We estimated the epidemic growth rate by analyzing data on the cases with illness onset between December 10 and January 4, because we expected the proportion of infections identified would increase soon after the formal announcement of the outbreak in Wuhan on December 31. We fitted a transmission model (formulated with the use of renewal equations) with zoonotic infections to onset dates that were not linked to the Huanan Seafood Wholesale Market, and we used this model to derive the epidemic growth rate, the epidemic doubling time, and the basic reproductive number (R0), which is defined as the expected number of additional cases that one case will generate, on average, over the course of its infectious period in an otherwise uninfected population. We used an informative prior distribution for the serial interval based on the serial interval of SARS with a mean of 8.4 and a standard deviation of 3.8.11 (link)Analyses of the incubation period, serial interval, growth rate, and R0 were performed with the use of MATLAB software (MathWorks). Other analyses were performed with the use of SAS software (SAS Institute) and R software (R Foundation for Statistical Computing).
Disease Outbreaks
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Most cited protocols related to «Disease Outbreaks»
We estimated the epidemic growth rate by analyzing data on the cases with illness onset between December 10 and January 4, because we expected the proportion of infections identified would increase soon after the formal announcement of the outbreak in Wuhan on December 31. We fitted a transmission model (formulated with the use of renewal equations) with zoonotic infections to onset dates that were not linked to the Huanan Seafood Wholesale Market, and we used this model to derive the epidemic growth rate, the epidemic doubling time, and the basic reproductive number (R0), which is defined as the expected number of additional cases that one case will generate, on average, over the course of its infectious period in an otherwise uninfected population. We used an informative prior distribution for the serial interval based on the serial interval of SARS with a mean of 8.4 and a standard deviation of 3.8.11 (link)Analyses of the incubation period, serial interval, growth rate, and R0 were performed with the use of MATLAB software (MathWorks). Other analyses were performed with the use of SAS software (SAS Institute) and R software (R Foundation for Statistical Computing).
Two of the simulated read sets were independently run through iMetAMOS [93 (link)] to automatically determine the best assembler. The consensus pick across both datasets was SPAdes version 3.0 [81 (link)], which was subsequently run on the remaining 30 simulated read sets using default parameters. The final contigs and scaffolds files were used as input to the genome alignment methods. For mapping methods, the raw simulated reads were used. For accuracy comparisons, Indels were ignored and called SNPs were required to be unambiguously aligned across all 32 genomes (that is, not part of a subset relationship; SNPs present but part of a subset relationship were ignored).
For S. Montevideo 12 closely related outbreak strains where sequenced once by US Food and Drug Administration using Roche Genome sequencer FLX system, Illumina MiSeq and Life Technologies Ion Torrent and made publicly available (
Genomic DNA (gDNA) was purified from the isolates using the Easy-DNA extraction kit (Invitrogen) and DNA concentrations determined using the Qubit dsDNA BR Assay Kit (Invitrogen). The isolates were sequenced twice on the MiSeq platform (Illumina) and Ion Torrent PGM (Life Technologies).
For Ion Torrent the isolates were sequenced following the manufacturer’s protocols for 200 bp gDNA fragment library preparation (Ion Xpress Plus gDNA and Amplicon Library 96 Preparation), template preparation (Ion OneTouch System), and sequencing (Ion PGM 200 Sequencing kit) using the 316 chip. For MiSeq the isolates chromosomal DNA of the isolates was used to create genomic libraries using the Nextera XT DNA sample preparation kit (Illumina, cat. No. FC-131-1024) and sequenced using v2, 2×250 bp chemistry on the Illumina MiSeq platform (Illumina, Inc., San Diego, CA).
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Most recents protocols related to «Disease Outbreaks»
Example 5
To investigate whether a Canine/FL/04-like influenza virus had circulated among greyhound populations in Florida prior to the January 2004 outbreak, archival sera from 65 racing greyhounds were tested for the presence of antibodies to Canine/FL/04 using the HI and MN assays. There were no detectable antibodies in 33 dogs sampled from 1996 to 1999. Of 32 dogs sampled between 2000 and 2003, 9 were seropositive in both assays—1 in 2000, 2 in 2002, and 6 in 2003 (Table 5). The seropositive dogs were located at Florida tracks involved in outbreaks of respiratory disease of unknown etiology from 1999 to 2003, suggesting that a Canine/FL/04-like virus may have been the causative agent of those outbreaks. To investigate this possibility further, we examined archival tissues from greyhounds that died from hemorrhagic bronchopneumonia in March 2003. Lung homogenates inoculated into MDCK cells and chicken embryos from one dog yielded H3N8 influenza virus, termed A/Canine/Florida/242/2003 (Canine/FL/03). Sequence analysis of the complete genome of Canine/FL/03 revealed >99% identity to Canine/FL/04 (Table 4), indicating that Canine/FL/04-like viruses had infected greyhounds prior to 2004.
Our participants had an average Teaching Experience of 14.7 years (SD = 8.9, N = 735), with an average index of Experience of Teaching with Technology of 3.4 of 5 (SD = 1.1, N = 735). Note that we assume normality for these two variables; tests for skewness and kurtosis for Teaching Experience resulted with satisfyingly low values of 0.67 and − 0.34, respectively, and for Experience of Teaching with Technology they were − 0.10 and − 0.61, respectively. Of the participants, 32% (238 of 735) had a leading role at school, being part of the management team. Regarding their Teaching Domains, we had similar ratios of teachers teaching STEM (33%, 241 of 735), Language (either mother tongue or second language, 30%, 224 of 735), and Social Sciences or Humanities (37%, 270 of 735).
Of our participants, 24% (177 of 735) were in a Risk Group for COVID-19. Regarding the factors that influenced their working from home, Familial Difficulties where the most common (M = 1.96, SD = 0.75, N = 714), followed by Emotional Difficulties (M = 1.73, SD = 0.68, N = 708), Physical Space Difficulties (M = 1.633, SD = 0.73, N = 728), and finally Technology Difficulties (M = 1.627, SD = 0.73, N = 724).
The current study included N = 735 teachers from 68 middle schools across Israel. As it is common in Israel to teach in both middle- and high-schools, our inclusion criteria included that at least 50% of the teaching hours were done in middle school grades. In order to survey teachers who had experienced the transition from traditional teaching to emergency remote teaching, another inclusion criteria was teaching during both the 2020/21 school year (when data was collected) and the prior year (i.e., before COVID-19 days).
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More about "Disease Outbreaks"
These outbreaks require close monitoring of emerging and re-emerging infectious diseases, analyzing transmission patterns, and implementing effective prevention and control strategies.
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Researchers can utilize this platform to explore a wide range of resources, including information from FBS, SAS 9.4, SAS version 9.4, QIAamp Viral RNA Mini Kit, DMEM, MiSeq platform, DNeasy Blood and Tissue Kit, QIAamp DNA Mini Kit, MEM, and Stata 12.0, to optimize their disease outbreak preparedness and response strategies.