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Comparative analysis of European bat lyssavirus 1 pathogenicity in the mouse model

PLoS Neglected Tropical Diseases News - 19 June 2017 - 9:00pm

by Elisa Eggerbauer, Florian Pfaff, Stefan Finke, Dirk Höper, Martin Beer, Thomas C. Mettenleiter, Tobias Nolden, Jens-Peter Teifke, Thomas Müller, Conrad M. Freuling

European bat lyssavirus 1 is responsible for most bat rabies cases in Europe. Although EBLV-1 isolates display a high degree of sequence identity, different sublineages exist. In individual isolates various insertions and deletions have been identified, with unknown impact on viral replication and pathogenicity. In order to assess whether different genetic features of EBLV-1 isolates correlate with phenotypic changes, different EBLV-1 variants were compared for pathogenicity in the mouse model. Groups of three mice were infected intracranially (i.c.) with 102 TCID50/ml and groups of six mice were infected intramuscularly (i.m.) with 105 TCID50/ml and 102 TCID50/ml as well as intranasally (i.n.) with 102 TCID50/ml. Significant differences in survival following i.m. inoculation with low doses as well as i.n. inoculation were observed. Also, striking variations in incubation periods following i.c. inoculation and i.m. inoculation with high doses were seen. Hereby, the clinical picture differed between general symptoms, spasms and aggressiveness depending on the inoculation route. Immunohistochemistry of mouse brains showed that the virus distribution in the brain depended on the inoculation route. In conclusion, different EBLV-1 isolates differ in pathogenicity indicating variation which is not reflected in studies of single isolates.

South African Ebola diagnostic response in Sierra Leone: A modular high biosafety field laboratory

PLoS Neglected Tropical Diseases News - 19 June 2017 - 9:00pm

by Janusz T. Paweska, Petrus Jansen van Vuren, Gunther H. Meier, Chantel le Roux, Ousman S. Conteh, Alan Kemp, Cardia Fourie, Prabha Naidoo, Serisha Naicker, Phumza Ohaebosim, Nadia Storm, Orienka Hellferscee, Lisa K. Ming Sun, Busisiwe Mogodi, Nishi Prabdial-Sing, Desiree du Plessis, Deidre Greyling, Shayne Loubser, Mark Goosen, Stewart D. McCulloch, Terence P. Scott, Alexandra Moerdyk, Wesley Dlamini, Kelfala Konneh, Idrissa L. Kamara, Dauda Sowa, Samuel Sorie, Brima Kargbo, Shabir A. Madhi


In August 2014, the National Institute for Communicable Diseases (NICD) in South Africa established a modular high-biosafety field Ebola diagnostic laboratory (SA FEDL) near Freetown, Sierra Leone in response to the rapidly increasing number of Ebola virus disease (EVD) cases.

Methods and findings

The SA FEDL operated in the Western Area of Sierra Leone, which remained a “hotspot” of the EVD epidemic for months. The FEDL was the only diagnostic capacity available to respond to the overwhelming demand for rapid EVD laboratory diagnosis for several weeks in the initial stages of the EVD crisis in the capital of Sierra Leone. Furthermore, the NICD set out to establish local capacity amongst Sierra Leonean nationals in all aspects of the FEDL functions from the outset. This led to the successful hand-over of the FEDL to the Sierra Leone Ministry of Health and Sanitation in March 2015. Between 25 August 2014 and 22 June 2016, the laboratory tested 11,250 specimens mostly from the Western Urban and Western Rural regions of Sierra Leone, of which 2,379 (21.14%) tested positive for Ebola virus RNA.


The bio-safety standards and the portability of the SA FEDL, offered a cost-effective and practical alternative for the rapid deployment of a field-operated high biocontainment facility. The SA FEDL teams demonstrated that it is highly beneficial to train the national staff in the course of formidable disease outbreak and accomplished their full integration into all operational and diagnostic aspects of the laboratory. This initiative contributed to the international efforts in bringing the EVD outbreak under control in Sierra Leone, as well as capacitating local African scientists and technologists to respond to diagnostic needs that might be required in future outbreaks of highly contagious pathogens.

Host gene expression analysis in Sri Lankan melioidosis patients

PLoS Neglected Tropical Diseases News - 19 June 2017 - 9:00pm

by Shivankari Krishnananthasivam, Nimanthi Jayathilaka, Harindra Darshana Sathkumara, Enoka Corea, Mohan Natesan, Aruna Dharshan De Silva


Melioidosis is a life threatening infectious disease caused by the gram-negative bacillus Burkholderia pseudomallei predominantly found in southeast Asia and northern Australia. Studying the host transcription profiles in response to infection is crucial for understanding disease pathogenesis and correlates of disease severity, which may help improve therapeutic intervention and survival. The aim of this study was to analyze gene expression levels of human host factors in melioidosis patients and establish useful correlation with disease biomarkers, compared to healthy individuals and patients with sepsis caused by other pathogens.


The study population consisted of 30 melioidosis cases, 10 healthy controls and 10 sepsis cases caused by other pathogens. Total RNA was extracted from peripheral blood mononuclear cells (PBMC’s) of study subjects. Gene expression profiles of 25 gene targets including 19 immune response genes and 6 epigenetic factors were analyzed by real time quantitative polymerase chain reaction (RT-qPCR).

Principal findings

Inflammatory response genes; TLR4, late onset inflammatory mediator HMGB1, genes associated with antigen presentation; MICB, PSMB2, PSMB8, PSME2, epigenetic regulators; DNMT3B, HDAC1, HDAC2 were significantly down regulated, whereas the anti-inflammatory gene; IL4 was up regulated in melioidosis patients compared to sepsis cases caused by other pathogens. Septicaemic melioidosis cases showed significant down regulation of IL8 compared sepsis cases caused by other pathogens. HMGB1, MICB, PSMB8, PSMB2, PSME2, HDAC1, HDAC2 and DNMT3B showed consistent down regulation of gene expression in melioidosis patients compared to other sepsis infection, irrespective of comorbidities such as diabetes, duration of clinical symptoms and antibiotic treatment.


Specific immune response genes and epigenetic regulators are differentially expressed among melioidosis patients and patients with sepsis caused by other pathogens. Therefore, these genes may serve as biomarkers for disease diagnosis to distinguish melioidosis from cases of sepsis due to other infections and therapeutic intervention for melioidosis.

Therapeutic administration of a recombinant human monoclonal antibody reduces the severity of chikungunya virus disease in rhesus macaques

PLoS Neglected Tropical Diseases News - 19 June 2017 - 9:00pm

by Rebecca Broeckel, Julie M. Fox, Nicole Haese, Craig N. Kreklywich, Soila Sukulpovi-Petty, Alfred Legasse, Patricia P. Smith, Michael Denton, Carsten Corvey, Shiv Krishnan, Lois M. A. Colgin, Rebecca M. Ducore, Anne D. Lewis, Michael K. Axthelm, Marie Mandron, Pierre Cortez, Jonathan Rothblatt, Ercole Rao, Ingo Focken, Kara Carter, Gopal Sapparapau, James E. Crowe Jr., Michael S. Diamond, Daniel N. Streblow

Chikungunya virus (CHIKV) is a mosquito-borne virus that causes a febrile syndrome in humans associated with acute and chronic debilitating joint and muscle pain. Currently no licensed vaccines or therapeutics are available to prevent or treat CHIKV infections. We recently isolated a panel of potently neutralizing human monoclonal antibodies (mAbs), one (4N12) of which exhibited prophylactic and post-exposure therapeutic activity against CHIKV in immunocompromised mice. Here, we describe the development of an engineered CHIKV mAb, designated SVIR001, that has similar antigen binding and neutralization profiles to its parent, 4N12. Because therapeutic administration of SVIR001 in immunocompetent mice significantly reduced viral load in joint tissues, we evaluated its efficacy in a rhesus macaque model of CHIKV infection. Rhesus macaques that were treated after infection with SVIR001 showed rapid elimination of viremia and less severe joint infiltration and disease compared to animals treated with SVIR002, an isotype control mAb. SVIR001 reduced viral burden at the site of infection and at distant sites and also diminished the numbers of activated innate immune cells and levels of pro-inflammatory cytokines and chemokines. SVIR001 therapy; however, did not substantively reduce the induction of CHIKV-specific B or T cell responses. Collectively, these results show promising therapeutic activity of a human anti-CHIKV mAb in rhesus macaques and provide proof-of-principle for its possible use in humans to treat active CHIKV infections.

Flavivirus and Filovirus EvoPrinters: New alignment tools for the comparative analysis of viral evolution

PLoS Neglected Tropical Diseases News - 16 June 2017 - 9:00pm

by Thomas Brody, Amarendra S. Yavatkar, Dong Sun Park, Alexander Kuzin, Jermaine Ross, Ward F. Odenwald


Flavivirus and Filovirus infections are serious epidemic threats to human populations. Multi-genome comparative analysis of these evolving pathogens affords a view of their essential, conserved sequence elements as well as progressive evolutionary changes. While phylogenetic analysis has yielded important insights, the growing number of available genomic sequences makes comparisons between hundreds of viral strains challenging. We report here a new approach for the comparative analysis of these hemorrhagic fever viruses that can superimpose an unlimited number of one-on-one alignments to identify important features within genomes of interest.

Methodology/Principal finding

We have adapted EvoPrinter alignment algorithms for the rapid comparative analysis of Flavivirus or Filovirus sequences including Zika and Ebola strains. The user can input a full genome or partial viral sequence and then view either individual comparisons or generate color-coded readouts that superimpose hundreds of one-on-one alignments to identify unique or shared identity SNPs that reveal ancestral relationships between strains. The user can also opt to select a database genome in order to access a library of pre-aligned genomes of either 1,094 Flaviviruses or 460 Filoviruses for rapid comparative analysis with all database entries or a select subset. Using EvoPrinter search and alignment programs, we show the following: 1) superimposing alignment data from many related strains identifies lineage identity SNPs, which enable the assessment of sublineage complexity within viral outbreaks; 2) whole-genome SNP profile screens uncover novel Dengue2 and Zika recombinant strains and their parental lineages; 3) differential SNP profiling identifies host cell A-to-I hyper-editing within Ebola and Marburg viruses, and 4) hundreds of superimposed one-on-one Ebola genome alignments highlight ultra-conserved regulatory sequences, invariant amino acid codons and evolutionarily variable protein-encoding domains within a single genome.


EvoPrinter allows for the assessment of lineage complexity within Flavivirus or Filovirus outbreaks, identification of recombinant strains, highlights sequences that have undergone host cell A-to-I editing, and identifies unique input and database SNPs within highly conserved sequences. EvoPrinter’s ability to superimpose alignment data from hundreds of strains onto a single genome has allowed us to identify unique Zika virus sublineages that are currently spreading in South, Central and North America, the Caribbean, and in China. This new set of integrated alignment programs should serve as a useful addition to existing tools for the comparative analysis of these viruses.

Minimal genetic change in <i>Vibrio cholerae</i> in Mozambique over time: Multilocus variable number tandem repeat analysis and whole genome sequencing

PLoS Neglected Tropical Diseases News - 16 June 2017 - 9:00pm

by Marcelino Garrine, Inácio Mandomando, Delfino Vubil, Tacilta Nhampossa, Sozinho Acacio, Shan Li, Joseph N. Paulson, Mathieu Almeida, Daryl Domman, Nicholas R. Thomson, Pedro Alonso, Oscar Colin Stine

Although cholera is a major public health concern in Mozambique, its transmission patterns remain unknown. We surveyed the genetic relatedness of 75 Vibrio cholerae isolates from patients at Manhiça District Hospital between 2002–2012 and 3 isolates from river using multilocus variable-number tandem-repeat analysis (MLVA) and whole genome sequencing (WGS). MLVA revealed 22 genotypes in two clonal complexes and four unrelated genotypes. WGS revealed i) the presence of recombination, ii) 67 isolates descended monophyletically from a single source connected to Wave 3 of the Seventh Pandemic, and iii) four clinical isolates lacking the cholera toxin gene. This Wave 3 strain persisted for at least eight years in either an environmental reservoir or circulating within the human population. Our data raises important questions related to where these isolates persist and how identical isolates can be collected years apart despite our understanding of high change rate of MLVA loci and the V. cholerae molecular clock.

Comparison of monocyte gene expression among patients with neurocysticercosis-associated epilepsy, Idiopathic Epilepsy and idiopathic headaches in India

PLoS Neglected Tropical Diseases News - 16 June 2017 - 9:00pm

by Vasudevan Prabhakaran, Douglas A. Drevets, Govindan Ramajayam, Josephine J. Manoj, Michael P. Anderson, Jay S. Hanas, Vedantam Rajshekhar, Anna Oommen, Hélène Carabin


Neurocysticercosis (NCC), a neglected tropical disease, inflicts substantial health and economic costs on people living in endemic areas such as India. Nevertheless, accurate diagnosis using brain imaging remains poorly accessible and too costly in endemic countries. The goal of this study was to test if blood monocyte gene expression could distinguish patients with NCC-associated epilepsy, from NCC-negative imaging lesion-free patients presenting with idiopathic epilepsy or idiopathic headaches.

Methods/Principal findings

Patients aged 18 to 51 were recruited from the Department of Neurological Sciences, Christian Medical College and Hospital, Vellore, India, between January 2013 and October 2014. mRNA from CD14+ blood monocytes was isolated from 76 patients with NCC, 10 Recovered NCC (RNCC), 29 idiopathic epilepsy and 17 idiopathic headaches patients. A preliminary microarray analysis was performed on six NCC, six idiopathic epilepsy and four idiopathic headaches patients to identify genes differentially expressed in NCC-associated epilepsy compared with other groups. This analysis identified 1411 upregulated and 733 downregulated genes in patients with NCC compared to Idiopathic Epilepsy. Fifteen genes up-regulated in NCC patients compared with other groups were selected based on possible relevance to NCC, and analyzed by qPCR in all patients’ samples. Differential gene expression among patients was assessed using linear regression models. qPCR analysis of 15 selected genes showed generally higher gene expression among NCC patients, followed by RNCC, idiopathic headaches and Idiopathic Epilepsy. Gene expression was also generally higher among NCC patients with single cyst granulomas, followed by mixed and single calcifications.


Expression of certain genes in blood monocytes can distinguish patients with NCC-related epilepsy from patients with active Idiopathic Epilepsy and idiopathic headaches patients. These findings are significant because they may lead to the development of new tools to screen for and monitor NCC patients without brain imaging.

Sterol 14α-demethylase mutation leads to amphotericin B resistance in <i>Leishmania mexicana</i>

PLoS Neglected Tropical Diseases News - 16 June 2017 - 9:00pm

by Roy Mwenechanya, Julie Kovářová, Nicholas J. Dickens, Mudaliar Manikhandan, Pawel Herzyk, Isabel M. Vincent, Stefan K. Weidt, Karl E. Burgess, Richard J. S. Burchmore, Andrew W. Pountain, Terry K. Smith, Darren J. Creek, Dong-Hyun Kim, Galina I. Lepesheva, Michael P. Barrett

Amphotericin B has emerged as the therapy of choice for use against the leishmaniases. Administration of the drug in its liposomal formulation as a single injection is being promoted in a campaign to bring the leishmaniases under control. Understanding the risks and mechanisms of resistance is therefore of great importance. Here we select amphotericin B-resistant Leishmania mexicana parasites with relative ease. Metabolomic analysis demonstrated that ergosterol, the sterol known to bind the drug, is prevalent in wild-type cells, but diminished in the resistant line, where alternative sterols become prevalent. This indicates that the resistance phenotype is related to loss of drug binding. Comparing sequences of the parasites’ genomes revealed a plethora of single nucleotide polymorphisms that distinguish wild-type and resistant cells, but only one of these was found to be homozygous and associated with a gene encoding an enzyme in the sterol biosynthetic pathway, sterol 14α-demethylase (CYP51). The mutation, N176I, is found outside of the enzyme’s active site, consistent with the fact that the resistant line continues to produce the enzyme’s product. Expression of wild-type sterol 14α-demethylase in the resistant cells caused reversion to drug sensitivity and a restoration of ergosterol synthesis, showing that the mutation is indeed responsible for resistance. The amphotericin B resistant parasites become hypersensitive to pentamidine and also agents that induce oxidative stress. This work reveals the power of combining polyomics approaches, to discover the mechanism underlying drug resistance as well as offering novel insights into the selection of resistance to amphotericin B itself.

Dengue seroprevalence and force of primary infection in a representative population of urban dwelling Indonesian children

PLoS Neglected Tropical Diseases News - 15 June 2017 - 9:00pm

by Ari Prayitno, Anne-Frieda Taurel, Joshua Nealon, Hindra Irawan Satari, Mulya Rahma Karyanti, Rini Sekartini, Soedjatmiko Soedjatmiko, Hartono Gunardi, Bernie Endyarni Medise, R. Tedjo Sasmono, James Mark Simmerman, Alain Bouckenooghe, Sri Rezeki Hadinegoro


Indonesia reports the second highest dengue disease burden in the world; these data are from passive surveillance reports and are likely to be significant underestimates. Age-stratified seroprevalence data are relatively unbiased indicators of past exposure and allow understanding of transmission dynamics.

Methodology/Principal Findings

To better understand dengue infection history and associated risk factors in Indonesia, a representative population-based cross-sectional dengue seroprevalence study was conducted in 1–18-year-old urban children. From October to November 2014, 3,210 children were enrolled from 30 geographically dispersed clusters. Serum samples were tested for anti-dengue IgG antibodies by indirect ELISA. A questionnaire investigated associations between dengue serologic status and household socio-demographic and behavioural factors. Overall, 3,194 samples were tested, giving an adjusted national seroprevalence in this urban population of 69.4% [95% CI: 64.4–74.3] (33.8% [95% CI: 26.4–41.2] in the 1–4-year-olds, 65.4% [95% CI: 69.1–71.7] in the 5–9-year-olds, 83.1% [95% CI: 77.1–89.0] in the 10–14-year-olds, and 89.0% [95% CI: 83.9–94.1] in the 15–18-year–olds). The median age of seroconversion estimated through a linear model was 4.8 years. Using a catalytic model and considering a constant force of infection we estimated 13.1% of children experience a primary infection per year. Through a hierarchical logistic multivariate model, the subject’s age group (1–4 vs 5–9 OR = 4.25; 1–4 vs. 10–14 OR = 12.60; and 1–4 vs 15–18 OR = 21.87; p<0.0001) and the number of cases diagnosed in the household since the subject was born (p = 0.0004) remained associated with dengue serological status.


This is the first dengue seroprevalence study in Indonesia that is targeting a representative sample of the urban paediatric population. This study revealed that more than 80% of children aged 10 years or over have experienced dengue infection at least once. Prospective incidence studies would likely reveal dengue burdens far in excess of reported incidence rates.

Co-occurrence of viruses and mosquitoes at the vectors’ optimal climate range: An underestimated risk to temperate regions?

PLoS Neglected Tropical Diseases News - 15 June 2017 - 9:00pm

by Marcus S. C. Blagrove, Cyril Caminade, Elisabeth Waldmann, Elizabeth R. Sutton, Maya Wardeh, Matthew Baylis

Mosquito-borne viruses have been estimated to cause over 100 million cases of human disease annually. Many methodologies have been developed to help identify areas most at risk from transmission of these viruses. However, generally, these methodologies focus predominantly on the effects of climate on either the vectors or the pathogens they spread, and do not consider the dynamic interaction between the optimal conditions for both vector and virus. Here, we use a new approach that considers the complex interplay between the optimal temperature for virus transmission, and the optimal climate for the mosquito vectors. Using published geolocated data we identified temperature and rainfall ranges in which a number of mosquito vectors have been observed to co-occur with West Nile virus, dengue virus or chikungunya virus. We then investigated whether the optimal climate for co-occurrence of vector and virus varies between “warmer” and “cooler” adapted vectors for the same virus. We found that different mosquito vectors co-occur with the same virus at different temperatures, despite significant overlap in vector temperature ranges. Specifically, we found that co-occurrence correlates with the optimal climatic conditions for the respective vector; cooler-adapted mosquitoes tend to co-occur with the same virus in cooler conditions than their warmer-adapted counterparts. We conclude that mosquitoes appear to be most able to transmit virus in the mosquitoes’ optimal climate range, and hypothesise that this may be due to proportionally over-extended vector longevity, and other increased fitness attributes, within this optimal range. These results suggest that the threat posed by vector-competent mosquito species indigenous to temperate regions may have been underestimated, whilst the threat arising from invasive tropical vectors moving to cooler temperate regions may be overestimated.

Whole genome sequencing distinguishes between relapse and reinfection in recurrent leprosy cases

PLoS Neglected Tropical Diseases News - 15 June 2017 - 9:00pm

by Mariane M. A. Stefani, Charlotte Avanzi, Samira Bührer-Sékula, Andrej Benjak, Chloé Loiseau, Pushpendra Singh, Maria A. A. Pontes, Heitor S. Gonçalves, Emerith M. Hungria, Philippe Busso, Jérémie Piton, Maria I. S. Silveira, Rossilene Cruz, Antônio Schetinni, Maurício B. Costa, Marcos C. L. Virmond, Suzana M. Diorio, Ida M. F. Dias-Baptista, Patricia S. Rosa, Masanori Matsuoka, Maria L. F. Penna, Stewart T. Cole, Gerson O. Penna


Since leprosy is both treated and controlled by multidrug therapy (MDT) it is important to monitor recurrent cases for drug resistance and to distinguish between relapse and reinfection as a means of assessing therapeutic efficacy. All three objectives can be reached with single nucleotide resolution using next generation sequencing and bioinformatics analysis of Mycobacterium leprae DNA present in human skin.


DNA was isolated by means of optimized extraction and enrichment methods from samples from three recurrent cases in leprosy patients participating in an open-label, randomized, controlled clinical trial of uniform MDT in Brazil (U-MDT/CT-BR). Genome-wide sequencing of M. leprae was performed and the resultant sequence assemblies analyzed in silico.

Principal findings

In all three cases, no mutations responsible for resistance to rifampicin, dapsone and ofloxacin were found, thus eliminating drug resistance as a possible cause of disease recurrence. However, sequence differences were detected between the strains from the first and second disease episodes in all three patients. In one case, clear evidence was obtained for reinfection with an unrelated strain whereas in the other two cases, relapse appeared more probable.


This is the first report of using M. leprae whole genome sequencing to reveal that treated and cured leprosy patients who remain in endemic areas can be reinfected by another strain. Next generation sequencing can be applied reliably to M. leprae DNA extracted from biopsies to discriminate between cases of relapse and reinfection, thereby providing a powerful tool for evaluating different outcomes of therapeutic regimens and for following disease transmission.

A misdiagnosed infection mimicking “tree man disease”

PLoS Neglected Tropical Diseases News - 15 June 2017 - 9:00pm

by Jo Anne Lim, Zulrusydi Ismail, Che Noraini Ibrahim, Soon Eu Chong, Wan Noor Hasbee Wan Abdullah

Lessons learned on Zika virus vectors

PLoS Neglected Tropical Diseases News - 15 June 2017 - 9:00pm

by Ricardo Lourenço-de-Oliveira, Anna-Bella Failloux

Giant elephantiasis and inguino-scrotal hernia

PLoS Neglected Tropical Diseases News - 15 June 2017 - 9:00pm

by Helder Miranda, Anna Claudia Colangelo, Mario Antunes, Marcella Schiavone, Stefano Merigliano, Damiano Pizzol

Burden of trachoma in five counties of Eastern Equatoria state, South Sudan: Results from population-based surveys

PLoS Neglected Tropical Diseases News - 14 June 2017 - 9:00pm

by Angelia M. Sanders, Aisha E. P. Stewart, Samuel Makoy, Joy J. Chebet, Peter Magok, Aja Kuol, Carla Blauvelt, Richard Lako, John Rumunu, E. Kelly Callahan, Scott D. Nash


In order to decrease the prevalence of trachoma within the country, the Republic of South Sudan has implemented components of the SAFE strategy in various counties since 2001. Five counties in Eastern Equatoria state were surveyed in order to monitor progress of programmatic interventions and determine if additional rounds of Mass Drug Administration with azithromycin were needed.

Methodology/ Principal findings

Five counties (Budi, Lafon, Kapoeta East, Kapoeta South and Kapoeta North) were surveyed from April to October 2015. A cross-sectional, multi-stage, cluster-random sampling was used. All present, consenting residents of selected households were examined for all clinical signs of trachoma using the World Health Organization (WHO) simplified grading system. 14,462 individuals from 3,446 households were surveyed. The prevalence of trachomatous inflammation-follicular (TF) in children ages one to nine years ranged from 17.4% (95% Confidence Interval (CI): 11.4%, 25.6%) in Budi county to 47.6%, (95% CI: 42.3%, 53.0%) in Kapoeta East county. Trachomatous trichiasis (TT) was also highly prevalent in those 15 years and older, ranging between 2.6% (95% CI: 1.6%, 4.0%) in Kapoeta South to 3.9% (95% CI: 2.4%, 6.1%) in Lafon. The presence of water and sanitation were low in all five counties, including two counties which had a complete absence of latrines in all surveyed clusters.

Conclusions/ Significance

To our knowledge, these were the first trachoma surveys conducted in the Republic of South Sudan since their independence in 2011. The results show that despite years of interventions, four of the five surveyed counties require a minimum of five additional years of SAFE strategy implementation, with the fifth requiring at minimum three more years.

First report of naturally infected <i>Aedes aegypti</i> with chikungunya virus genotype ECSA in the Americas

PLoS Neglected Tropical Diseases News - 14 June 2017 - 9:00pm

by André Luis Costa-da-Silva, Rafaella Sayuri Ioshino, Vivian Petersen, Antonio Fernando Lima, Marielton dos Passos Cunha, Michael R. Wiley, Jason T. Ladner, Karla Prieto, Gustavo Palacios, Danuza Duarte Costa, Lincoln Suesdek, Paolo Marinho de Andrade Zanotto, Margareth Lara Capurro


The worldwide expansion of new emergent arboviruses such as Chikungunya and Zika reinforces the importance in understanding the role of mosquito species in spreading these pathogens in affected regions. This knowledge is essential for developing effective programs based on species specificity to avoid the establishment of endemic transmission cycles sustained by the identified local vectors. Although the first autochthonous transmission of Chikungunya virus was described in 2014 in the north of Brazil, the main outbreaks were reported in 2015 and 2016 in the northeast of Brazil.

Methodology/Principal findings

During 5 days of February 2016, we collected mosquitoes in homes of 6 neighborhoods of Aracaju city, the capital of Sergipe state. Four mosquito species were identified but Culex quinquefasciatus and Aedes aegypti were the most abundant. Field-caught mosquitoes were tested for Chikungunya (CHIKV), Zika (ZIKV) and Dengue viruses (DENV) by qRT-PCR and one CHIKV-infected Ae. aegypti female was detected. The complete sequence of CHIKV genome was obtained from this sample and phylogenetic analysis revealed that this isolate belongs to the East-Central-South-African (ECSA) genotype.


Our study describes the first identification of a naturally CHIKV-infected Ae. aegypti in Brazil and the first report of a CHIKV from ECSA genotype identified in this species in the Americas. These findings support the notion of Ae. aegypti being a vector involved in CHIKV outbreaks in northeast of Brazil.

Comparative genomics of <i>Cryptococcus neoformans</i> var. <i>grubii</i> associated with meningitis in HIV infected and uninfected patients in Vietnam

PLoS Neglected Tropical Diseases News - 14 June 2017 - 9:00pm

by Jeremy N. Day, Seet Qihui, Lam Tuan Thanh, Phan Hai Trieu, Anh Duong Van, Nha Hoang Thu, Tran Thi Hong Chau, Nguyen P. H. Lan, Nguyen Van Vinh Chau, Philip M. Ashton, Guy E. Thwaites, Maciej F. Boni, Marcel Wolbers, Niranjan Nagarajan, Patrick B. O. Tan, Stephen Baker

The vast burden of cryptococcal meningitis occurs in immunosuppressed patients, driven by HIV, and is caused by Cryptococcus neoformans var. grubii. We previously reported cryptococcal meningitis in Vietnam arising atypically in HIV uninfected, apparently immunocompetent patients, caused by a single amplified fragment length polymorphism (AFLP) cluster of C. neoformans var. grubii (VNIγ). This variant was less common in HIV infected individuals; it remains unclear why this lineage is associated with apparently immunocompetent patients. To study this host tropism we aimed to further our understanding of clinical phenotype and genomic variation within Vietnamese C. neoformans var. grubii. After performing MLST on C. neoformans clinical isolates we identified 14 sequence types (STs); ST5 correlated with the VNIγ cluster. We next compared clinical phenotype by lineage and found HIV infected patients with cryptococcal meningitis caused by ST5 organisms were significantly more likely to have lymphadenopathy (11% vs. 4%, p = 0.05 Fisher’s exact test) and higher blood lymphocyte count (median 0.76 versus 0.55 X109 cells/L, p = 0.001, Kruskal-Wallis test). Furthermore, survivors of ST5 infections had evidence of worse disability outcomes at 70 days (72.7% (40/55) in ST5 infections versus 57.1% (52/91) non-ST5 infections (OR 2.11, 95%CI 1.01 to 4.41), p = 0.046). To further investigate the relationship between strain and disease phenotype we performed genome sequencing on eight Vietnamese C. neoformans var. grubii. Eight genome assemblies exhibited >99% nucleotide sequence identity and we identified 165 kbp of lineage specific to Vietnamese isolates. ST5 genomes harbored several strain specific regions, incorporating 19 annotated coding sequences and eight hypothetical proteins. These regions included a phenolic acid decarboxylase, a DEAD-box ATP-dependent RNA helicase 26, oxoprolinases, a taurine catabolism dioxygenase, a zinc finger protein, membrane transport proteins and various drug transporters. Our work outlines the complexity of genomic pathogenicity in cryptococcal infections and identifies a number of gene candidates that may aid the disaggregation of the pathways associated with the pathogenesis of Cryptococcus neoformans var. grubii.

The ubiquitin-conjugating enzyme CDC34 is essential for cytokinesis in contrast to putative subunits of a SCF complex in <i>Trypanosoma brucei</i>

PLoS Neglected Tropical Diseases News - 13 June 2017 - 9:00pm

by Federico Rojas, Joanna Koszela, Jacqueline Búa, Briardo Llorente, Richard Burchmore, Manfred Auer, Jeremy C. Mottram, María Teresa Téllez-Iñón

The ubiquitin-proteasome system is a post-translational regulatory pathway for controlling protein stability and activity that underlies many fundamental cellular processes, including cell cycle progression. Target proteins are tagged with ubiquitin molecules through the action of an enzymatic cascade composed of E1 ubiquitin activating enzymes, E2 ubiquitin conjugating enzymes, and E3 ubiquitin ligases. One of the E3 ligases known to be responsible for the ubiquitination of cell cycle regulators in eukaryotes is the SKP1-CUL1-F-box complex (SCFC). In this work, we identified and studied the function of homologue proteins of the SCFC in the life cycle of Trypanosoma brucei, the causal agent of the African sleeping sickness. Depletion of trypanosomal SCFC components TbRBX1, TbSKP1, and TbCDC34 by RNAi resulted in decreased growth rate and contrasting cell cycle abnormalities for both procyclic (PCF) and bloodstream (BSF) forms. Depletion of TbRBX1 in PCF cells interfered with kinetoplast replication, whilst depletion of TbSKP1 arrested PCF and BSF cells in the G1/S transition. Silencing of TbCDC34 in BSF cells resulted in a block in cytokinesis and caused rapid clearance of parasites from infected mice. We also show that TbCDC34 is able to conjugate ubiquitin in vitro and in vivo, and that its activity is necessary for T. brucei infection progression in mice. This study reveals that different components of a putative SCFC have contrasting phenotypes once depleted from the cells, and that TbCDC34 is essential for trypanosome replication, making it a potential target for therapeutic intervention.

Identification of antigenic <i>Sarcoptes scabiei</i> proteins for use in a diagnostic test and of non-antigenic proteins that may be immunomodulatory

PLoS Neglected Tropical Diseases News - 12 June 2017 - 9:00pm

by Marjorie S. Morgan, S. Dean Rider Jr., Larry G. Arlian


Scabies, caused by the mite, Sarcoptes scabiei, infects millions of humans, and many wild and domestic mammals. Scabies mites burrow in the lower stratum corneum of the epidermis of the skin and are the source of substances that are antigenic or modulate aspects of the protective response of the host. Ordinary scabies is a difficult disease to diagnose.


The goal of this project was to identify S. scabiei proteins that may be candidate antigens for use in a diagnostic test or may be used by the mite to modulate the host’s protective response.


An aqueous extract of S. scabiei was separated by 2-dimensional electrophoresis and proteins were identified by mass spectrometry. A parallel immunoblot was probed with serum from patients with ordinary scabies to identify IgM and/or IgG-binding antigens. The genes coding for 23 selected proteins were cloned into E. coli and the expressed recombinant proteins were screened with serum from patients with confirmed ordinary scabies.


We identified 50 different proteins produced by S. scabiei, 34 of which were not previously identified, and determined that 66% were recognized by patient IgM and/or IgG. Fourteen proteins were screened for use in a diagnostic test but none possessed enough sensitivity and specificity to be useful. Six of the 9 proteins selected for the possibility that they may be immunomodulatory were not recognized by antibodies in patient serum.


Thirty-three proteins that bound IgM and/or IgG from the serum of patients with ordinary scabies were identified. None of the 14 tested were useful for inclusion in a diagnostic test. The identities of 16 proteins that are not recognized as antigens by infected patients were also determined. These could be among the molecules that are responsible for this mite’s ability to modulate its host’s innate and adaptive immune responses.

Challenges in developing methods for quantifying the effects of weather and climate on water-associated diseases: A systematic review

PLoS Neglected Tropical Diseases News - 12 June 2017 - 9:00pm

by Giovanni Lo Iacono, Ben Armstrong, Lora E. Fleming, Richard Elson, Sari Kovats, Sotiris Vardoulakis, Gordon L. Nichols

Infectious diseases attributable to unsafe water supply, sanitation and hygiene (e.g. Cholera, Leptospirosis, Giardiasis) remain an important cause of morbidity and mortality, especially in low-income countries. Climate and weather factors are known to affect the transmission and distribution of infectious diseases and statistical and mathematical modelling are continuously developing to investigate the impact of weather and climate on water-associated diseases. There have been little critical analyses of the methodological approaches. Our objective is to review and summarize statistical and modelling methods used to investigate the effects of weather and climate on infectious diseases associated with water, in order to identify limitations and knowledge gaps in developing of new methods. We conducted a systematic review of English-language papers published from 2000 to 2015. Search terms included concepts related to water-associated diseases, weather and climate, statistical, epidemiological and modelling methods. We found 102 full text papers that met our criteria and were included in the analysis. The most commonly used methods were grouped in two clusters: process-based models (PBM) and time series and spatial epidemiology (TS-SE). In general, PBM methods were employed when the bio-physical mechanism of the pathogen under study was relatively well known (e.g. Vibrio cholerae); TS-SE tended to be used when the specific environmental mechanisms were unclear (e.g. Campylobacter). Important data and methodological challenges emerged, with implications for surveillance and control of water-associated infections. The most common limitations comprised: non-inclusion of key factors (e.g. biological mechanism, demographic heterogeneity, human behavior), reporting bias, poor data quality, and collinearity in exposures. Furthermore, the methods often did not distinguish among the multiple sources of time-lags (e.g. patient physiology, reporting bias, healthcare access) between environmental drivers/exposures and disease detection. Key areas of future research include: disentangling the complex effects of weather/climate on each exposure-health outcome pathway (e.g. person-to-person vs environment-to-person), and linking weather data to individual cases longitudinally.