Molecular Characterisation of Chikungunya Virus Infections in Trinidad and Comparison of Clinical and Laboratory Features with Dengue and Other Acute Febrile Cases

<div><p>Local transmission of Chikungunya virus (CHIKV) was first documented in Trinidad and Tobago (T&T) in July 2014 preceding a large epidemic. At initial presentation, it is difficult to distinguish chikungunya fever (CHIKF) from other acute undifferentiated febrile illnesses (AUFIs), including life-threatening dengue disease. We characterised and compared dengue virus (DENV) and CHIKV infections in 158 patients presenting with suspected dengue fever (DF) and CHIKF at a major hospital in T&T, and performed phylogenetic analyses on CHIKV genomic sequences recovered from 8 individuals. The characteristics of patients with and without PCR-confirmed CHIKV were compared using Pearson’s χ^<i>2</i> and student’s t-tests, and adjusted odds ratios (aORs) and 95% confidence intervals (CIs) were determined using logistic regression. We then compared signs and symptoms of people with RT-qPCR-confirmed CHIKV and DENV infections using the Mann-Whitney U, Pearson’s χ^<i>2</i> and Fisher’s exact tests. Among the 158 persons there were 8 (6%) RT-qPCR-confirmed DENV and 30 (22%) RT-qPCR-confirmed CHIKV infections. Phylogenetic analyses showed that the CHIKV strains belonged to the Asian genotype and were most closely related to a British Virgin Islands strain isolated at the beginning of the 2013/14 outbreak in the Americas. Compared to persons who were RT-qPCR-negative for CHIKV, RT-qPCR-positive individuals were significantly more likely to have joint pain (aOR: 4.52 [95% CI: 1.28–16.00]), less likely to be interviewed at a later stage of illness (days post onset of fever—aOR: 0.56 [0.40–0.78]) and had a lower white blood cell count (aOR: 0.83 [0.71–0.96]). Among the 38 patients with RT-qPCR-confirmed CHIKV or DENV, there were no significant differences in symptomatic presentation. However when individuals with serological evidence of recent DENV or CHIKV infection were included in the analyses, there were key differences in clinical presentation between CHIKF and other AUFIs including DF, which can be used to triage patients for appropriate care in the clinical setting.</p></div

Bivariable associations between select characteristics of patients of the APCF of the EWMSC, T&T (Dec 2013 –Nov 2014) and having a confirmed infection^ⱡ with CHIKV.

<p>Bivariable associations between select characteristics of patients of the APCF of the EWMSC, T&T (Dec 2013 –Nov 2014) and having a confirmed infection<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004199#t001fn002" target="_blank">^ⱡ</a> with CHIKV.</p

Total number of patients enrolled and number of CHIKV and DENV RT-qPCR positive cases by week.

<p>The green line graph indicates the number of patients enrolled per week. Histogram bars indicate the number of individuals confirmed as RT-qPCR positive for CHIKV (blue) or DENV (red) by RT-qPCR. Weeks 41–43 in 2014 are excluded as no patient enrolment was attempted during this period.</p

Bivariable associations between symptoms and clinical characteristics of patients of the APCF of the EWMSC, T&T (Dec 2013 –Nov 2014) and having a confirmed infection^ⱡ with either DENV or CHIKV.

<p>Bivariable associations between symptoms and clinical characteristics of patients of the APCF of the EWMSC, T&T (Dec 2013 –Nov 2014) and having a confirmed infection<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004199#t003fn002" target="_blank">^ⱡ</a> with either DENV or CHIKV.</p

Multivariable associations with having a confirmed infection^ⱡ with CHIKV in patients of the APCF of the EWMSC, T&T (Dec 2013 –Nov 2014).

<p>Multivariable associations with having a confirmed infection<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004199#t002fn001" target="_blank">^ⱡ</a> with CHIKV in patients of the APCF of the EWMSC, T&T (Dec 2013 –Nov 2014).</p

Positive predictive values (PPVs), negative predictive values (NPVs), sensitivity, specificity and likelihood ratios of clinical features used to distinguish patients of the APCF of the EWMSC, T&T (Dec 2013 –Nov 2014) with DF ^ⱡ infection from patients with CHIKF^ⱡ.

<p>Positive predictive values (PPVs), negative predictive values (NPVs), sensitivity, specificity and likelihood ratios of clinical features used to distinguish patients of the APCF of the EWMSC, T&T (Dec 2013 –Nov 2014) with DF <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004199#t005fn001" target="_blank">^ⱡ</a> infection from patients with CHIKF<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004199#t005fn001" target="_blank">^ⱡ</a>.</p

Positive predictive values (PPVs), negative predictive values (NPVs), sensitivity, specificity and likelihood ratios of clinical features used to distinguish patients of the APCF of the EWMSC, T&T (Dec 2013 –Nov 2014) with DF ^ⱡ and CHIKF ^ⱡ from patients with other AUFIs.

<p>Positive predictive values (PPVs), negative predictive values (NPVs), sensitivity, specificity and likelihood ratios of clinical features used to distinguish patients of the APCF of the EWMSC, T&T (Dec 2013 –Nov 2014) with DF <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004199#t004fn001" target="_blank">^ⱡ</a> and CHIKF <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004199#t004fn001" target="_blank">^ⱡ</a> from patients with other AUFIs.</p

Maximum clade credibility (MCC) phylogeny based on the complete coding region of 74 CHIKV sequences.

<p>The three major CHIKV genotypes are labelled, as well as the IOL within the ECSA clade. Sequences generated from this study (Genbank accession numbers (KR046227 –KR046234) are labelled in blue. Nodes with clade credibilities (posterior probabilities) ≥ 0.95 are labelled accordingly. The clade credibility for the node supporting the Trinidad and BVI sequences is shown in the insert together with the mean estimated time to most recent common ancestor (tMRCA) in years (with 95% HPD in brackets).</p