Correction: Recommended reporting items for epidemic forecasting and prediction research: The EPIFORGE 2020 guidelines.

[This corrects the article DOI: 10.1371/journal.pmed.1003793.].

Molecular survey of Anaplasma and Ehrlichia species in livestock ticks from Kassena-Nankana, Ghana; with a first report of Anaplasma capra and Ehrlichia minasensis.

Tick-borne pathogens harm livestock production and pose a significant risk to public health. To combat these effects, it is necessary to identify the circulating pathogens to create effective control measures. This study identified Anaplasma and Ehrlichia species in ticks collected from livestock in the Kassena-Nankana Districts between February 2020 and December 2020. A total of 1550 ticks were collected from cattle, sheep and goats. The ticks were morphologically identified, pooled and screened for pathogens using primers that amplify a 345 bp fragment of the 16SrRNA gene and Sanger sequencing. The predominant tick species collected was Amblyomma variegatum (62.98%). From the 491 tick pools screened, 34 (6.92%) were positive for Ehrlichia and Anaplasma. The pathogens identified were Ehrlichia canis (4.28%), Ehrlichia minasensis (1.63%), Anaplasma capra (0.81%) and Anaplasma marginale (0.20%). This study reports the first molecular identification of the above-mentioned Ehrlichia and Anaplasma species in ticks from Ghana. With the association of human infections with the zoonotic pathogen A. capra, livestock owners are at risk of infections, calling for the development of effective control measures.

Virus genomes reveal factors that spread and sustained the Ebola epidemic.

The 2013-2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact. Here we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region by analysing 1,610 Ebola virus genomes, which represent over 5% of the known cases. We test the association of geography, climate and demography with viral movement among administrative regions, inferring a classic 'gravity' model, with intense dispersal between larger and closer populations. Despite attenuation of international dispersal after border closures, cross-border transmission had already sown the seeds for an international epidemic, rendering these measures ineffective at curbing the epidemic. We address why the epidemic did not spread into neighbouring countries, showing that these countries were susceptible to substantial outbreaks but at lower risk of introductions. Finally, we reveal that this large epidemic was a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help to inform interventions in future epidemics.

First record of Babesia and Theileria parasites in ticks from Kassena-Nankana, Ghana.

Ticks are efficient vectors for transmitting pathogens that negatively affect livestock production and pose a risk to public health. In this study, Babesia and Theileria species were identified in ticks collected from cattle, sheep and goats from the Kassena-Nankana Districts of Ghana between February and December 2020. A total of 1550 ticks were collected, morphologically identified, pooled and screened for pathogens using primers that amplify a 560 bp fragment of the ssrRNA gene and Sanger sequencing. Amblyomma variegatum (62.98%) was the predominant tick species. From the 491 tick pools screened, 12/15 (2.44%) positive pools were successfully sequenced. The pathogen DNA identified were Theileria ovis in eight (15.38%) pools of Rhipicephalus evertsi evertsi, Theileria velifera in two (0.78%) pools of A. variegatum and Babesia occultans and Babesia sp. Xinjiang in one (1.72%) pool each of Hyalomma truncatum. It was further observed that T. ovis occurred in ticks collected from only sheep (p < 0.001) which were females (p = 0.023) and < =1 year old (p = 0.040). This study reports the first identification of these pathogens in ticks within Kassena-Nankana. With the constant trade of livestock, there is a need for effective tick control measures to prevent infection spread.

Effects of Functional Electrical Stimulation Cycling Combined With Arm Cranking Exercise on Cardiorespiratory Fitness in People With Central Nervous System Disorders: A Systematic Review and Meta-analysis.

OBJECTIVE: To examine the evidence regarding the potential of hybrid functional electrical stimulation (FES) cycling for improving cardiorespiratory fitness for people with a mobility disability related to a central nervous system (CNS) disorder. DATA SOURCES: Nine electronic databases: MEDLINE, EMBASE, Web of Science, CINAHL, PsycInfo, SPORTDiscus, Pedro, Cochrane, and Scopus, were searched from inception until October 2022. STUDY SELECTION: Search terms included multiple sclerosis, spinal cord injury (SCI), stroke, Parkinson's disease, cerebral palsy, synonyms of FES cycling, arm crank ergometry (ACE) or hybrid exercise, and V̇o2. All experimental studies, including randomized controlled trials that included an outcome measure related to peak or sub-maximal V̇o2 were eligible. DATA EXTRACTION: From a total of 280 articles, 13 were studies included. The Downs and Black Checklist was used to assess study quality. Random effects (Hedges' g) meta-analyses were undertaken to determine whether there were differences in V̇o2peak during acute bouts of hybrid FES cycling vs other modes of exercise and changes resulting from longitudinal training. DATA SYNTHESIS: During acute bouts of exercise, hybrid FES cycling was moderately more effective than ACE (effect size [ES] of 0.59 (95% CI 0.15-1.02, P=.008) in increasing V̇o2peak from rest. There was a large effect on the increase of V̇o2peak from rest for hybrid FES cycling compared with FES cycling (ES of 2.36 [95% CI 0.83-3.40, P=.003]). Longitudinal training with hybrid FES cycling showed a significant improvement in V̇o2peak from pre to post intervention with a large, pooled ES of 0.83 (95% CI 0.24-1.41, P=.006). CONCLUSIONS: Hybrid FES cycling produced higher V̇o2peak compared with ACE or FES cycling during acute bouts of exercise. Hybrid FES cycling can improve cardiorespiratory fitness in people with SCI. Additionally, there is emerging evidence that hybrid FES cycling might increase aerobic fitness in people with mobility disability related to CNS disorders.

Occurrence of Rickettsia spp. and Coxiella burnetii in ixodid ticks in Kassena-Nankana, Ghana.

Ticks are arthropods of veterinary and medical importance which spread zoonotic pathogens that link animal and human health. In this study, ticks were collected from 448 livestock between February and December 2020 in the Kassena-Nankana Districts of Ghana and screened for the presence of zoonotic pathogens DNA using PCR and sequencing approaches. In total, 1550 ticks were collected and morphologically identified. Three tick genera were identified with Amblyomma variegatum (63%) as the predominant tick species collected. DNA was extracted from 491 tick pools and screened for the presence of DNA of Rickettsia spp. based on the 115 bp fragment of the 17 kDa surface protein and 639 bp of the Outer membrane protein A (ompA) gene and the 295 bp fragment of the transposase gene of Coxiella burnetii IS1111a element. From the 491 pools screened, the DNA of Rickettsia spp. and C. burnetii was detected in 56.8 and 3.7%, respectively. Coinfections were identified in 2.4% of the tick pools. Characterization of the Rickettsia spp. in this study based on the ompA gene showed that the DNA of Rickettsia africae and Rickettsia aeschlimannii accounted for 39.7 and 14.7%, respectively, and were 100% similar to sequences in GenBank. Most R. africae and C. burnetii infections occurred in ticks collected in the wet season, whereas R. aeschlimannii occurred mostly in the dry season. These pathogens are potential public health threats, thus there is a need to implement control measures to reduce the risk of infections in vulnerable populations.

First record of Rhipicephalus (Boophilus) microplus in Ghana, a potential risk to livestock production.

Ticks are a public health threat due to their tendency to spread pathogens that affect humans and animals. With reports of Rhipicephalus (Boophilus) microplus invasion in neighbouring countries, there is the risk of this species invading Ghana through livestock trade. Previous identification of tick species in Ghana has been based on morphological identification, which can be ineffective, especially with damaged tick specimens or engorged nymphs. This study focused on the Kassena-Nankana District, which serves as a trade route for cattle into Ghana, to determine the presence of R. microplus. Three genera of ticks were identified as Amblyomma (70.9%), Hyalomma (21.3%) and Rhipicephalus (7.8%). The engorged nymphs that could not be identified morphologically were analyzed using primers that target the mitochondrial 16S rRNA gene. This study reports the first record of R. (B.) microplus in Ghana. Furthermore, R. microplus constituted 54.8% of the Boophilus species collected in this study. This finding is an addition to the diverse tick species previously collected in Ghana, most of which are of veterinary and public health importance. With reports of acaricide resistance in R. microplus and its role in spreading infectious pathogens, the detection of this species in Ghana cannot be overlooked. Nationwide surveillance will be essential to ascertain its distribution, its effects on cattle production, and the control measures adopted.

Recommended reporting items for epidemic forecasting and prediction research: The EPIFORGE 2020 guidelines.

BACKGROUND: The importance of infectious disease epidemic forecasting and prediction research is underscored by decades of communicable disease outbreaks, including COVID-19. Unlike other fields of medical research, such as clinical trials and systematic reviews, no reporting guidelines exist for reporting epidemic forecasting and prediction research despite their utility. We therefore developed the EPIFORGE checklist, a guideline for standardized reporting of epidemic forecasting research. METHODS AND FINDINGS: We developed this checklist using a best-practice process for development of reporting guidelines, involving a Delphi process and broad consultation with an international panel of infectious disease modelers and model end users. The objectives of these guidelines are to improve the consistency, reproducibility, comparability, and quality of epidemic forecasting reporting. The guidelines are not designed to advise scientists on how to perform epidemic forecasting and prediction research, but rather to serve as a standard for reporting critical methodological details of such studies. CONCLUSIONS: These guidelines have been submitted to the EQUATOR network, in addition to hosting by other dedicated webpages to facilitate feedback and journal endorsement.

Pilot Study of Enhancing Cardiorespiratory Exercise Response in People With Advanced Multiple Sclerosis With Hybrid Functional Electrical Stimulation.

OBJECTIVE: To investigate through a pilot study the acute cardiorespiratory responses during functional electrical stimulation (FES) cycling, arm crank ergometry (ACE), and a combination of ACE and FES cycling (hybrid FES cycling) in people with advanced multiple sclerosis (MS) to provide preliminary guidance for effective aerobic exercise prescription. DESIGN: Acute repeated measures. SETTING: Laboratory setting. PARTICIPANTS: Inclusion criteria was a diagnosis of MS, with Expanded Disability Status Scale (EDSS) 6.0-8.5. Included were 9 participants (N=9; 7 female, age 54.7±8.8y, EDSS 7.2±0.7). INTERVENTIONS: Participants were assessed on 3 different exercise modalities (FES cycling, ACE, hybrid FES cycling) at 40%, 60%, 80%, and 100% of mode-specific peak workload. MAIN OUTCOME MEASURES: Oxygen consumption and heart rate were measured at each workload. RESULTS: Hybrid FES cycling evoked a significantly higher oxygen consumption relative to body weight (V̇o2relative) (mL/kg/min) and heart rate (beats per minute [BPM]) at most workloads compared with ACE or FES cycling. At the 100% workload, heart rate for hybrid FES cycling was 125 BPM (range, 113-148 BPM) and was significantly higher than ACE at 99 BPM (range, 95-119 BPM) (P=.008) and FES cycling at 94 BPM (range, 79-100 BPM) (P=.008). Similarly, at the 100% workload, V̇o2relative for hybrid FES cycling was 11.8 mL/kg/min (range, 7.6-17.6 mL/kg/min) and was significantly higher than ACE at 8.9 mL/kg/min (range, 5.3-12.5 mL/kg/min) (P=.012) and FES cycling at 6.8 mL/kg/min (range, 4.1-9.2 mL/kg/min) (P=.012). CONCLUSIONS: This pilot study showed that hybrid FES cycling can elicit a greater cardiorespiratory response than ACE or FES cycling in people with advanced MS. Thus, hybrid FES cycling might provide a potent enough stimulus to induce clinically relevant changes in cardiorespiratory fitness. Training studies are warranted to document the magnitude and sustainability of aerobic capacity adaptations to hybrid FES cycling and associated health outcomes in advanced MS.

Molecular Evidence of Sexual Transmission of Ebola Virus.

A suspected case of sexual transmission from a male survivor of Ebola virus disease (EVD) to his female partner (the patient in this report) occurred in Liberia in March 2015. Ebola virus (EBOV) genomes assembled from blood samples from the patient and a semen sample from the survivor were consistent with direct transmission. The genomes shared three substitutions that were absent from all other Western African EBOV sequences and that were distinct from the last documented transmission chain in Liberia before this case. Combined with epidemiologic data, the genomic analysis provides evidence of sexual transmission of EBOV and evidence of the persistence of infective EBOV in semen for 179 days or more after the onset of EVD. (Funded by the Defense Threat Reduction Agency and others.).

Cynomolgus macaque (Macaca fascicularis) immunoglobulin heavy chain locus description.

Cynomolgus macaques (Macaca fascicularis) have become an important animal model for biomedical research. In particular, it is the animal model of choice for the development of vaccine candidates associated with emerging dangerous pathogens. Despite their increasing importance as animal models, the cynomolgus macaque genome is not fully characterized, hindering molecular studies for this model. More importantly, the lack of knowledge about the immunoglobulin (IG) locus organization directly impacts the analysis of the humoral response in cynomolgus macaques. Recent advances in next generation sequencing (NGS) technologies to analyze IG repertoires open the opportunity to deeply characterize the humoral immune response. However, the IG locus organization for the animal is required to completely dissect IG repertoires. Here, we describe the localization and organization of the rearranging IG heavy (IGH) genes on chromosome 7 of the cynomolgus macaque draft genome. Our annotation comprises 108 functional genes which include 63 variable (IGHV), 38 diversity (IGHD), and 7 joining (IGHJ) genes. For validation, we provide RNA transcript data for most of the IGHV genes and all of the annotated IGHJ genes, as well as proteomic data to validate IGH constant genes. The description and annotation of the rearranging IGH genes for the cynomolgus macaques will significantly facilitate scientific research. This is particularly relevant to dissect the immune response during vaccination or infection with dangerous pathogens such as Ebola, Marburg and other emerging pathogens where non-human primate models play a significant role for countermeasure development.

Monitoring of Ebola Virus Makona Evolution through Establishment of Advanced Genomic Capability in Liberia.

To support Liberia's response to the ongoing Ebola virus (EBOV) disease epidemic in Western Africa, we established in-country advanced genomic capabilities to monitor EBOV evolution. Twenty-five EBOV genomes were sequenced at the Liberian Institute for Biomedical Research, which provided an in-depth view of EBOV diversity in Liberia during September 2014-February 2015. These sequences were consistent with a single virus introduction to Liberia; however, shared ancestry with isolates from Mali indicated at least 1 additional instance of movement into or out of Liberia. The pace of change is generally consistent with previous estimates of mutation rate. We observed 23 nonsynonymous mutations and 1 nonsense mutation. Six of these changes are within known binding sites for sequence-based EBOV medical countermeasures; however, the diagnostic and therapeutic impact of EBOV evolution within Liberia appears to be low.

Possible sexual transmission of Ebola virus - Liberia, 2015.

On March 20, 2015, 30 days after the most recent confirmed Ebola Virus Disease (Ebola) patient in Liberia was isolated, Ebola was laboratory confirmed in a woman in Monrovia. The investigation identified only one epidemiologic link to Ebola: unprotected vaginal intercourse with a survivor. Published reports from previous outbreaks have demonstrated Ebola survivors can continue to harbor virus in immunologically privileged sites for a period of time after convalescence. Ebola virus has been isolated from semen as long as 82 days after symptom onset and viral RNA has been detected in semen up to 101 days after symptom onset. One instance of possible sexual transmission of Ebola has been reported, although the accompanying evidence was inconclusive. In addition, possible sexual transmission of Marburg virus, a filovirus related to Ebola, was documented in 1968. This report describes the investigation by the Government of Liberia and international response partners of the source of Liberia's latest Ebola case and discusses the public health implications of possible sexual transmission of Ebola virus. Based on information gathered in this investigation, CDC now recommends that contact with semen from male Ebola survivors be avoided until more information regarding the duration and infectiousness of viral shedding in body fluids is known. If male survivors have sex (oral, vaginal, or anal), a condom should be used correctly and consistently every time.

Functional electrical stimulation combined with voluntary cycling accentuates VO2 response in people with severe multiple sclerosis: A pilot study.

BACKGROUND: Lower limb muscle weakness and reduced balance due to disease progression in multiple sclerosis (MS) may make robust aerobic exercise difficult. Functional electrical stimulation (FES) cycling combined with voluntary cycling may allow people with severe MS to enhance the intensity of aerobic exercise. The aim of this study was to investigate the cardiorespiratory, power, and participant-reported perceptions during acute bouts of FES cycling, voluntary cycling, and FES cycling combined with voluntary cycling (FES assist cycling). METHODS: Participants with severe MS (Expanded Disability Status Scale [EDSS] ≥ 6.0) undertook three exercise trials on a leg cycle ergometer. Trial 1 involved 30 min of FES cycling; Trial 2 involved two 10-minute bouts of voluntary cycling separated by 10 min rest; and Trial 3 was a combination of trials 1 and 2 (FES assist cycling). Outcome measures included VO2 (volume of oxygen consumption), cycle power output, heart rate, RPE, and post-exercise perceptions of pain and fatigue. RESULTS: Ten people with severe MS participated (9 female; age 52.4 ± 9.98 y; EDSS 7.1 ± 0.6). The average VO2 during the 30-minute trials was significantly higher for FES assist cycling compared to voluntary cycling (429.7 ± 111.0 vs 388.5 ± 101.0 mL/min, 95% CI 23.4 to 113.0 mL/min, p = 0.01), with a large effect size (Hedges' g = 1.04). Participants reported similar rates of perceived exertion at the end of FES cycling (13 ± 2), voluntary cycling (14 ± 2), and FES assist cycling (15 ± 1); p = 0.14. Self-reported pain was higher during both FES cycling (5.4 vs 0.3; 95% CI 3.4 to 6.7, p = 0.01, Hedges' g = 2.07) and FES assist cycling (4.2 vs. 0.3; 95% CI 2.3 to 5.5, p = 0.01, Hedges' g = 1.71) than voluntary cycling, both with large effect sizes. There was no difference in self-reported fatigue at the end of each trial (p = 0.21). CONCLUSION: This study found FES assist cycling produced significantly higher VO2 values than voluntary cycling, although the clinical significance of these differences is unknown. Participants performed FES assist cycling at a self-reported RPE consistent with moderate to vigorous intensity, however it was considered light-intensity exercise when expressed by METS. FES assist cycling was no more fatiguing post-exercise than the other modes.

The effects of hybrid functional electrical stimulation interval training on aerobic fitness and fatigue in people with advanced multiple sclerosis: An exploratory pilot training study.

BACKGROUND: Improving aerobic fitness in people with advanced multiple sclerosis (MS) may reduce fatigue, and lower the risk of cardiovascular disease, as has been found for people with mild to moderate MS. Training targeting aerobic fitness can be challenging due to paresis, access to suitable equipment and fatigue. The aim of this study was to investigate whether people with advanced multiple sclerosis could perform functional electrical stimulation (FES) cycling combined with arm crank interval exercise (hybrid FES interval training) training, and its effects on aerobic fitness and fatigue. METHODS: Hybrid FES interval training was performed 2 d/wk for 12 weeks. Each session consisted of 40 min of continuous FES cycling with arm crank intervals of 30 s work/30 s rest added concurrently for 20 min. The intensity target was a minimum of 60 % of arm crank power and 'hard' measured by rate of perceived exertion (RPE). Attendance, compliance to intensity and time targets, adverse events, and drop outs were measured. Aerobic fitness was assessed by an arm crank maximal test. Fatigue was measured via the Modified Fatigue Impact Scale (MFIS). RESULTS: Seven participants (6 female; age 57.1 ± 7.8y; Expanded Disability Status Scale 7.1 ± 0.8) with advanced MS attended 80 ± 10.4 % of the scheduled exercise sessions and there were no adverse events or drop outs. Average RPE at the end of each training session was 15.1 ± 2.1, representing vigorous intensity exercise. Aerobic fitness did not change pre- to post-intervention (14.2 ± 5.7 to 14.8 ± 6.0 mL/kg/min [p = 0.43]), and resulted in a small effect size (ES) (0.30). The reduction in fatigue during the intervention (31.0 ± 10.4 to 21.7 ± 11.4 [p = 0.10]), resulted in a moderate to large ES (-0.77). CONCLUSION: Hybrid FES interval training could be performed 2 days per week for 12 weeks and represented vigorous intensity exercise, but there was no change in aerobic fitness. The reduction in participants' perceptions of fatigue represented a moderate to large ES, indicating hybrid FES interval training might be suitable for people with advanced MS who need exercise equipment appropriate for their condition. CLINICAL TRIAL REGISTRATION: This study was registered with Australian and New Zealand Clinical Trials Register (U1111-1194-2040).

Characterization of the ZBTB42 gene in humans and mice.

A 12 kb haplotype upstream of the key signaling protein gene, AKT1, has been associated with insulin resistance and metabolic syndrome (Devaney et al. 2010). The region contains the first exon and promoter sequences of AKT1, but also includes the complete transcript unit for a highly conserved yet uncharacterized zinc finger-containing protein (ZBTB42). One of the component SNPs of the 12 kb haplotype metabolic syndrome haplotype changes a conserved amino acid in the predicted ZBTB42 protein, increasing the potential significance of the ZBTB42 transcript unit for contributing to disease risk. Using RT-PCR of human and mouse cells, we verified that the two exon ZBTB42 was expressed and correctly spliced in human skeletal muscle, and murine C2C12 cells. Production of peptide antibodies showed the expected protein in human (47 kD) and mouse (49 kD) immunoblots, and murine tissue distribution showed strongest expression in muscle and ovary. Immunostaining showed nuclear localization of the ZBTB42 protein in human muscle. Confocal imaging analyses of murine muscle showed ZBTB42 distributed in the nucleoplasm, with particular enrichment in nuclei underlying the neuromuscular junctions. The genetic association data of metabolic syndrome, coupled with the molecular characterization of the ZBTB42 transcript unit and encoded protein presented here, suggests that ZBTB42 may be involved in metabolic syndrome phenotypes.

Identification and evaluation of epidemic prediction and forecasting reporting guidelines: A systematic review and a call for action.

INTRODUCTION: High quality epidemic forecasting and prediction are critical to support response to local, regional and global infectious disease threats. Other fields of biomedical research use consensus reporting guidelines to ensure standardization and quality of research practice among researchers, and to provide a framework for end-users to interpret the validity of study results. The purpose of this study was to determine whether guidelines exist specifically for epidemic forecast and prediction publications. METHODS: We undertook a formal systematic review to identify and evaluate any published infectious disease epidemic forecasting and prediction reporting guidelines. This review leveraged a team of 18 investigators from US Government and academic sectors. RESULTS: A literature database search through May 26, 2019, identified 1467 publications (MEDLINE n = 584, EMBASE n = 883), and a grey-literature review identified a further 407 publications, yielding a total 1777 unique publications. A paired-reviewer system screened in 25 potentially eligible publications, of which two were ultimately deemed eligible. A qualitative review of these two published reporting guidelines indicated that neither were specific for epidemic forecasting and prediction, although they described reporting items which may be relevant to epidemic forecasting and prediction studies. CONCLUSIONS: This systematic review confirms that no specific guidelines have been published to standardize the reporting of epidemic forecasting and prediction studies. These findings underscore the need to develop such reporting guidelines in order to improve the transparency, quality and implementation of epidemic forecasting and prediction research in operational public health.

Persistence of Ebola virus after the end of widespread transmission in Liberia: an outbreak report.

BACKGROUND: Outbreak response efforts for the 2014-15 Ebola virus disease epidemic in west Africa brought widespread transmission to an end. However, subsequent clusters of infection have occurred in the region. An Ebola virus disease cluster in Liberia in November, 2015, that was identified after a 15-year-old boy tested positive for Ebola virus infection in Monrovia, raised the possibility of transmission from a persistently infected individual. METHODS: Case investigations were done to ascertain previous contact with cases of Ebola virus disease or infection with Ebola virus. Molecular investigations on blood samples explored a potential linkage between Ebola virus isolated from cases in this November, 2015, cluster and epidemiologically linked cases from the 2014-15 west African outbreak, according to the national case database. FINDINGS: The cluster investigated was the family of the index case (mother, father, three siblings). Ebola virus genomes assembled from two cases in the November, 2015, cluster, and an epidemiologically linked Ebola virus disease case in July, 2014, were phylogenetically related within the LB5 sublineage that circulated in Liberia starting around August, 2014. Partial genomes from two additional individuals, one from each cluster, were also consistent with placement in the LB5 sublineage. Sequencing data indicate infection with a lineage of the virus from a former transmission chain in the country. Based on serology and epidemiological and genomic data, the most plausible scenario is that a female case in the November, 2015, cluster survived Ebola virus disease in 2014, had viral persistence or recurrent disease, and transmitted the virus to three family members a year later. INTERPRETATION: Investigation of the source of infection for the November, 2015, cluster provides evidence of Ebola virus persistence and highlights the risk for outbreaks after interruption of active transmission. These findings underscore the need for focused prevention efforts among survivors and sustained capacity to rapidly detect and respond to new Ebola virus disease cases to prevent recurrence of a widespread outbreak. FUNDING: US Centers for Disease Control and Prevention, Defense Threat Reduction Agency, and WHO.

Reduced evolutionary rate in reemerged Ebola virus transmission chains.

On 29 June 2015, Liberia's respite from Ebola virus disease (EVD) was interrupted for the second time by a renewed outbreak ("flare-up") of seven confirmed cases. We demonstrate that, similar to the March 2015 flare-up associated with sexual transmission, this new flare-up was a reemergence of a Liberian transmission chain originating from a persistently infected source rather than a reintroduction from a reservoir or a neighboring country with active transmission. Although distinct, Ebola virus (EBOV) genomes from both flare-ups exhibit significantly low genetic divergence, indicating a reduced rate of EBOV evolution during persistent infection. Using this rate of change as a signature, we identified two additional EVD clusters that possibly arose from persistently infected sources. These findings highlight the risk of EVD flare-ups even after an outbreak is declared over.