 participants to measure their immune response to the BA.5 and XBB.1.9 before and after the corresponding waves. Our findings revealed the Omicron variants, mainly the BA.5.2.48 lineage, causing infections in over 90% of individuals across different age groups within a month. This rapid spread led to the establishment of widespread immunity, limiting the virus's ability to further adaptive mutation and dissemination. While similar immune responses to BA.5 were observed across all age groups after the initial wave, children aged 3 to 11 developed a stronger cross immune response to the XBB.1.9 strain, possibly explaining their lower infection rates in the following XBB.1 wave. Reinfection with Omicron XBB.1 variant triggered a more potent neutralizing immune response among older adults. These findings highlight the impact of age-specific immune responses on viral spread in potential future waves.


Assuntos
COVID-19 , Genoma Viral , SARS-CoV-2 , Humanos , COVID-19/imunologia , COVID-19/epidemiologia , COVID-19/virologia , SARS-CoV-2/imunologia , SARS-CoV-2/genética , China/epidemiologia , Criança , Pré-Escolar , Adulto , Adolescente , Pessoa de Meia-Idade , Adulto Jovem , Genoma Viral/genética , Masculino , Feminino , Anticorpos Antivirais/imunologia , Anticorpos Antivirais/sangue , Epidemiologia Molecular , Lactente , Idoso , Pandemias , Filogenia
2.
Viruses ; 16(4)2024 04 22.
Artigo em Inglês | MEDLINE | ID: mdl-38675989

RESUMO

BACKGROUND: After the adjustment of COVID-19 epidemic policy, mainland China experienced two consecutive waves of Omicron variants within a seven-month period. In Guangzhou city, as one of the most populous regions, the viral infection characteristics, molecular epidemiology, and the dynamic of population immunity are still elusive. METHODS: We launched a prospective cohort study in the Guangdong Provincial CDC from December 2022 to July 2023. Fifty participants who received the same vaccination regimen and had no previous infection were recruited. RESULTS: 90% of individuals were infected with Omicron BA.5* variants within three weeks in the first wave. Thirteen cases (28.26%) experienced infection with XBB.1* variants, occurring from 14 weeks to 21 weeks after the first wave. BA.5* infections exhibited higher viral loads in nasopharyngeal sites compared to oropharyngeal sites. Compared to BA.5* infections, the XBB.1* infections had significantly milder clinical symptoms, lower viral loads, and shorter durations of virus positivity. The infection with the BA.5* variant elicited varying levels of neutralizing antibodies against XBB.1* among different individuals, even with similar levels of BA.5* antibodies. The level of neutralizing antibodies specific to XBB.1* determined the risk of reinfection. CONCLUSIONS: The rapid large-scale infections of the Omicron variants have quickly established herd immunity among the population in mainland China. In the future of the COVID-19 epidemic, a lower infection rate but a longer duration can be expected. Given the large population size and ongoing diversified herd immunity, it remains crucial to closely monitor the molecular epidemiology of SARS-CoV-2 for the emergence of new variants of concern in this region. Additionally, the timely evaluation of the immune status across different age groups is essential for informing future vaccination strategies and intervention policies.


Assuntos
Anticorpos Neutralizantes , Anticorpos Antivirais , COVID-19 , SARS-CoV-2 , Carga Viral , Humanos , COVID-19/epidemiologia , COVID-19/virologia , COVID-19/imunologia , China/epidemiologia , SARS-CoV-2/genética , SARS-CoV-2/imunologia , SARS-CoV-2/classificação , Masculino , Feminino , Adulto , Pessoa de Meia-Idade , Anticorpos Neutralizantes/sangue , Anticorpos Neutralizantes/imunologia , Estudos Prospectivos , Anticorpos Antivirais/sangue , Estudos de Coortes , Adulto Jovem , Idoso
3.
Psychol Res Behav Manag ; 17: 367-378, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38327872

RESUMO

Purpose: To explore the potential classification of Problematic Mobile Social Media Usage (PMSMU) in Chinese college students, analyze whether there is group heterogeneity in PMSMU, and discuss the differences in the latent profile of PMSMU in fear of missing out, online positive feedback, and boredom proneness. Methods: A total of 2591 Chinese college students were investigated using the Problematic Mobile Social Media Usage Questionnaire, Fear of Missing Out (FOMO) Scale, Online Positive Feedback Scale and Short-form Boredom Proneness Scale, and heterogeneity was tested by latent profile analysis. Results: The PMSMU of college students can be divided into three latent profiles: no-problem use group (26.44%), mild problem use group (56.66%), and severe problem use group (16.91%). Male students, as compared to female students, showed a significantly lower likelihood of being classified as mild problematic users (OR=0.50, p<0.001) and severe problematic users (OR=0.29, p<0.001). Additionally, students with higher levels of FOMO, a stronger craving for online positive feedback, and increased boredom proneness are more likely to belong to the severe problematic use group (OR=2.91, p<0.001; OR=1.42, p<0.01; OR=8.72, p<0.001). Conclusion: The results of this study highlight the factors influencing the heterogeneity of individual PMSMU. Specifically, female college students and those with a higher fear of missing out, greater susceptibility to boredom, and a stronger craving for positive online feedback are more likely to exhibit severe PMSMU. These findings provide valuable empirical evidence for developing preventive strategies to address PMSMU among college students.

4.
Curr Res Food Sci ; 7: 100569, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37664003

RESUMO

The peptide MOp2 obtained from Moringa oleifera seeds showed good antimicrobial activity. However, the stability of its activity has not yet been studied. In the present study, MOp2-loaded thiolated chitosan-stabilized (CMOp2) Pickering emulsion was prepared and applied to prolong the shelf life of grass carp. The encapsulation rate of MOp2 was 57.7% in CMOp2. In addition, the effects of different concentrations of CMOp2 solid particles and pH on droplet size, zeta optional and storage stability of Pickering emulsions were evaluated; the best condition for preparing Pickering emulsion through experiment was 1.75% CMOp2 solid particles at pH 9.5. Moreover, morphological observations and rheological analysis indicated that Pickering emulsions were considered a water-in-oil emulsion with typical non-Newtonian fluid characteristics. Furthermore, the prepared Pickering emulsion could significantly inhibit the growth of Escherichia coli and Staphylococcus aureus. Besides, Pickering emulsion effectively prevented spoilage of grass carp, and the Pickering emulsion-treated group reduced its pH, TVB-N and color values, inhibited microbial growth, and extended shelf life to 9 day at the storage of 4 °C. Overall, the present findings provide a reference for the application of MOp2-loaded Pickering emulsions in food preservation.

5.
J Epidemiol Glob Health ; 13(3): 539-546, 2023 09.
Artigo em Inglês | MEDLINE | ID: mdl-37535238

RESUMO

BACKGROUND: Since the Non-pharmaceutical Intervention (NPI) by COVID-19 emerged, influenza activity has been somewhat altered. OBJECTIVES: The aim of this study was to explore changes in influenza activities in the context of COVID-19 based on the sentinel hospitals/units in Guangdong, southern China. METHODS: The surveillance data in influenza-like illness (ILI) were collected from 21 cities in Guangdong between September 2017 and August 2021, while 43 hospitals/units were selected to analyze the predominant types of influenza, population characteristics, and seasonal features by three methods (the concentration ratio, the seasonal index, and the circulation distribution), based on a descriptive epidemiological approach. RESULTS: During the four consecutive influenza seasons, a total of 157345 ILIs were tested, of which 9.05% were positive for influenza virus (n = 14238), with the highest positive rates for both IAV (13.20%) and IBV (5.41%) in the 2018-2019 season. After the emergence of COVID-19, influenza cases decreased near to zero from March 2020 till March 2021, and the dominant type of influenza virus changed from IAV to IBV. The highest positive rate of influenza existed in the age-group of 5 ~ < 15 years in each season for IAV (P < 0.001), which was consistent with that for IBV (P < 0.001). The highest annual positive rates for IBV emerged in eastern Guangdong, while the highest annual positive rates of IAV in different seasons existed in different regions. Furthermore, compared with the epidemic period (ranged from December to June) during 2017-2019, the period ended three months early (March 2020) in 2019-2020, and started by five months behind (April 2021) during 2020-2021. CONCLUSION: The highest positive rates in 5 ~ < 15 age-group suggested the susceptible in this age-group mostly had infected with infected B/Victoria. Influenced by the emergence of COVID-19 and NPI responses, the epidemic patterns and trends of influenza activities have changed in Guangdong, 2017-2021.


Assuntos
COVID-19 , Epidemias , Influenza Humana , Humanos , Adolescente , Influenza Humana/epidemiologia , Influenza Humana/prevenção & controle , COVID-19/epidemiologia , Epidemias/prevenção & controle , China/epidemiologia , Cidades , Estações do Ano , Vigilância de Evento Sentinela
6.
Exp Cell Res ; 429(1): 113650, 2023 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-37209990

RESUMO

The retina may undergo structural and functional damage as a result of hypoxia, which could lead to permanent blindness. As competing endogenous RNAs (ceRNAs), lncRNAs are essential in eye disorders. The biological function of lncRNA MALAT 1 and its potential mechanisms in hypoxic-ischemic retinal diseases are still unknown. MALAT 1 and miR-625-3p expression alterations in hypoxia-treated RPE cells were examined using qRT-PCR. The target binding relationships between MALAT 1 and miR-625-3p, as well as between miR-625-3p and HIF-1α, were identified utilizing bioinformatics analysis and dual luciferase reporter assay. We observed that si-MALAT 1 and miR-625-3p mimic both reduced apoptosis and epithelial-mesenchymal transition (EMT) in hypoxic RPE cells, whereas si-MALAT 1 was reversed by miR-625-3p inhibitor. Further, we carried out a mechanistic investigation, and rescue assays demonstrated that MALAT 1 sponging miR-625-3p influenced HIF-1α expression and consequently took part in the NF-κB/Snail signaling pathway, which regulated apoptosis and EMT. In conclusion, our research had shown that the MALAT 1/miR-625-3p/HIF-1α axis drove the progression of hypoxic-ischemic retinal disorders and may serve as a promising predictive biomarker for their therapeutic and diagnostic targets.


Assuntos
MicroRNAs , RNA Longo não Codificante , Humanos , NF-kappa B/genética , NF-kappa B/metabolismo , MicroRNAs/metabolismo , RNA Longo não Codificante/genética , Transição Epitelial-Mesenquimal/genética , Movimento Celular/genética , Transdução de Sinais/genética , Hipóxia , Proliferação de Células/genética , Subunidade alfa do Fator 1 Induzível por Hipóxia/genética , Subunidade alfa do Fator 1 Induzível por Hipóxia/metabolismo
7.
Virol J ; 19(1): 197, 2022 11 25.
Artigo em Inglês | MEDLINE | ID: mdl-36434614

RESUMO

Currently, the majority of the global population has been vaccinated with the COVID-19 vaccine, and characterization studies of antibodies in vivo from Omicron breakthrough infection and naive infection populations are urgently needed to provide pivotal clues about accurate diagnosis, treatment, and next-generation vaccine design against SARS-CoV-2 infection. We showed that after infection with Omicron-BA.2, the antibody levels of specific IgM against the Wuhan strain and specific IgG against Omicron were not significantly elevated within 27 days of onset. Interestingly, in this study, the levels of humoral immunity against Omicron-specific IgM were significantly increased after breakthrough infection, suggesting that the detection of Omicron-specific IgM antibodies can be used as a test criterion of Omicron breakthrough infection. In addition, we observed that serums from unvaccinated individuals and the majority of vaccinated infections possessed only low or no neutralizing activity against Omicron at the onset of Omicron breakthrough infections, and at the later stage of Omicron-BA.2 breakthrough infection, levels of neutralization antibody against the Wuhan and Omicron strains were elevated in infected individuals. The findings of this study provide important clues for the diagnosis of Omicron breakthrough infections, antibody characterization studies and vaccine design against COVID-19.


Assuntos
Formação de Anticorpos , COVID-19 , Humanos , SARS-CoV-2 , Anticorpos Antivirais , Vacinas contra COVID-19 , Imunoglobulina M
10.
J Med Virol ; 94(12): 6065-6072, 2022 12.
Artigo em Inglês | MEDLINE | ID: mdl-35931461

RESUMO

Various variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been emerging and circulating in different parts of the world. Millions of vaccine doses have been administered globally, which reduces the morbidity and mortality of coronavirus disease-2019 efficiently. Here, we assess the immune responses of individuals after two shots of BBIBP-CorV or CoronaVac inactivated vaccine. We measured neutralizing antibody responses after the second vaccination by using authentic SARS-CoV-2 and its viral variants. All the serum samples efficiently neutralized SARS-CoV-2 wild-type lineage, in contrast, a part of serum samples failed to neutralize Alpha, Beta, Gamma, Delta, or Eta lineages, and only several serum samples were able to neutralize Omicron lineage virus strains (BA.1 and BA.2) with low neutralization titer. As compared with the neutralization of SARS-CoV-2 wild-type lineage, the neutralization of all other SARS-CoV-2 variant lineages was significantly lower. Considering that all the SARS-CoV-2 mutation viruses challenged the antibody neutralization induced by BBIBP-CorV and CoronaVac, it is necessary to carry out a third booster vaccination to increase the humoral immune response against the SARS-CoV-2 mutation viruses.


Assuntos
COVID-19 , Vacinas Virais , Anticorpos Neutralizantes , Anticorpos Antivirais , COVID-19/prevenção & controle , Vacinas contra COVID-19 , Humanos , SARS-CoV-2/genética , Vacinas de Produtos Inativados
11.
Front Microbiol ; 13: 945133, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35836420

RESUMO

Coronavirus disease 2019 (COVID-19) pandemic caused by SARS-CoV-2 variants is a new and unsolved threat; therefore, it is an urgent and unmet need to develop a simple and rapid method for detecting and tracking SARS-CoV-2 variants. The spike gene of SARS-CoV-2 was amplified by isothermal recombinase-aided amplification (RAA) followed by the cleavage of CRISPR-Cas12a in which five allele-specific crRNAs and two Omicron-specific crRNAs were designed to detect and distinguish major SARS-CoV-2 variants of concerns (VOCs), including alpha, beta, delta variants, and Omicron sublineages BA.1 and BA.2. The whole reaction can be carried out in one tube at 39°C within 1.5-2 h, and the results can be read out by a fluorescence meter or naked eyes. Our results show that the RAA/CRISPR-Cas12a-based assay could readily distinguish the signature mutations, i.e., K417N, T478K, E484K, N501Y, and D614G, with a sensitivity of 100.0% and a specificity of 94.9-100.0%, respectively. The assay had a low limit of detection (LOD) of 104 copies/reaction and a concordance of 92.59% with Sanger sequencing results when detecting 54 SARS-CoV-2 positive clinical samples. The two Omicron-specific crRNAs can readily and correctly distinguish Omicron BA.1 and BA.2 sublineages with a LOD of as low as 20 copies/reaction. Furthermore, no cross-reaction was observed for all crRNAs analyzed when detecting clinical samples infected with 11 common respiratory pathogens. The combination of isothermal amplification and CRISPR-Cas12a-mediated assay is suitable for rapid detection of major SARS-CoV-2 variants in point-of-care testing and in resource-limiting settings. This simple assay could be quickly updated for emerging variants and implemented to routinely monitor and track the spread of SARS-CoV-2 variants.

12.
J Med Virol ; 94(9): 4224-4233, 2022 09.
Artigo em Inglês | MEDLINE | ID: mdl-35585023

RESUMO

We aimed to analyze the efficacy and safety of an inactivated SARS-CoV-2 vaccine in people living with HIV (PLWH). A total of 143 PLWH and 50 healthy individuals were included in this study. A commercially available magnetic chemiluminescence enzyme immunoassay kit was used to detect serum IgG and IgM antibodies against SARS-CoV-2. Serum levels of SARS-CoV-2-specific IgG were significantly higher in the control group than in the PLWH group (p = 0.001). Overall, 76% of individuals in the control group were detected with seropositivity IgG against SARS-CoV-2 compared to 58% in the PLWH group (p = 0.024). In PLWH with IgG seropositivity, CD4+ T-cell counts before antiretroviral therapy (ART) was higher (p = 0.015). Multivariable analysis indicated that CD4+ T cells at IgG detection (odds ratio [OR] = 1.004, p = 0.006) and time after vaccination (OR = 0.977, p = 0.014) were independently associated with seropositivity IgG against SARS-CoV-2 in PLWH. Neutralizing antibody (nAb) titers in PLWH against wild-type SARS-CoV-2 were similar to those in the control group (p = 0.160). The proportion of seropositive nAbs against wild-type SARS-CoV-2 was also similar (95% in the control group vs. 97% in the PLWH group, p = 0.665). Similar results were obtained when nAb was detected against the delta variants with similar titers (p = 0.355) and a similar proportion of seropositive nAbs were observed (p = 0.588). All the side effects observed in our study were mild and self-limiting. The inactivated COVID-19 vaccine appears to be safe with good immunogenicity in Chinese PLWH.


Assuntos
COVID-19 , Vacinas Virais , Anticorpos Neutralizantes , Anticorpos Antivirais , COVID-19/prevenção & controle , Vacinas contra COVID-19/efeitos adversos , Estudos Transversais , Humanos , Imunogenicidade da Vacina , Imunoglobulina G , SARS-CoV-2
13.
J Med Virol ; 94(9): 4533-4538, 2022 09.
Artigo em Inglês | MEDLINE | ID: mdl-35614018

RESUMO

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants could induce immune escape by mutations of the spike protein which are threatening to weaken vaccine efficacy. A booster vaccination is expected to increase the humoral immune response against SARS-CoV-2 variants in the population. We showed that immunization with two doses of wild type receptor-binding domain (RBD) protein, and booster vaccination with wild type or variant RBD protein all significantly increased binding and neutralizing antibody titers against wild type SARS-CoV-2 and its variants in mice. Only the booster immunization by Omicron (BA.1)RBD induced a strong antibody titer against the omicron virus strain and comparable antibody titers against all the other virus strains. These findings might shed the light on coronavirus disease 2019 booster immunogens.


Assuntos
Vacinas contra COVID-19 , COVID-19 , Imunidade Humoral , Animais , Anticorpos Neutralizantes , Anticorpos Antivirais , COVID-19/prevenção & controle , Vacinas contra COVID-19/imunologia , Humanos , Imunização Secundária , Camundongos , SARS-CoV-2/genética , Glicoproteína da Espícula de Coronavírus/genética , Vacinação
14.
ACS Synth Biol ; 11(5): 1811-1823, 2022 05 20.
Artigo em Inglês | MEDLINE | ID: mdl-35481381

RESUMO

Objectives: Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants pose a great threat and burden to global public health. Here, we evaluated a clustered regularly interspaced short palindromic repeat-associated enzyme 12a (CRISPR-Cas12a)-based method for detecting major SARS-CoV-2 variants of concern (VOCs) in SARS-CoV-2 positive clinical samples. Methods: Allele-specific CRISPR RNAs (crRNAs) targeting the signature mutations in the spike protein of SARS-CoV-2 are designed. A total of 59 SARS-CoV-2 positive oropharyngeal swab specimens were used to evaluate the performance of the CRISPR-Cas12a-mediated assay to identify major SARS-CoV-2 VOCs. Results: Compared with Sanger sequencing, the eight allele-specific crRNAs analyzed can specifically identify the corresponding mutations with a positive predictive value of 83.3-100% and a negative predictive value of 85.7-100%. Our CRISPR-Cas12a-mediated assay distinguished wild-type and four major VOCs (Alpha, Beta, Delta, and Omicron) of SARS-CoV-2 with a sensitivity of 93.8-100.0% and a specificity of 100.0%. The two methods showed a concordance of 98.3% (58/59) with a κ value of 0.956-1.000, while seven (11.9%) samples were found to be positive for extra mutations by the CRISPR-based assay. Furthermore, neither virus titers nor the sequences adjacent to the signature mutations were associated with the variation of fluorescence intensity detected or the false-positive reaction observed when testing clinical samples. In addition, there was no cross-reaction observed when detecting 33 SARS-CoV-2 negative clinical samples infected with common respiratory pathogens. Conclusions: The CRISPR-Cas12a-based genotyping assay is highly sensitive and specific when detecting both the SARS-CoV-2 wild-type strain and major VOCs. It is a simple and rapid assay that can monitor and track the circulating SARS-CoV-2 variants and the dynamics of the coronavirus disease 2019 (COVID-19) pandemic and can be easily implemented in resource-limited settings.


Assuntos
COVID-19 , SARS-CoV-2 , COVID-19/diagnóstico , Sistemas CRISPR-Cas/genética , Humanos , Mutação , SARS-CoV-2/genética
16.
Biosens Bioelectron ; 205: 114098, 2022 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-35189535

RESUMO

BACKGROUND: The newly emerged SARS-CoV-2 variant of concern (VOC) Omicron is spreading quickly worldwide, which manifests an urgent need of simple and rapid assay to detect and diagnose Omicron infection and track its spread. METHODS: To design allele-specific CRISPR RNAs (crRNAs) targeting the signature mutations in the spike protein of Omicron variant, and to develop a CRISPR-Cas12a-based assay to specifically detect Omicron variant. RESULTS: Our system showed a low limit of detection of 2 copies per reaction for the plasmid DNA of Omicron variant, and could readily detect Omicron variant in 5 laboratory-confirmed clinical samples and distinguish them from 57 SARS-CoV-2 positive clinical samples (4 virus isolates and 53 oropharyngeal swab specimens) infected with wild-type (N = 8) and the variants of Alpha (N = 17), Beta (N = 17) and Delta (N = 15). The testing results could be measured by fluorescent detector or judged by naked eyes. In addition, no cross-reaction was observed when detecting 16 clinical samples infected with 9 common respiratory pathogens. CONCLUSIONS: The rapid assay could be easily set up in laboratories already conducting SARS-CoV-2 nucleic acid amplification tests and implemented routinely in resource-limited settings to monitor and track the spread of Omicron variant.


Assuntos
Técnicas Biossensoriais , COVID-19 , COVID-19/diagnóstico , Sistemas CRISPR-Cas/genética , Humanos , SARS-CoV-2/genética
17.
Nat Commun ; 13(1): 460, 2022 01 24.
Artigo em Inglês | MEDLINE | ID: mdl-35075154

RESUMO

The SARS-CoV-2 Delta variant has spread rapidly worldwide. To provide data on its virological profile, we here report the first local transmission of Delta in mainland China. All 167 infections could be traced back to the first index case. Daily sequential PCR testing of quarantined individuals indicated that the viral loads of Delta infections, when they first become PCR-positive, were on average ~1000 times greater compared to lineage A/B infections during the first epidemic wave in China in early 2020, suggesting potentially faster viral replication and greater infectiousness of Delta during early infection. The estimated transmission bottleneck size of the Delta variant was generally narrow, with 1-3 virions in 29 donor-recipient transmission pairs. However, the transmission of minor iSNVs resulted in at least 3 of the 34 substitutions that were identified in the outbreak, highlighting the contribution of intra-host variants to population-level viral diversity during rapid spread.


Assuntos
COVID-19/transmissão , Busca de Comunicante/métodos , Surtos de Doenças/prevenção & controle , SARS-CoV-2/isolamento & purificação , Animais , COVID-19/epidemiologia , COVID-19/virologia , Chlorocebus aethiops , Humanos , RNA-Seq/métodos , Reação em Cadeia da Polimerase Via Transcriptase Reversa , SARS-CoV-2/genética , SARS-CoV-2/fisiologia , Fatores de Tempo , Células Vero , Carga Viral/genética , Carga Viral/fisiologia , Replicação Viral/genética , Replicação Viral/fisiologia , Eliminação de Partículas Virais/genética , Eliminação de Partículas Virais/fisiologia
18.
Microbiol Spectr ; 9(3): e0101721, 2021 12 22.
Artigo em Inglês | MEDLINE | ID: mdl-34787487

RESUMO

A big challenge for the control of COVID-19 pandemic is the emergence of variants of concern (VOCs) or variants of interest (VOIs) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which may be more transmissible and/or more virulent and could escape immunity obtained through infection or vaccination. A simple and rapid test for SARS-CoV-2 variants is an unmet need and is of great public health importance. In this study, we designed and analytically validated a CRISPR-Cas12a system for direct detection of SARS-CoV-2 VOCs. We further evaluated the combination of ordinary reverse transcription-PCR (RT-PCR) and CRISPR-Cas12a to improve the detection sensitivity and developed a universal system by introducing a protospacer adjacent motif (PAM) near the target mutation sites through PCR primer design to detect mutations without PAM. Our results indicated that the CRISPR-Cas12a assay could readily detect the signature spike protein mutations (K417N/T, L452R/Q, T478K, E484K/Q, N501Y, and D614G) to distinguish alpha, beta, gamma, delta, kappa, lambda, and epsilon variants of SARS-CoV-2. In addition, the open reading frame 8 (ORF8) mutations (T/C substitution at nt28144 and the corresponding change of amino acid L/S) could differentiate L and S lineages of SARS-CoV-2. The low limit of detection could reach 10 copies/reaction. Our assay successfully distinguished 4 SARS-CoV-2 strains of wild type and alpha (B.1.1.7), beta (B.1.351), and delta (B.1.617.2) variants. By testing 32 SARS-CoV-2-positive clinical samples infected with the wild type (n = 5) and alpha (n = 11), beta (n = 8), and delta variants (n = 8), the concordance between our assay and sequencing was 100%. The CRISPR-based approach is rapid and robust and can be adapted for screening the emerging mutations and immediately implemented in laboratories already performing nucleic acid amplification tests or in resource-limited settings. IMPORTANCE We described CRISPR-Cas12-based multiplex allele-specific assay for rapid SARS-CoV-2 variant genotyping. The new system has the potential to be quickly developed, continuously updated, and easily implemented for screening of SARS-CoV-2 variants in resource-limited settings. This approach can be adapted for emerging mutations and implemented in laboratories already conducting SARS-CoV-2 nucleic acid amplification tests using existing resources and extracted nucleic acid.


Assuntos
Teste para COVID-19/métodos , COVID-19/virologia , Sistemas CRISPR-Cas , SARS-CoV-2/classificação , SARS-CoV-2/genética , SARS-CoV-2/isolamento & purificação , Alelos , COVID-19/diagnóstico , Bases de Dados de Ácidos Nucleicos , Humanos , Programas de Rastreamento , Mutação , Reação em Cadeia da Polimerase , Saúde Pública , Glicoproteína da Espícula de Coronavírus/genética
19.
Curr Med Sci ; 41(2): 228-235, 2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-33877539

RESUMO

Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) with unknown origin spread rapidly to 222 countries, areas or territories. To investigate the genomic evolution and variation in the early phase of COVID-19 pandemic in Guangdong, 60 specimens of SARS-CoV-2 were used to perform whole genome sequencing, and genomics, amino acid variation and Spike protein structure modeling analyses. Phylogenetic analysis suggested that the early variation in the SARS-CoV-2 genome was still intra-species, with no evolution to other coronaviruses. There were one to seven nucleotide variations (SNVs) in each genome and all SNVs were distributed in various fragments of the genome. The Spike protein bound with human receptor, an amino acid salt bridge and a potential furin cleavage site were found in the SARS-CoV-2 using molecular modeling. Our study clarified the characteristics of SARS-CoV-2 genomic evolution, variation and Spike protein structure in the early phase of local cases in Guangdong, which provided reference for generating prevention and control strategies and tracing the source of new outbreaks.


Assuntos
COVID-19/genética , Evolução Molecular , SARS-CoV-2/crescimento & desenvolvimento , Glicoproteína da Espícula de Coronavírus/genética , COVID-19/epidemiologia , COVID-19/virologia , China/epidemiologia , Furina/genética , Genoma Viral/genética , Humanos , Pandemias , Filogenia , Ligação Proteica/genética , SARS-CoV-2/patogenicidade
20.
J Thorac Dis ; 13(1): 39-49, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-33569183

RESUMO

BACKGROUND: There have been many studies on the effectiveness and complications of airway stent, but few had focused on factors that affect survival after stent placement. This study intended to assess the factors associated with the survival in patients with malignant central airway obstruction (MCAO) after airway metallic stent placement. METHODS: The clinical data of adult MCAO patients who underwent stent placement form February 2003 to June 2017 in the First Affiliated Hospital of Soochow University in China were retrospectively analyzed. The survival rates were compared using Log-rank tests. Potential prognostic factors were identified using multivariate Cox hazard regression models. RESULTS: Total 102 MCAO patients were included in this study. The median survival time of these patients after airway metallic stent placement was 4.1 months. Multivariate analysis showed that MCAO patients receiving radiotherapy [hazard ratio (HR) 0.554; 95% confidence interval (CI): 0.308-0.999] or chemoradiotherapy (HR 0.251; 95% CI: 0.126-0.499) after stenting had better prognosis. However, ECOG PS ≥3 score prior to the stenting (HR 2.193; 95% CI: 1.364-3.526) and stents placed in both trachea and main bronchus (HR 2.458; 95% CI: 1.384-4.366) were associated with worse survival. CONCLUSIONS: In our results, survival of MCAO patients after airway metallic stenting was related to ECOG PS score prior to the stenting, the site of stent placement and we have hereby proposed for the first time that having opportunity to receive radiotherapy or chemoradiotherapy after stenting contribute to better prognosis.

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