Schematic representation of detection of 100 fg of <i>Y. pestis</i> DNA in seven Array Card channels across one Array Card.

a<p>Numbered PCR represents assays evaluated in an alternate study. Named PCRs this study.</p>b<p>C_T value: PCR cycle number at which fluorescence first detected. # = negative result.</p

Quantification of B. anthracis (Ames) DNA by pXO2 MGB PCR replicates incorporated within the TaqMan Array Cards.

<p>Trendline and R2 value generated from mean CT values by Microsoft Excel.</p

Summary of PCR results from Array Card and Singleplex PCR experiments.

a<p><i>B. mallei</i> genome calculation performed using ATCC 23344 genome size. <i>B. pseudomallei</i> calucalation using 1106B genome size. Other genome calculations performed using genome sizes of stated strains.</p>b<p>No. of PCR positives from <i>n</i> replicates. nt - Not tested.</p>c<p>C_T value: PCR cycle number at which fluorescence first detected. Mean of positives only. Variance of mean in paranthesis.</p>d<p>Detection rate defined as at least one agent PCR positive replicate in the Array Card channel.</p

Ranking of each method, as determined by statistical analysis, by individual sample type and combined sample types.

<p>Ranking of each method, as determined by statistical analysis, by individual sample type and combined sample types.</p

Sample types used in this study.

<p>Sample types used in this study.</p

Results from Bg sp PCR when tested against DNA extracts produced from a 100 µL (0.001% w/v) Bg aliquot (with an added 1 µL microbiological loopful of grated deodorant) and 100 µL (0.001% w/v) Bg aliquots removed from a cotton swab.

a<p>No. of PCR positives from <i>n</i> replicates.</p>b<p>C_T value: PCR cycle number at which fluorescence first detected in a 50 cycle PCR. Mean of positive results only. Variance of mean in parenthesis.</p

Results from Bg sp PCR when tested against DNA extracts produced from liquid sample types spiked with two concentrations of <i>B. atropheaus</i> spores.

a<p>weight/volume Bg spores/liquid.</p>b<p>No. of PCR positives from <i>n</i> replicates.</p>c<p>C_T value: PCR cycle number at which fluorescence first detected in a 50 cycle PCR. Mean of positive results only. Variance of mean in parenthesis.</p

Results from Bg sp PCR when tested against DNA extracts produced from powder sample types spiked with two concentrations of <i>B. atropheaus.</i>

a<p>weight/weight powder/Bg spores.</p>b<p>No. of PCR positives from <i>n</i> replicates.</p>c<p>C_T value: PCR cycle number at which fluorescence first detected in a 50 cycle PCR. Mean of positive results only. Variance of mean in parenthesis.</p

Data and R code used in epidemiological analyses.

Since 2014, Brazil has experienced an unprecedented epidemic caused by chikungunya virus (CHIKV), with several waves of East-Central-South-African (ECSA) lineage transmission reported across the country. In 2018, Rio de Janeiro state, the third most populous state in Brazil, reported 41% of all chikungunya cases in the country. Here we use evolutionary and epidemiological analysis to estimate the timescale of CHIKV-ECSA-American lineage and its epidemiological patterns in Rio de Janeiro. We show that the CHIKV-ECSA outbreak in Rio de Janeiro derived from two distinct clades introduced from the Northeast region in mid-2015 (clade RJ1, n = 63/67 genomes from Rio de Janeiro) and mid-2017 (clade RJ2, n = 4/67). We detected evidence for positive selection in non-structural proteins linked with viral replication in the RJ1 clade (clade-defining: nsP4-A481D) and the RJ2 clade (nsP1-D531G). Finally, we estimate the CHIKV-ECSA’s basic reproduction number (R0) to be between 1.2 to 1.6 and show that its instantaneous reproduction number (Rt) displays a strong seasonal pattern with peaks in transmission coinciding with periods of high Aedes aegypti transmission potential. Our results highlight the need for continued genomic and epidemiological surveillance of CHIKV in Brazil, particularly during periods of high ecological suitability, and show that selective pressures underline the emergence and evolution of the large urban CHIKV-ECSA outbreak in Rio de Janeiro.</div

BEAST xml files and outputs generated in this study.

BEAST xml files and outputs generated in this study.</p