Genomic Assays for Identification of Chikungunya Virus in Blood Donors, Puerto Rico, 2014

Multiplex detection and identification of viral, bacterial, and protozoan pathogens in human blood and plasma using an expanded high-density resequencing microarray platform

Introduction: Nucleic acid tests for blood donor screening have improved the safety of the blood supply; however, increasing numbers of emerging pathogen tests are burdensome. Multiplex testing platforms are a potential solution. Methods: The Blood Borne Pathogen Resequencing Microarray Expanded (BBP-RMAv.2) can perform multiplex detection and identification of 80 viruses, bacteria and parasites. This study evaluated pathogen detection in human blood or plasma. Samples spiked with selected pathogens, each with one of 6 viruses, 2 bacteria and 5 protozoans were tested on this platform. The nucleic acids were extracted, amplified using multiplexed sets of primers, and hybridized to a microarray. The reported sequences were aligned to a database to identify the pathogen. To directly compare the microarray to an emerging molecular approach, the amplified nucleic acids were also submitted to nanopore next generation sequencing (NGS). Results: The BBP-RMAv.2 detected viral pathogens at a concentration as low as 100 copies/ml and a range of concentrations from 1,000 to 100,000 copies/ml for all the spiked pathogens. Coded specimens were identified correctly demonstrating the effectiveness of the platform. The nanopore sequencing correctly identified most samples and the results of the two platforms were compared. Discussion: These results indicated that the BBP-RMAv.2 could be employed for multiplex detection with potential for use in blood safety or disease diagnosis. The NGS was nearly as effective at identifying pathogens in blood and performed better than BBP-RMAv.2 at identifying pathogen-negative samples.

Monolithic affinity columns in 3D printed microfluidics for chikungunya RNA detection

Mosquito-borne pathogens plague much of the world, yet rapid and simple diagnosis is not available for many affected patients. Using a custom stereolithography 3D printer, we created microfluidic devices with affinity monoliths that could retain, noncovalently attach a fluorescent tag, and detect oligonucleotide and viral RNA. We optimized the fluorescent binding and sample load times using an oligonucleotide sequence from chikungunya virus (CHIKV). We also tested the specificity of CHIKV capture relative to genetically similar Sindbis virus. Moreover, viral RNA from both viruses was flowed through capture columns to study the efficiency and specificity of the column for viral CHIKV. We detected ~107 loaded viral genome copies, which was similar to levels in clinical samples during acute infection. These results show considerable promise for development of this platform into a rapid mosquito-borne viral pathogen detection system.

Infectious diseases and the impact on transfusion medicine: A historical review and lessons for the future

Blood transfusion saves millions of lives each year. It is a well-established treatment, and many procedures are applied to avoid transmitted infections. However, throughout the history of transfusion medicine, many infectious diseases arose or were recognised, bringing up an impact on the blood supply, as the difficulties in diagnosing new diseases, the decrease in blood donors, the challenges for the medical team, the risks for the receptor and the related costs. This study aims to review historically the principal infectious diseases transmitted through the blood that circulated worldwide in the 20th and 21st centuries, considering the impact on the blood banks. Despite the current blood bank control of transfusion risks and the hemovigilance improvements, transmitted and emerging infections can still compromise the blood bank supply, as we have witnessed during the first waves of the COVID-19 pandemic. Moreover, new pathogens will continue emerging, and we must be prepared for the future.

Prevalence of Chikungunya, Dengue and Zika viruses in blood donors: a systematic literature review and meta-analysis

BACKGROUND

Blood transfusion centres should understand the epidemiology of emerging diseases that are transmissible through the transfusion of blood components. The risk of transmission of arboviruses through this route has become apparent in recent years. The aim of our study is to summarise the reported prevalence (viraemic rate, seroprevalence and/or antigen detection) of Chikungunya (CHIKV), Dengue (DENV) and Zika (ZIKV) viruses in blood donors according to screening test used and world region.

MATERIALS AND METHODS

We conducted a systematic literature review and meta-analysis having searched for information in the main bibliographic databases (MEDLINE, Embase, and Scopus). The prevalence for each of the viruses was calculated according to the screening test used and geographic location.

RESULTS

We included 18 records on CHIKV, 71 on DENV, and 27 on ZIKV. The highest prevalences of RNA for CHIKV were 1.9% in Puerto Rico (2014), 1.0% in Thailand (2009), and 1.0% in French Polynesia (2014-15). The highest prevalences of RNA for DENV were 5.5% in Saudi Arabia (2015-16), 2.3% in Madeira, Portugal (2012-13), and 0.6% in Brazil (2012). The highest prevalences of RNA for ZIKV were 2.8% in French Polynesia (2013-14), 2.7% in Brazil (2015-16), and 1.8% in Martinique (2016). Overall seroprevalence, as assessed by IgG antibodies, was 21.6% for CHIKV, 24.0% for DENV, and 5.1% for ZIKV.

DISCUSSION

Our study shows a high proportion of donors who are viraemic and asymptomatic, especially during outbreaks, with prevalences surpassing 5% for DENV, 1% for CHIKV, and 2% for ZIKV. These data confirm a clear threat to blood transfusion safety. The elevated seroprevalence for these three arboviruses is also indicative of their wide circulation in populations, correlating with an increased risk of infected but asymptomatic donors. Health centres and institutions must address this threat, especially in tropical regions where the biggest outbreaks occur.

Mitigating the risk of transfusion-transmitted infections with vector-borne agents solely by means of pathogen reduction

Background

This study evaluated whether pathogen reduction technology (PRT) in plasma and platelets using amotosalen/ultraviolet A light (A/UVA) or in red blood cells using amustaline/glutathione (S‐303/GSH) may be used as the sole mitigation strategy preventing transfusion‐transmitted West Nile (WNV), dengue (DENV), Zika (ZIKV), and chikungunya (CHIKV) viral, and Babesia microti, Trypanosoma cruzi, and Plasmodium parasitic infections.

Methods

Antibody (Ab) status and pathogen loads (copies/mL) were obtained for donations from US blood donors testing nucleic acid (NAT)‐positive for WNV, DENV, ZIKV, CHIKV, and B. microti. Infectivity titers derived from pathogen loads were compared to published PRT log₁₀ reduction factors (LRF); LRFs were also reviewed for Plasmodium and T. cruzi. The potential positive impact on donor retention following removal of deferrals from required questioning and testing for WNV, Babesia, Plasmodium, and T. cruzi was estimated for American Red Cross (ARC) donors.

Results

A/UVA and S‐303/GSH reduced infectivity to levels in accordance with those recognized by FDA as suitable to replace testing for all agents evaluated. If PRT replaced deferrals resulting from health history questions and/or NAT for WNV, Babesia, Plasmodium, and T. cruzi, 27,758 ARC donors could be retained allowing approximately 50,000 additional donations/year based on 1.79 donations/donor for calendar year 2019 (extrapolated to an estimated 125,000 additional donations nationally).

Conclusion

Pathogen loads in donations from US blood donors demonstrated that robust PRT may provide an opportunity to replace deferrals associated with donor questioning and NAT for vector‐borne agents allowing for significant donor retention and likely increased blood availability.

Lack of Evidence of Chikungunya Virus Infection among Blood Donors during the Chikungunya Outbreak in Lazio Region, Italy, 2017

Background: The latest European Chikungunya virus (CHIKV) outbreak occurred in Italy in 2017, in the municipalities of Anzio and Rome (Lazio Region), with a secondary outbreak in the Calabrian Region. Most CHIKV infections are symptomatic but about 15% of people who acquire the infection may be asymptomatic. A retrospective study was conducted with the aim of assessing the prevalence of recent/ongoing CHIKV infections on the blood donor population in the Lazio Region, during the 2017 outbreak (including in the period before it was detected). Methods: The study was conducted on 4595 plasma samples from donors who donated in 14 different Blood Establishments in the Lazio Region, in the period June–November 2017. A total of 389 of these samples were collected in provinces not affected by the outbreak and were used as negative controls. All samples were tested for IgM detection by the use of an ELISA test, and positive samples were tested for confirmation through the use of a PRNT. Molecular tests were performed on sera that were found to be IgM-positive or borderline. Results: A total of 41 (0.89%) blood donors tested positive for IgM. None of these positive IgM ELISA results was confirmed either by PRNT or by molecular tests. Conclusions: Our study has shown no evidence of recent/ongoing CHIKV infection in blood donors of the affected area.

Chikungunya and Mayaro infective viruses in components of blood

OBJECTIVE

Evaluate the infectivity of Alphavirus Chikungunya and Mayaro in blood products in plaque forming units (UFP/ml).

BACKGROUND

Arboviruses are responsible for sporadic diseases or epidemics which cause serious public health issues. Due to the high number of asymptomatic infections and high viremia, blood donors may pass on these viruses by transfusion.

METHODS/MATERIALS

This study used blood bags that would be discarded after evaluation and certification of the absence of infections. The blood products obtained by centrifuging a unit of whole blood were called blood components. All blood bags were infected with viable viruses (previously quantified) compatible with Chikungunya and Mayaro viremia.

RESULTS

Blood bags inoculated with both Chikungunya and Mayaro viruses were able to keep infective viruses during the processing of blood products (red blood cell concentrate, platelet concentrate and fresh frozen plasma) and also after the recommended storage for each component, which may infect individuals transfused with those.

CONCLUSION

The results indicate that in order to prevent infections by Mayaro and Chikungunya viruses in blood products it is necessary to stimulate the development and use of diagnostic tests for these pathogens in donated blood.

Molecular techniques for the genomic viral RNA detection of West Nile, Dengue, Zika and Chikungunya arboviruses: a narrative review

Introduction: Molecular technology has played an important role in arboviruses diagnostics. PCR-based methods stand out in terms of sensitivity, specificity, cost, robustness, and accessibility, and especially the isothermal amplification (IA) method is ideal for field-adaptable diagnostics in resource-limited settings (RLS).Areas covered: In this review, we provide an overview of the various molecular methods for West Nile, Zika, Dengue and Chikungunya. We summarize literature works reporting the assessment and use of in house and commercial assays. We describe limitations and challenges in the usage of methods and opportunities for novel approaches such as NNext-GenerationSequencing (NGS).Expert opinion: The rapidity and accuracy of differential diagnosis is essential for a successful clinical management, particularly in co-circulation area of arboviruses. Several commercial diagnostic molecular assays are available, but many are not affordable by RLS and not usable as Point-of-care/Point-of-need (POC/PON) such as RReal-TimeRT-PCR, Array-based methods and NGS. In contrast, the IA-based system fits better for POC/PON but it is still not ideal for the multiplexing detection system. Improvement in the characterization and validation of current molecular assays is needed to optimize their translation to the point of care.

The Putative Roles and Functions of Indel, Repetition and Duplication Events in Alphavirus Non-Structural Protein 3 Hypervariable Domain (nsP3 HVD) in Evolution, Viability and Re-Emergence

Alphavirus non-structural proteins 1–4 (nsP1, nsP2, nsP3, and nsP4) are known to be crucial for alphavirus RNA replication and translation. To date, nsP3 has been demonstrated to mediate many virus–host protein–protein interactions in several fundamental alphavirus mechanisms, particularly during the early stages of replication. However, the molecular pathways and proteins networks underlying these mechanisms remain poorly described. This is due to the low genetic sequence homology of the nsP3 protein among the alphavirus species, especially at its 3′ C-terminal domain, the hypervariable domain (HVD). Moreover, the nsP3 HVD is almost or completely intrinsically disordered and has a poor ability to form secondary structures. Evolution in the nsP3 HVD region allows the alphavirus to adapt to vertebrate and insect hosts. This review focuses on the putative roles and functions of indel, repetition, and duplication events that have occurred in the alphavirus nsP3 HVD, including characterization of the differences and their implications for specificity in the context of virus–host interactions in fundamental alphavirus mechanisms, which have thus directly facilitated the evolution, adaptation, viability, and re-emergence of these viruses.

Global transmission and evolutionary dynamics of the Chikungunya virus

Chikungunya virus (CHIKV) is a re-emerging pathogen of global importance. We attempted to gain an insight into the organisation, distribution and mutational load of the virus strains reported from different parts of the world. We describe transmission dynamics and genetic characterisation of CHIKV across the globe during the last 65 years from 1952 to 2017. The evolutionary pattern of CHIKV was analysed using the E1 protein gene through phylogenetic, Bayesian and Network methods with a dataset of 265 sequences from various countries. The time to most recent common ancestor of the virus was estimated to be 491 years ago with an evolutionary rate of 2.78 × 10-4 substitutions/site/year. Genetic characterisation of CHIKV strains was carried out in terms of variable sites, selection pressure and epitope mapping. The neutral selection pressure on the E1 gene of the virus suggested a stochastic process of evolution. We identified six potential epitope peptides in the E1 protein showing substantial interaction with human MHC-I and MHC-II alleles. The present study augments global epidemiological and population dynamics of CHIKV warranting undertaking of appropriate control measures. The identification of epitopic peptides can be useful in the development of epitope-based vaccine strategies against this re-emerging viral pathogen.

Autocidal gravid ovitraps protect humans from chikungunya virus infection by reducing Aedes aegypti mosquito populations

Background

Public health responses to outbreaks of dengue, chikungunya, and Zika virus have been stymied by the inability to control the primary vector, Aedes aegypti mosquitos. Consequently, the need for novel approaches to Aedes vector control is urgent. Placement of three autocidal gravid ovitraps (AGO traps) in ~85% of homes in a community was previously shown to sustainably reduce the density of female Ae. aegypti by >80%. Following the introduction of chikungunya virus (CHIKV) to Puerto Rico, we conducted a seroprevalence survey to estimate the prevalence of CHIKV infection in communities with and without AGO traps and evaluate their effect on reducing CHIKV transmission.

Methods and findings

Multivariate models that calculated adjusted prevalence ratios (aPR) showed that among 175 and 152 residents of communities with and without AGO traps, respectively, an estimated 26.1% and 43.8% had been infected with CHIKV (aPR = 0.50, 95% CI: 0.37–0.91). After stratification by time spent in their community, protection from CHIKV infection was strongest among residents who reported spending many or all weekly daytime hours in their community:10.3% seropositive in communities with AGO traps vs. 48.7% in communities without (PR = 0.21, 95% CI: 0.11–0.41). The age-adjusted rate of fever with arthralgia attributable to CHIKV infection was 58% (95% CI: 46–66%). The monthly number of CHIKV-infected mosquitos and symptomatic residents were diminished in communities with AGO traps compared to those without.

Conclusions

These findings indicate that AGO traps are an effective tool that protects humans from infection with a virus transmitted by Ae. aegypti mosquitos. Future studies should evaluate their protective effectiveness in large, urban communities.

Aedes species mosquitos transmit pathogens of public health importance, including dengue, Zika, and chikungunya viruses. No tools exist to control these mosquitos that sustainably and effectively prevent human infections. Autocidal gravid ovitraps (AGO traps) have been shown to sustainably reduce Aedes populations by >80%. After chikungunya virus was introduced into Puerto Rico, we conducted serosurveys in communities with and without AGO traps. We observed a two-fold lower prevalence of chikungunya virus infection among residents of communities with AGO traps compared to communities without. Among infected residents of communities with traps, a significant proportion likely had been infected while outside their community. These findings indicate that AGO traps are an effective tool that protects humans from infection with pathogens transmitted by Aedes mosquitos.

The Potential Impact of Chikungunya Virus Outbreaks on Blood Transfusion

Chikungunya virus (CHIKV) is responsible for large periodic epidemics in both endemic and nonendemic areas where competent mosquitoes are present. Transmission of CHIKV by transfusion during explosive outbreaks has never been documented, and the true impact of CHIKV infection on blood transfusion during an outbreak is unknown. Considerations include not only transfusions in the active outbreak areas but also returning travelers to nonendemic areas. Because there are no documented cases of transfusion-transmitted CHIKV, there are no standard guidelines regarding transfusion policies during a chikungunya fever outbreak. We review current information from studies during outbreaks with the goal of estimating the potential effect of different blood safety interventions (eg, querying donors for possible CHIKV exposure, chikungunya fever-related symptoms, screening for CHIKV RNA).

GloPID-R report on Chikungunya, O'nyong-nyong and Mayaro virus, part I: Biological diagnostics

The GloPID-R (Global Research Collaboration for Infectious Disease Preparedness) Chikungunya (CHIKV), O'nyong-nyong (ONNV) and Mayaro virus (MAYV) Working Group is investigating the natural history, epidemiology and medical management of infection by these viruses, to identify knowledge gaps and to propose recommendations for direct future investigations and rectification measures. Here, we present the first report dedicated to diagnostic aspects of CHIKV, ONNV and MAYV. Regarding diagnosis of the disease at the acute phase, molecular assays previously described for the three viruses require further evaluation, standardized protocols and the availability of international standards representing the genetic diversity of the viruses. Detection of specific IgM would benefit from further investigations to clarify the extent of cross-reactivity among the three viruses, the sensitivity of the assays, and the possible interfering role of cryoglobulinaemia. Implementation of reference panels and external quality assessments for both molecular and serological assays is necessary. Regarding sero-epidemiological studies, there is no reported high-throughput assay that can distinguish among these different viruses in areas of potential co-circulation. New specific tools and/or improved standardized protocols are needed to enable large-scale epidemiological studies of public health relevance to be performed. Considering the high risk of future CHIKV, MAYV and ONNV outbreaks, the Working Group recommends that a major investigation should be initiated to fill the existing diagnostic gaps.

A systematic review of individual and community mitigation measures for prevention and control of chikungunya virus

BACKGROUND

Chikungunya is a mosquito-borne virus transmitted by mosquitoes from the Aedes genus. The virus, endemic to parts of Asia and Africa, has recently undergone an emergence in other parts of the world where it was previously not found including Indian Ocean Islands, Europe, the Western Pacific and the Americas. There is no vaccine against chikungunya virus, which means that prevention and mitigation rely on personal protective measures and community level interventions including vector control.

METHODOLOGY/PRINCIPAL FINDINGS

A systematic review (SR) was conducted to summarize the literature on individual and community mitigation and control measures and their effectiveness. From a scoping review of the global literature on chikungunya, there were 91 articles that investigated mitigation or control strategies identified at the individual or community level. Of these, 81 were confirmed as relevant and included in this SR. The majority of the research was published since 2010 (76.5%) and was conducted in Asia (39.5%). Cross sectional studies were the most common study design (36.6%). Mitigation measures were placed into six categories: behavioural protective measures, insecticide use, public education, control of blood and blood products, biological vector control and quarantine of infected individuals. The effectiveness of various mitigation measures was rarely evaluated and outcomes were rarely quantitative, making it difficult to summarize results across studies and between mitigation strategies. Meta-analysis of the proportion of individuals engaging in various mitigation measures indicates habitat removal is the most common measure used, which may demonstrate the effectiveness of public education campaigns aimed at reducing standing water.

CONCLUSIONS/SIGNIFICANCE

Further research with appropriate and consistent outcome measurements are required in order to determine which mitigation measures, or combination of mitigation measures, are the most effective at protecting against exposure to chikungunya virus.

Risk factors for hospitalization of patients with chikungunya virus infection at sentinel hospitals in Puerto Rico

Background

Hospitalization of patients during outbreaks of chikungunya virus has been reported to be uncommon (0.5–8.7%), but more frequent among infants and the elderly. CHIKV was first detected in Puerto Rico in May 2014. We enrolled patients with acute febrile illness (AFI) presenting to two hospital emergency departments in Puerto Rico and tested them for CHIKV infection to describe the frequency of detection of CHIKV-infected patients, identify risk factors for hospitalization, and describe patients with severe manifestations.

Methodology/Principal findings

Serum specimens were collected from patients with AFI and tested by rRT-PCR. During May–December 2014, a total of 3,035 patients were enrolled, and 1,469 (48.4%) had CHIKV infection. A total of 157 (10.7%) CHIKV-infected patients were hospitalized, six (0.4%) were admitted to the intensive care unit, and two died (0.1%). Common symptoms among all CHIKV-infected patients were arthralgia (82.6%), lethargy (80.6%), and myalgia (80.5%). Compared to patients aged 1–69 years (7.3%), infant (67.2%) and elderly (17.3%) patients were nine and two times more likely to be hospitalized, respectively (relative risk [RR] and 95% confidence interval [CI] = 9.16 [7.05–11.90] and 2.36 [1.54–3.62]). Multiple symptoms of AFI were associated with decreased risk of hospitalization, including arthralgia (RR = 0.31 [0.23–0.41]) and myalgia (RR = 0.29 [0.22–0.39]). Respiratory symptoms were associated with increased risk of hospitalization, including rhinorrhea (RR = 1.68 [1.24–2.27) and cough (RR = 1.77 [1.31–2.39]). Manifestations present among <5% of patients but associated with patient hospitalization included cyanosis (RR = 2.20 [1.17–4.12) and seizures (RR = 3.23 [1.80–5.81).

Discussion

Among this cohort of CHIKV-infected patients, hospitalization was uncommon, admission to the ICU was infrequent, and death was rare. Risk of hospitalization was higher in patients with symptoms of respiratory illness and other manifestations that may not have been the result of CHIKV infection.

Chikungunya is an emerging infectious disease caused by a virus (chikungunya virus, CHIKV) transmitted through the bite of infected mosquitos; typical symptoms are fever and joint pain. After CHIKV was first detected in Puerto Rico in 2014, an epidemic quickly spread across the island. Because previous reports identified varying frequencies of hospitalization of CHIKV-infected patients, we used an existing hospital-based disease detection system to better understand the frequency and reasons for hospitalization of CHIKV-infected patients in Puerto Rico. Among 1,469 patients with laboratory-confirmed CHIKV infection, 11% were hospitalized, most of whom were infants or elderly. Six CHIKV-infected patients were admitted to the intensive care unit, and two died. Although several illness characteristics were associated with hospitalization, most of these were not typical of chikungunya and instead suggested underlying or concomitant respiratory disease. By enrolling patients when they presented to the emergency department and testing them for evidence of CHIKV infection, we determined that hospitalization in this population occurred in roughly one-in-ten CHIKV-infected patients, one-in-two hundred were admitted to the intensive care unit, and one-in-one thousand died. These findings provide information on the spectrum of disease caused by CHIKV, and identified underlying or concomitant respiratory illness as a risk factor associated with hospitalization.

Duplex nucleic acid test for the detection of chikungunya and dengue RNA viruses in blood donations

BACKGROUND

Chikungunya (CHIKV) and dengue (DENV) viruses are primarily mosquito‐borne, but transfusion transmission can occur (DENV) or is likely (CHIKV). In the absence of commercially available blood screening assays, a variety of strategies to ensure recipient safety in the face of expanding CHIKV and/or DENV outbreaks have been used.

STUDY DESIGN AND METHODS

Performance of cobas CHIKV/DENV, a qualitative RNA detection assay for use on the cobas 6800/8800 Systems, was evaluated at two sites (Roche Molecular Systems, Inc. [RMS], and the American Red Cross [ARC]). Analytical sensitivity, genotype inclusion, correlation with other assays, and reproducibility used clinical CHIKV‐ or DENV‐positive samples and secondary standards for DENV Types 1 to 4 and for three CHIKV genotypes (Asian; East Central South African; and West African); each secondary standard was traceable to international reference panels or reagents. Evaluation of analytic specificity assessed other microorganisms for interference and cross‐reactivity; clinical specificity was determined by individually testing 10,528 volunteer blood donations from the continental United States.

RESULTS

The 50 and 95% limit of detection (LoD) obtained by RMS for CHIKV, Asian genotype was 1.8 and 6.8 Detectable Units (DU)/mL, respectively, and 0.14 and 0.63 International Units (IU)/mL, respectively for DENV‐1. No significant differences in detection occurred by testing at a second site, the ARC (2.4 and 10.5 DU/mL for CHIKV and 0.15 and 0.60 IU/mL for DENV). Clinical specificity was 100% (95% confidence interval, 99.965%‐100%) for CHIKV and DENV.

CONCLUSIONS

The high sensitivity and specificity of the cobas CHIKV/DENV test, as demonstrated in these evaluations, indicate its suitability for blood donation screening.

The Emergence of Zoonotic Pathogens as Agents of Concern in Transfusion Medicine

A variety of emerging infections are of interest to transfusion medicine clinicians, but zoonotic pathogens, those maintained in nonhuman hosts and transmitted to humans, have dominated recent discussions, especially emerging acute viral infections that can or might spread around a shrinking globe with unprecedented speed, in an infected human or an infected vector or reservoir host. Further, advanced pathogen discovery techniques (e.g., metagenomics) allow the identification of potential pathogens before their recognition as clinically relevant to transfusion medicine. In the aftermath of our experiences with HIV and posttransfusion hepatitis, our windows for response to such agents and infections have contracted rapidly. These characteristics pose difficult challenges for our development of surveillance and control regimes capable of timely, but appropriately nuanced, responses. This monograph surveys a selection of such agents, exploring their apparent relevance to transfusion medicine, closing with a framework for an ongoing approach to their surveillance, recognition, threat evaluation, and mitigation.

Amustaline (S-303) treatment inactivates high levels of Chikungunya virus in red-blood-cell components

BACKGROUND AND OBJECTIVES

Chikungunya virus (CHIKV) infections have been reported in all continents, and the potential risk for CHIKV transfusion-transmitted infections (TTIs) was demonstrated by the detection of CHIKV RNA-positive donations in several countries. TTIs can be reduced by pathogen inactivation (PI) of blood products. In this study, we evaluated the efficacy of amustaline and glutathione (S-303/GSH) to inactivate CHIKV in red-blood-cell concentrates (RBCs).

MATERIAL AND METHODS

Red-blood-cells were spiked with high level of CHIKV. Infectious titres and RNA loads were measured before and after PI treatment. Residual CHIKV infectivity was also assessed after five successive cell culture passages.

RESULTS

The mean CHIKV titres in RBCs before inactivation was 5·81 ± 0·18 log₁₀ 50% tissue culture infectious dose (TCID₅₀ )/mL, and the mean viral RNA load was 10·49 ± 0·15 log₁₀ genome equivalent (GEq)/mL. No CHIKV TCID was detected after S-303 treatment nor was replicative CHIKV particles and viral RNA present after five cell culture passages of samples obtained immediately after S-303 treatment.

CONCLUSION

Chikungunya virus was previously shown to be inactivated by the PI technology using amotosalen and ultraviolet A light for the treatment of plasma and platelets. This new study demonstrates that S-303/GSH can inactivate high titres of CHIKV in RBCs.

Analytical and clinical performance of a Chikungunya qRT-PCR for Central and South America

Chikungunya was introduced into the Americas in 2015 causing a pandemic across the continent. Testing during the acute phase of infection relies on qRT-PCR, but available assays have a number of limitations. A qRT-PCR assay specific to the chikungunya E1 gene was designed using sequence data from contemporary strains. A probit analysis established the 95% limit of detection as 19.6 copies per reaction. We compared the assay with a US Centers for Disease Control (CDC) chikungunya qRT-PCR as the reference standard. The assay had a sensitivity and specificity of 98.4% and 100% in 90 samples retrospectively collected in Guatemala. In a further 74 febrile samples prospectively collected in Ecuador and Guatemala the test had a sensitivity and specificity of 100% and 98.4%, respectively. Sequencing the nsp4 gene of the discordant positive sample indicated the presence of chikungunya RNA, and mismatches to the primer binding sites of the CDC assay.

Transfusion Reactions

Transfusion reactions are common occurrences, and clinicians who order or transfuse blood components need to be able to recognize adverse sequelae of transfusion. The differential diagnosis of any untoward clinical event should always consider adverse sequelae of transfusion, even when transfusion occurred weeks earlier. There is no pathognomonic sign or symptom that differentiates a transfusion reaction from other potential medical problems, so vigilance is required during and after transfusion when a patient presents with a change in clinical status. This review covers the presentation, mechanisms, and management of transfusion reactions that are commonly encountered, and those that can be life-threatening.

Guillain-Barré Syndrome and Healthcare Needs during Zika Virus Transmission, Puerto Rico, 2016

To assist with public health preparedness activities, we estimated the number of expected cases of Zika virus in Puerto Rico and associated healthcare needs. Estimated annual incidence is 3.2–5.1 times the baseline, and long-term care needs are predicted to be 3–5 times greater than in years with no Zika virus.

Distinct Zika Virus Lineage in Salvador, Bahia, Brazil

Sequencing of isolates from patients in Bahia, Brazil, where most Zika virus cases in Brazil have been reported, resulted in 11 whole and partial Zika virus genomes. Phylogenetic analyses revealed a well-supported Bahia-specific Zika virus lineage, which indicates sustained Zika virus circulation in Salvador, Bahia’s capital city, since mid-2014.

High Incidence of Chikungunya Virus and Frequency of Viremic Blood Donations during Epidemic, Puerto Rico, USA, 2014

Deaths were rarely observed, but newborns and other vulnerable populations are at risk for severe complications.

Chikungunya virus (CHIKV) caused large epidemics throughout the Caribbean in 2014. We conducted nucleic acid amplification testing (NAAT) for CHIKV RNA (n = 29,695) and serologic testing for IgG against CHIKV (n = 1,232) in archived blood donor samples collected during and after an epidemic in Puerto Rico in 2014. NAAT yields peaked in October with 2.1% of donations positive for CHIKV RNA. A total of 14% of NAAT-reactive donations posed a high risk for virus transmission by transfusion because of high virus RNA copy numbers (10⁴–10⁹ RNA copies/mL) and a lack of specific IgM and IgG responses. Testing of minipools of 16 donations would not have detected 62.5% of RNA-positive donations detectable by individual donor testing, including individual donations without IgM and IgG. Serosurveys before and after the epidemic demonstrated that nearly 25% of blood donors in Puerto Rico acquired CHIKV infections and seroconverted during the epidemic.

Coinfections of Zika and Chikungunya Viruses in Bahia, Brazil, Identified by Metagenomic Next-Generation Sequencing

Metagenomic next-generation sequencing (mNGS) of samples from 15 patients with documented Zika virus (ZIKV) infection in Bahia, Brazil, from April 2015 to January 2016 identified coinfections with chikungunya virus (CHIKV) in 2 of 15 ZIKV-positive cases by PCR (13.3%). While generally nonspecific, the clinical presentation corresponding to these two CHIKV/ZIKV coinfections reflected infection by the virus present at a higher titer. Aside from CHIKV and ZIKV, coinfections of other viral pathogens were not detected. The mNGS approach is promising for differential diagnosis of acute febrile illness and identification of coinfections, although targeted arbovirus screening may be sufficient in the current ZIKV outbreak setting.

Zika Virus

Zika virus (ZIKV) is an arthropod-borne virus (arbovirus) in the genus Flavivirus and the family Flaviviridae. ZIKV was first isolated from a nonhuman primate in 1947 and from mosquitoes in 1948 in Africa, and ZIKV infections in humans were sporadic for half a century before emerging in the Pacific and the Americas. ZIKV is usually transmitted by the bite of infected mosquitoes. The clinical presentation of Zika fever is nonspecific and can be misdiagnosed as other infectious diseases, especially those due to arboviruses such as dengue and chikungunya. ZIKV infection was associated with only mild illness prior to the large French Polynesian outbreak in 2013 and 2014, when severe neurological complications were reported, and the emergence in Brazil of a dramatic increase in severe congenital malformations (microcephaly) suspected to be associated with ZIKV. Laboratory diagnosis of Zika fever relies on virus isolation or detection of ZIKV-specific RNA. Serological diagnosis is complicated by cross-reactivity among members of the Flavivirus genus. The adaptation of ZIKV to an urban cycle involving humans and domestic mosquito vectors in tropical areas where dengue is endemic suggests that the incidence of ZIKV infections may be underestimated. There is a high potential for ZIKV emergence in urban centers in the tropics that are infested with competent mosquito vectors such as Aedes aegypti and Aedes albopictus.

Two human immunodeficiency virus Type 2 cases in US blood donors including serologic, molecular, and genomic characterization of an epidemiologically unusual case

BACKGROUND

Blood donation screening for human immunodeficiency virus Type 2 (HIV-2) has been in place in the United States since 1992. However, only three HIV-2 antibody-positive donors have been reported to date, all detected via HIV-1 cross-reactivity.

STUDY DESIGN AND METHODS

Here we identify two additional HIV-2-positive donors by routine anti-HIV-1 and anti-HIV-2 screening, including a first-time male donor living in Georgia having recently immigrated to the United States from West Africa (from a 1998 donation) and a Taiwanese female repeat donor (nurse) living in California with no travel outside of Taiwan or apparent connections to West Africa (from a 2015 donation). Neither donor acknowledged any risk factors, and both remained asymptomatic through follow-up. The second donor was further investigated by serologic, molecular, and genomic assays because of her unusual demographics. She was documented to harbor HIV-2 RNA, albeit sporadically by HIV-2-specific nucleic acid tests (35%-100% of replicates) and at very low levels (<9.6 IU/mL). Metagenomic next-generation sequencing (mNGS) confirmed the identification of a Group B HIV-2 strain, with recovered reads covering 46.9% of the predicted genome.

CONCLUSIONS

The estimated frequency of an HIV-2-positive blood donor in the United States is one in 57 million donations. Due to the low frequency and low pathogenicity of HIV-2, public health and blood donation screening efforts must focus on HIV-1 detection and prevention. However, detection of HIV-2 infection in a donor with no apparent link to West Africa suggests that the United States must remain vigilant for HIV-2 virus infections. Ultradeep mNGS may be useful in the future for comprehensive identification of rare transfusion-transmissible agents.

Advances in multiplex nucleic acid diagnostics for blood-borne pathogens: promises and pitfalls

The large number of blood-borne viruses, bacteria and parasites currently of concern, as well as many newly emerging pathogens, presents a daunting challenge to protection of the safety of blood for transfusion and diagnosing infectious diseases. Focusing on nucleic acid diagnostic tests, multiplex devices are coming into use with many more in various developmental stages that promise to offer solutions to the clinical need. The characteristics, advantages and disadvantages of platforms in clinical use and at the research and development stage are examined here. The presence of multiple assays and associated reagents operating simultaneously on one platform, implementation in traditional clinical laboratories and regulatory review will present special challenges. Fortunately, clinical laboratories have made dramatic technical progress in the last two decades and regulatory agencies have publicly expressed support for development of multiplex devices.

Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

We report unbiased metagenomic detection of chikungunya virus (CHIKV), Ebola virus (EBOV), and hepatitis C virus (HCV) from four human blood samples by MinION nanopore sequencing coupled to a newly developed, web-based pipeline for real-time bioinformatics analysis on a computational server or laptop (MetaPORE). At titers ranging from 10⁷–10⁸ copies per milliliter, reads to EBOV from two patients with acute hemorrhagic fever and CHIKV from an asymptomatic blood donor were detected within 4 to 10 min of data acquisition, while lower titer HCV virus (1 × 10⁵ copies per milliliter) was detected within 40 min. Analysis of mapped nanopore reads alone, despite an average individual error rate of 24 % (range 8–49 %), permitted identification of the correct viral strain in all four isolates, and 90 % of the genome of CHIKV was recovered with 97–99 % accuracy. Using nanopore sequencing, metagenomic detection of viral pathogens directly from clinical samples was performed within an unprecedented <6 hr sample-to-answer turnaround time, and in a timeframe amenable to actionable clinical and public health diagnostics.

Probable and possible transfusion-transmitted dengue associated with NS1 antigen-negative but RNA confirmed-positive red blood cells

BACKGROUND

In the absence of active blood donation screening, dengue viruses (DENV) have been implicated in only a limited number of transfusion transmissions worldwide. This study attempted to identify if blood from donors testing negative by an NS1-antigen (Ag) enzyme-linked immunosorbent assay (ELISA) but confirmed positive for DENV RNA caused DENV-related disease in recipients during the epidemic years of 2010 to 2012 in Puerto Rico.

STUDY DESIGN AND METHODS

Donation aliquots testing negative by an investigational NS1-Ag ELISA were stored frozen and retested retrospectively using a research transcription-mediated amplification assay (TMA) detecting DENV RNA. All RNA-reactive donations were subject to confirmatory RNA and antibody testing. Recipient tracing was conducted for all components manufactured from TMA-reactive components. Medical chart review, recipient interview, and follow-up sampling occurred for 42 recipients transfused with TMA-reactive components.

RESULTS

Six of 42 recipients developed new-onset fever in the 2 weeks posttransfusion; three (50%) received RNA confirmed-positive, NS1-Ag-negative red blood cell (RBC) units. One recipient of a high-titer unit (7 × 10(7) DENV-4 RNA copies/mL) developed severe dengue, and a second recipient had only fever recorded but had a negative sepsis work-up. New fever attributable to DENV infection in a third recipient was confounded by fever potentially attributable to posttransfusion sepsis.

CONCLUSIONS

In our retrospective study, NS1-Ag detected 20% of all RNA confirmed-positive donations demonstrating limitations of NS1-Ag ELISA for blood donation screening. We identified one recipient with a clinical syndrome compatible with severe dengue who had received an NS1-Ag-negative but RNA confirmed-positive RBC unit. This investigation illustrates the difficulty in confirming transfusion transmission in dengue-endemic areas among severely ill transfusion recipients.