Your browser doesn't support javascript.
Show: 20 | 50 | 100
Results 1 - 11 de 11
Filter
1.
Geoscience Frontiers ; : 101384, 2022.
Article in English | ScienceDirect | ID: covidwho-1757360

ABSTRACT

Underground subway platforms are among the world’s busiest public transportation systems, but the airborne transmission mechanism of respiratory infections on these platforms has been rarely studied. Here, computational fluid dynamics (CFD) modeling is used to investigate the airflow patterns and infection risks in an island platform under two common ventilation modes: Mode 1- both sides have air inlets and outlets;Mode 2- air inlets are present at the two sides and outlets are present in the middle. Under the investigated scenario, airflow structure is characterized by the ventilation jet and human thermal plumes. Their interaction with the infector’s breathing jet imposes the front passenger under the highest exposure risk by short-range airborne route, with intake fractions up to 2.57% (oral breathing) or 0.63% (nasal breathing) under Mode 1;oral breathing of the infector may impose higher risks for the front passenger compared with nasal breathing. Pathogen are efficiently diluted as they travel further, in particular to adjacent crowds. The maximum and median value of intake fractions of passengers in adjacent crowds are respectively 0.093% and 0.016% (oral breathing), and 0.073% and 0.014% (nasal breathing) under Mode 1. Compared with Mode 1, the 2nd mode minimizes the interaction of ventilation jet and breathing jet, where the maximum intake fraction is only 0.34%, and the median value in the same crowd and other crowds are reduced by 23-63%. Combining published quanta generation rate data of COVID-19 and influenza infectors, the predicted maximum and median infection risks for passengers in the same crowds are respectively 1.46%−40.23% and 0.038%−1.67% during the 3−10 min waiting period, which are more sensitive to ventilation rate and exposure time compared with return air. This study can provide practical guidance for the prevention of respiratory infections in subway platforms.

2.
Biosens Bioelectron ; 205: 114098, 2022 Jun 01.
Article in English | MEDLINE | ID: covidwho-1693895

ABSTRACT

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.


Subject(s)
Biosensing Techniques , COVID-19 , COVID-19/diagnosis , CRISPR-Cas Systems/genetics , Humans , SARS-CoV-2/genetics
3.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-307605

ABSTRACT

Background: To analyze the efficacy and safety of SARS-CoV-2 inactivated vaccine in people living with HIV (PLWH).Methods: A total of 143 PLWH were included in the study. All patients were confirmed with HIV-1 infection. We also enrolled 50 healthy individuals vaccinated with two doses of SARS-CoV-2 vaccine as controls. A commercially available magnetic chemiluminescence enzyme immunoassay kit was used to detected serum IgG and IgM against SARS-CoV-2.Findings: 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 achieved IgG seroconversion after vaccination compared with 58% in the PLWH group (P=0.024). The time after vaccination in IgG seronegative PLWH was significantly longer compared with PLWH with IgG seropositive (43.38 ± 34.96 vs 30.27 ± 20.12 days, P=0.005). In PLWH with IgG seropositivity, CD4+ T cell counts before antiretroviral therapy (ART) (P=0.015) and at IgG detection (P<0.001) were higher. Multivariable analysis indicated CD4+ T cells at IgG detection (OR=1.004, P=0.006) and time after vaccination (OR=0.977, P=0.014) were independently associated with humoral response in PLWH after vaccination. Neutralizing antibody (NeuAb) titers in PLWH against wild type SARS-CoV-2 were similar compared with the Control group (P=0.160). The proportion of seropositive NeuAb against wild type SARS-CoV-2 were also similar (95% in Control group vs 97% in PLWH group, P=0.665). Similar results were obtained when NeuAb were detected against the delta variants with similar titers (P=0.355) and with similar proportion of humoral response (P=0.588). All side effects observed in our study were mild and self-limiting. There was no significant difference in occurrence of side effects in the control and PLWH groups. Interpretation: The inactivated COVID-19 vaccine appears to be safe with good immunogenicity in PLWH.Funding: This study was supported by Clinical Research Startup Program of Southern Medical University by High-level University Construction Funding of Guangdong Provincial Department of Education (No. LC2016PY003).Declaration of Interest: None of the authors have competing interests to disclose.Ethical Approval: The study was performed in accordance with the Declaration of Helsinki and was approved by the Institutional Ethics Committee of Nanfang Hospital (NFEC-2021-178).

4.
Nat Commun ; 13(1): 460, 2022 01 24.
Article in English | MEDLINE | ID: covidwho-1651070

ABSTRACT

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.


Subject(s)
COVID-19/transmission , Contact Tracing/methods , Disease Outbreaks/prevention & control , SARS-CoV-2/isolation & purification , Animals , COVID-19/epidemiology , COVID-19/virology , Chlorocebus aethiops , Humans , RNA-Seq/methods , Reverse Transcriptase Polymerase Chain Reaction , SARS-CoV-2/genetics , SARS-CoV-2/physiology , Time Factors , Vero Cells , Viral Load/genetics , Viral Load/physiology , Virus Replication/genetics , Virus Replication/physiology , Virus Shedding/genetics , Virus Shedding/physiology
6.
2021.
Preprint in English | Other preprints | ID: ppcovidwho-295289

ABSTRACT

Summary We report the first local transmission of the SARS-CoV-2 Delta variant in mainland China. All 167 infections could be traced back to the first index case. Daily sequential PCR testing of the quarantined subjects indicated that the viral loads of Delta infections, when they first become PCR+, were on average ∼1000 times greater compared to A/B lineage infections during initial epidemic wave in China in early 2020, suggesting potentially faster viral replication and greater infectiousness of Delta during early infection. We performed high-quality sequencing on samples from 126 individuals. Reliable epidemiological data meant that, for 111 transmission events, the donor and recipient cases were known. The estimated transmission bottleneck size was 1-3 virions with most minor intra-host single nucleotide variants (iSNVs) failing to transmit to the recipients. However, transmission heterogeneity of SARS-CoV-2 was also observed. The transmission of minor iSNVs resulted in at least 4 of the 30 substitutions identified in the outbreak, highlighting the contribution of intra-host variants to population level viral diversity during rapid spread. Disease control activities, such as the frequency of population testing, quarantine during pre-symptomatic infection, and level of virus genomic surveillance should be adjusted in order to account for the increasing prevalence of the Delta variant worldwide.

7.
Microbiol Spectr ; 9(3): e0101721, 2021 12 22.
Article in English | MEDLINE | ID: covidwho-1522923

ABSTRACT

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.


Subject(s)
COVID-19 Testing/methods , COVID-19/virology , CRISPR-Cas Systems , SARS-CoV-2/classification , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Alleles , COVID-19/diagnosis , Databases, Nucleic Acid , Humans , Mass Screening , Mutation , Polymerase Chain Reaction , Public Health , Spike Glycoprotein, Coronavirus/genetics
9.
Curr Med Sci ; 41(2): 228-235, 2021 Apr.
Article in English | MEDLINE | ID: covidwho-1193157

ABSTRACT

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.


Subject(s)
COVID-19/genetics , Evolution, Molecular , SARS-CoV-2/growth & development , Spike Glycoprotein, Coronavirus/genetics , COVID-19/epidemiology , COVID-19/virology , China/epidemiology , Furin/genetics , Genome, Viral/genetics , Humans , Pandemics , Phylogeny , Protein Binding/genetics , SARS-CoV-2/pathogenicity
10.
J Med Virol ; 92(10): 2221-2226, 2020 10.
Article in English | MEDLINE | ID: covidwho-505569

ABSTRACT

In this study, we designed a set of SARS-CoV-2 enrichment probes to increase the capacity for sequence-based virus detection and obtain the comprehensive genome sequence at the same time. This universal SARS-CoV-2 enrichment probe set contains 502 120 nt single-stranded DNA biotin-labeled probes designed based on all available SARS-CoV-2 viral sequences and it can be used to enrich for SARS-CoV-2 sequences without prior knowledge of type or subtype. Following the CDC health and safety guidelines, marked enrichment was demonstrated in a virus strain sample from cell culture, three nasopharyngeal swab samples (cycle threshold [Ct ] values: 32.36, 36.72, and 38.44) from patients diagnosed with COVID-19 (positive control) and four throat swab samples from patients without COVID-19 (negative controls), respectively. Moreover, based on these high-quality sequences, we discuss the heterozygosity and viral expression during coronavirus replication and its phylogenetic relationship with other selected high-quality samples from the Genome Variation Map. Therefore, this universal SARS-CoV-2 enrichment probe system can capture and enrich SARS-CoV-2 viral sequences selectively and effectively in different samples, especially clinical swab samples with a relatively low concentration of viral particles.


Subject(s)
COVID-19/diagnosis , DNA Probes/metabolism , DNA, Single-Stranded/genetics , Genome, Viral , SARS-CoV-2/genetics , Whole Genome Sequencing/methods , Biotin/chemistry , COVID-19/pathology , COVID-19/virology , DNA Probes/chemical synthesis , DNA, Single-Stranded/metabolism , Genotype , Humans , Mutation , Nasopharynx/virology , Phylogeny , Reverse Transcriptase Polymerase Chain Reaction/standards , SARS-CoV-2/classification , SARS-CoV-2/isolation & purification , SARS-CoV-2/pathogenicity , Sensitivity and Specificity
11.
Chin. J. Microbiol. Immunol. ; 3(40): 174-177, 20200331.
Article in Chinese | WHO COVID, ELSEVIER | ID: covidwho-142790

ABSTRACT

Objective: To obtain the genome sequences of SARS-CoV-2 in respiratory specimens in Guangdong Province with next-generation sequencing (NGS) and analyze the factors influencing sequencing. Methods: Eight upper and lower respiratory tract specimens were collected from patients with SARS-CoV-2 infection in Guangdong Province in January 2020. RNA library construction was used to obtain the genome sequences of SARS-CoV-2. A bio-informatics software package (CLC Genomics Workbench 12.0) was used to analyze and compare the genomic sequences. Results: Five SARS-CoV-2 genome sequences were obtained from the eight specimens and two were obtained from lower respiratory tract specimens. The nucleotide homology to SARS-CoV-2 was 97.74%-99.90%. The Ct values were lower, while the sequencing depth, coverage, relative abundance and genome integrity were higher in sequencing the SARS-CoV-2 in lower respiratory tract specimens. Conclusions: The low Ct value of SARS-CoV-2 in the samples was good for sequencing.

SELECTION OF CITATIONS
SEARCH DETAIL