Emergence of #Chikungunya Virus, #Pakistan, 2016–2017 (Emerg Infect Dis., abstract)

[Source: US Centers for Disease Control and Prevention (CDC), Emerging Infectious Diseases Journal, full page: (LINK). Abstract, edited.]

Volume 26, Number 2—February 2020 / Dispatch

Emergence of Chikungunya Virus, Pakistan, 2016–2017

Nazish Badar, Muhammad Salman, Jamil Ansari, Uzma Aamir, Muhammad Masroor Alam, Yasir Arshad, Nighat Mushtaq, Aamer Ikram, and Javaria Qazi

Author affiliations: National Institute of Health, Islamabad, Pakistan (N. Badar, M. Salman, J. Ansari, U. Aamir, M.M. Alam, Y. Arshad, N. Mushtaq, A. Ikram); Quaid-I-Azam University, Islamabad (N. Badar, J. Qazi)

 

Abstract

During December 2016–May 2017, an outbreak of chikungunya virus infection occurred across Pakistan. The East/Central/South African genotype was predominant. This study provides baseline data on the virus strain and emphasizes the need for active surveillance and implementation of preventive interventions to contain future outbreaks.

Keywords: Chikungunya fever; Pakistan.

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Unbiased #Metagenomic #Sequencing for #Pediatric #Meningitis in #Bangladesh Reveals #Neuroinvasive #Chikungunya Virus #Outbreak and Other Unrealized Pathogens (MBio, abstract)

[Source: MBio, full page: (LINK). Abstract, edited.]

Unbiased Metagenomic Sequencing for Pediatric Meningitis in Bangladesh Reveals Neuroinvasive Chikungunya Virus Outbreak and Other Unrealized Pathogens

Senjuti Saha, Akshaya Ramesh, Katrina Kalantar, Roly Malaker, Md Hasanuzzaman, Lillian M. Khan, Madeline Y. Mayday, M. S. I. Sajib, Lucy M. Li, Charles Langelier, Hafizur Rahman, Emily D. Crawford, Cristina M. Tato, Maksuda Islam, Yun-Fang Juan, Charles de Bourcy, Boris Dimitrov, James Wang, Jennifer Tang, Jonathan Sheu, Rebecca Egger, Tiago Rodrigues De Carvalho, Michael R. Wilson, Samir K. Saha, Joseph L. DeRisi

Nisha Duggal, Editor

DOI: 10.1128/mBio.02877-19

 

ABSTRACT

The burden of meningitis in low-and-middle-income countries remains significant, but the infectious causes remain largely unknown, impeding institution of evidence-based treatment and prevention decisions. We conducted a validation and application study of unbiased metagenomic next-generation sequencing (mNGS) to elucidate etiologies of meningitis in Bangladesh. This RNA mNGS study was performed on cerebrospinal fluid (CSF) specimens from patients admitted in the largest pediatric hospital, a World Health Organization sentinel site, with known neurologic infections (n = 36), with idiopathic meningitis (n = 25), and with no infection (n = 30), and six environmental samples, collected between 2012 and 2018. We used the IDseq bioinformatics pipeline and machine learning to identify potentially pathogenic microbes, which we then confirmed orthogonally and followed up through phone/home visits. In samples with known etiology and without infections, there was 83% concordance between mNGS and conventional testing. In idiopathic cases, mNGS identified a potential bacterial or viral etiology in 40%. There were three instances of neuroinvasive Chikungunya virus (CHIKV), whose genomes were >99% identical to each other and to a Bangladeshi strain only previously recognized to cause febrile illness in 2017. CHIKV-specific qPCR of all remaining stored CSF samples from children who presented with idiopathic meningitis in 2017 (n = 472) revealed 17 additional CHIKV meningitis cases, exposing an unrecognized meningitis outbreak. Orthogonal molecular confirmation, case-based clinical data, and patient follow-up substantiated the findings. Case-control CSF mNGS surveys can complement conventional diagnostic methods to identify etiologies of meningitis, conduct surveillance, and predict outbreaks. The improved patient- and population-level data can inform evidence-based policy decisions.

 

IMPORTANCE

Globally, there are an estimated 10.6 million cases of meningitis and 288,000 deaths every year, with the vast majority occurring in low- and middle-income countries. In addition, many survivors suffer from long-term neurological sequelae. Most laboratories assay only for common bacterial etiologies using culture and directed PCR, and the majority of meningitis cases lack microbiological diagnoses, impeding institution of evidence-based treatment and prevention strategies. We report here the results of a validation and application study of using unbiased metagenomic sequencing to determine etiologies of idiopathic (of unknown cause) cases. This included CSF from patients with known neurologic infections, with idiopathic meningitis, and without infection admitted in the largest children’s hospital of Bangladesh and environmental samples. Using mNGS and machine learning, we identified and confirmed an etiology (viral or bacterial) in 40% of idiopathic cases. We detected three instances of Chikungunya virus (CHIKV) that were >99% identical to each other and to a strain previously recognized to cause systemic illness only in 2017. CHIKV qPCR of all remaining stored 472 CSF samples from children who presented with idiopathic meningitis in 2017 at the same hospital uncovered an unrecognized CHIKV meningitis outbreak. CSF mNGS can complement conventional diagnostic methods to identify etiologies of meningitis, and the improved patient- and population-level data can inform better policy decisions.

Keywords: Chikungunya fever; Meningitis; Pediatrics; Bangladesh; Neuroinvasion.

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Analysis of humoral immune responses in #chikungunya virus (CHIKV) infected patients and individuals vaccinated with a candidate CHIKV #vaccine (J Infect Dis., abstract)

[Source: Journal of Infectious Diseases, full page: (LINK). Abstract, edited.]

Analysis of humoral immune responses in chikungunya virus (CHIKV) infected patients and individuals vaccinated with a candidate CHIKV vaccine

Lisa Henss, Constanze Yue, Christine von Rhein, Roland Tschismarov, Lia Laura Lewis-Ximenez, Albert Dölle, Sally A Baylis, Barbara S Schnierle

The Journal of Infectious Diseases, jiz658, https://doi.org/10.1093/infdis/jiz658

Published: 12 December 2019

 

Abstract

Background

Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes severe flu like symptoms. The acute symptoms disappear after one week, but chronic arthralgia can persist for years. Here, humoral immune responses in CHIKV-infected patients and vaccinees were analyzed.

Methods

Alphavirus neutralization activity was analyzed with pseudotyped lentiviral vectors and antibody epitope mapping was performed with a peptide array.

Results

Greatest CHIKV neutralization activity was observed 60-92 days after onset of symptoms. The amount of CHIKV-specific antibodies, their binding avidity and cross-reactivity with other alphaviruses increased over time. CHIKV and o’nyong-nyong virus (ONNV) were both neutralized to a similar extent. Linear antibody binding epitopes were mainly found in E2 domain B and the acid-sensitive regions (ASRs). In addition, serum samples from healthy volunteers vaccinated with a measles-vectored chikungunya vaccine candidate, MV-CHIK, were analyzed. Neutralization activity in the samples from the vaccine cohort was 2–6-fold lower than in samples from CHIKV-infected patients. In contrast to infection, vaccination only induced cross-neutralization with ONNV and the E2 ASR1 was the major antibody target.

Conclusion

These data could assist vaccine design and enable the identification of correlates of protection necessary for vaccine efficacy.

alphavirus, chikungunya, antibody, neutralization

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This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

Keywords: Chikungunya fever; Alphavirus; o’nyong-nyong virus; Vaccines.

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#ALS-like #Syndrome after #Chikungunya (Cureus, abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Cureus. 2019 Oct 9;11(10):e5876. doi: 10.7759/cureus.5876.

Amyotrophic Lateral Sclerosis-like Syndrome after Chikungunya.

Andrade FC1, Vergetti V1, Cozza G2, Falcao MC1, Azevedo G3.

Author information: 1 Medicine, Faculdade Pernambucana De Saude, Recife, BRA. 2 Medicine, Faculdade Pernambuca De Saude, Recife, BRA. 3 Neurosurgery, Hospital Getulio Vargas, Recife, BRA.

 

Abstract

Amyotrophic lateral sclerosis (ALS)-like syndrome refers to a group of conditions whose outcome is similar to that of amyotrophic lateral sclerosis, but with different characteristics in the initial phase and response to therapy. The involvement of an earlier age group, the subacute course, and the stabilization or improvement of the clinical condition during the treatment are most important. There is still no evidence of an association between amyotrophic lateral sclerosis-like syndrome and chikungunya (CHK) infection in the literature. This report was intended to review this syndrome and present a case that occurred after the epidemic of CHK in Pernambuco in 2016. CHK is a fast-onset febrile illness characterized by intense asthenia, arthralgia, myalgia, headache, and skin rash. Reports range from encephalitis, optic neuritis, myeloradiculitis to Guillain-Barré syndrome, generating drastic sequelae such as mental deficiency, blindness, and persistent paralysis. This is the first case report of a possible association of ALS-like syndrome and chikungunya infection. CHK infection may cause ALS-like syndrome. There is a need for further research in this field to develop therapies for neurological complications such as that of CHK.

Copyright © 2019, Andrade et al.

KEYWORDS: amyotrophic lateral sclerosis; arbovirus; chikungunya fever; critically ill; diagnostic techniques

PMID: 31763099 PMCID: PMC6834095 DOI: 10.7759/cureus.5876

Keywords: Chikungunya fever; Amyotrophic Lateral Scleroris; Neurology.

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Correlation of the basic reproduction number (#R0) and #eco-environmental #variables in #Colombian municipalities with #chikungunya #outbreaks during 2014-2016 (PLoS Negl Trop Dis., abstract)

[Source: PLoS Neglected Tropical Diseases, full page: (LINK). Abstract, edited.]

OPEN ACCESS /  PEER-REVIEWED / RESEARCH ARTICLE

Correlation of the basic reproduction number (R0) and eco-environmental variables in Colombian municipalities with chikungunya outbreaks during 2014-2016

Víctor Hugo Peña-García , Rebecca C. Christofferson

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Published: November 7, 2019 / DOI: https://doi.org/10.1371/journal.pntd.0007878 / This is an uncorrected proof.

 

Abstract

Chikungunya virus (CHIKV) emerged in Colombia in 2014 into a population presumed fully susceptible. This resulted in a quick and intense spread across Colombia, resulting in an epidemic that affected an estimated 450,000 people. The reported Colombian cases accounted for over 49% of all the cases reported to the PAHO. Eco-environmental factors are known to be associated with the spread of arboviruses such as CHIKV, and likely contribute to the differences in transmission profiles that were observed across several municipalities. To determine the association of eco-environmental factors and CHIKV, the basic reproduction number (R0) in 85 municipalities, which accounted for 65.6% of reported CHIKV cases in Colombia, was estimated. Estimates of R0 ranged from 1 to 9, where over 76% of municipalities had R0 values between 1 and 2. When we looked at the distribution of R0, the cumulative proportions were 20% with R0>2, 14% with R0>3, and 9% with R0>4. Next, we determined that there were different patterns of correlation between environmental and/or ecological variables and R0 when we considered different R0 lower-thresholds. Broadly, we found that temperature-related variables are significantly and positively correlated to R0 regardless of the lower threshold, while other variables like duration of outbreak and size of the urban area are inversely related to R0. Specifically, we conclude that high values of temperature-related variables where R0 > 1 will result in a fast growth of cases in a shorter time period (with faster cessation of outbreak transmission) but will result overall in a fewer total cases compared to outbreak areas (R0 > 1, but classified as lower). Thus, in the absence of vector control, a less explosive outbreak may be more advantageous for the virus in terms of transmission.

 

Author summary

Chikungunya virus emerged in Colombia in 2014 into a presumed fully susceptible population and rapidly spread in the country. Numerous municipalities were differently affected by this virus across the country. The main purpose of this work was understanding why those differences were produced and, in turn, what are the variables addressing such differences. For this purpose, we estimated for 85 municipalities the basic reproduction number (R0), a crucial parameter to understand epidemics that is expressed as the number of secondary cases produced by a primary case. Such parameter was correlated with numerous variables resulting evident a crucial role of temperature in the increase of R0. Interestingly, other variables like size of the urban area and cases showed to be negatively correlated with R0. Results shows that high temperatures produce high R0, but those municipalities that showed high R0 showed an explosive epidemic with faster increase of cases that ceased equally fast, so the duration of epidemic is short producing small amount of cases. In this way, more cases are expected with municipalities with lower values of R0, which is suitably explained by the tortoise-hare model, where the less explosive outbreak results to be more advantageous for the virus.

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Citation: Peña-García VH, Christofferson RC (2019) Correlation of the basic reproduction number (R0) and eco-environmental variables in Colombian municipalities with chikungunya outbreaks during 2014-2016. PLoS Negl Trop Dis 13(11): e0007878. https://doi.org/10.1371/journal.pntd.0007878

Editor: Nathan D. Grubaugh, Yale School of Public Health, UNITED STATES

Received: July 25, 2019; Accepted: October 25, 2019; Published: November 7, 2019

Copyright: © 2019 Peña-García, Christofferson. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All data are available, and where to get it and how are in the methods. Maps were created in ArcGIS 10.4.1 from publicly available dataset described.

Funding: This work was supported by NIH/NIGMS grant R01GM12207 (PI: RCC) (https://www.nigms.nih.gov). And by the National Aeronautics and Space Administration (NASA) grant number 80NSSC18k0517. The funders played no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

Keywords: Chikungunya Fever; Colombia.

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#Chikungunya and O’nyong-nyong Viruses in #Uganda: Implications for Diagnostics (Open Forum Infect Dis., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Open Forum Infect Dis. 2019 Jan 3;6(3):ofz001. doi: 10.1093/ofid/ofz001. eCollection 2019 Mar.

Chikungunya and O’nyong-nyong Viruses in Uganda: Implications for Diagnostics.

Clements TL1, Rossi CA1, Irish AK2, Kibuuka H3, Eller LA3, Robb ML4, Kataaha P5, Michael NL6, Hensley LE7, Schoepp RJ1.

Author information: 1 US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland. 2 College of Public Health, University of Iowa, Iowa City, Iowa. 3 Makerere University Walter Reed Project, Kampala, Uganda. 4 Henry M. Jackson Foundation, Rockville, Maryland. 5 Nakasero Blood Bank, Kampala, Uganda. 6 Walter Reed Army Institute of Research, Rockville, Maryland. 7 National Institute of Allergy and Infectious Diseases-Integrated Research Facility, Frederick, Maryland.

 

Abstract

BACKGROUND:

A serosurvey of healthy blood donors provided evidence of hemorrhagic fever and arthropod-borne virus infections in Uganda.

METHODS:

Antibody prevalence to arthropod-borne and hemorrhagic fever viruses in human sera was determined using enzyme-linked immunosorbent assay (ELISA) and plaque reduction neutralization test (PRNT).

RESULTS:

The greatest antibody prevalence determined by ELISA was to chikungunya virus (CHIKV) followed in descending order by West Nile virus (WNV), Crimean-Congo hemorrhagic fever virus (CCHFV), Ebola virus (EBOV), dengue virus (DEN), yellow fever virus (YFV), Rift Valley fever virus (RVFV), Marburg virus (MARV), and Lassa virus (LASV). Further investigation of CHIKV-positive sera demonstrated that the majority of antibody responses may likely be the result of exposure to the closely related alphavirus o’nyong-nyong virus (ONNV).

CONCLUSIONS:

As the use of highly specific and sensitive polymerase chain reaction-based assays becomes the diagnostic standard without the corresponding use of the less sensitive but more broadly reactive immunological-based assays, emerging and re-emerging outbreaks will be initially missed, illustrating the need for an orthogonal system for the detection and identification of viruses causing disease.

Published by Oxford University Press on behalf of Infectious Diseases Society of America 2019.

KEYWORDS: CHIKV; ONNV; Uganda; chikungunya; diagnostics; o’nyong-nyong; serosurvey

PMID: 31660384 PMCID: PMC6411207 [Available on 2020-01-03] DOI: 10.1093/ofid/ofz001

Keywords: Alphavirus; Chikungunya fever; O’nyong-nyong virus; Serosurvey; Uganda.

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#Genetic and #Phylogenetic Characterization of a #Chikungunya Virus Imported into #Shenzhen, #China (Virol Sin., abstract)

[Source: Virologica Sinica, full page: (LINK). Abstract, edited.]

Genetic and Phylogenetic Characterization of a Chikungunya Virus Imported into Shenzhen, China

Authors: Yang Yang, Zhixiang Xu, Haixia Zheng, Jingdong Song, Ying Wu, Zhou Tong, Jing Yuan, Gary Wong, William J. Liu, Yuhai Bi, Yingxia Liu, George F. Gao

LETTER / First Online: 21 October 2019

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Dear Editor,

Chikungunya virus (CHIKV) is a mosquito-borne virus belonging to the family Togaviridae, genus Alphavirus, and was first isolated in Tanzania in the 1950s (Silva and Dermody 2017; Weaver and Lecuit 2015). Human infections with CHIKV typically result in a rapid-onset febrile disease, with symptoms that include fever, headache, rash, severe joint and muscle pain, as well as prolonged periods of disability in some patients (Weaver and Lecuit 2015; Silva and Dermody 2017). Unlike other arboviral diseases such as dengue and Zika fever, the majority of CHIKV infections in humans results in clinical symptoms, with ~15% of human infections who are asymptomatic with seroconversion (Schwartz and Albert 2010; Weaver and Lecuit 2015). CHIKV has been reported in more than 110 countries and territories in Asia, Africa, Europe, and the Americas (CDC 2019), and has evolved into three main lineages, including West African, Asian, and East Central South African (ECSA) (Silva and Dermody 2017…

(…)

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Yang Yang, Zhixiang Xu and Haixia Zheng contributed equally to this study.

Electronic supplementary material

The online version of this article ( https://doi.org/10.1007/s12250-019-00166-5) contains supplementary material, which is available to authorized users.

 

Notes

Acknowledgements

This work was supported by the grants from the National Natural Science Foundation (NSFC) of China (81802004), the Shenzhen Science and Technology Research and Development Project (JCYJ20160427153238750), the National Science and Technology Major Project (2018ZX10711001, 2017ZX10103011), Strategic Priority Research Program of the Chinese Academy of Sciences (CAS) (XDB29010102), the Sanming Project of Medicine in Shenzhen (SZSM201412003). Y.B. is supported by the NSFC Outstanding Young Scholars (31822055).

 

Compliance with Ethical Standards

Animal and Human Rights Statement

All procedures performed in studies involving human participants were in accordance with the guidelines approved by the Ethics Committees from Shenzhen Third People’s Hospital (SZTHEC2016001) and with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards. Informed consent was obtained from the participant enrolled in the study.

Keywords: Chikungunya fever; China.

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