Publications by authors named "Jeffrey A Bailey"

121 Publications

Single-cell RNA-seq reveals transcriptomic heterogeneity mediated by host-pathogen dynamics in lymphoblastoid cell lines.

Elife 2021 Jan 27;10. Epub 2021 Jan 27.

Department of Molecular Genetics and Microbiology, Center for Virology, Duke University School of Medicine, Durham, United States.

Lymphoblastoid cell lines (LCLs) are generated by transforming primary B cells with Epstein-Barr virus (EBV) and are used extensively as model systems in viral oncology, immunology, and human genetics research. In this study, we characterized single-cell transcriptomic profiles of five LCLs and present a simple discrete-time simulation to explore the influence of stochasticity on LCL clonal evolution. Single-cell RNA sequencing (scRNA-seq) revealed substantial phenotypic heterogeneity within and across LCLs with respect to immunoglobulin isotype; virus-modulated host pathways involved in survival, activation, and differentiation; viral replication state; and oxidative stress. This heterogeneity is likely attributable to intrinsic variance in primary B cells and host-pathogen dynamics. Stochastic simulations demonstrate that initial primary cell heterogeneity, random sampling, time in culture, and even mild differences in phenotype-specific fitness can contribute substantially to dynamic diversity in populations of nominally clonal cells.
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http://dx.doi.org/10.7554/eLife.62586DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7867410PMC
January 2021

Clinical Readiness Program: Refocusing the Military Health System.

Mil Med 2021 01;186(Suppl 1):32-39

Department of Surgery at Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA.

Introduction: The Military Health System serves to globally provide health services and trained medical forces. Military providers possess variable levels of deployment preparedness. The aim of the Clinical Readiness Program is to develop and assess the knowledge, skills, and abilities (KSAs) needed for combat casualty care.

Methods: The Clinical Readiness Program developed a KSA metric for general and orthopedic surgery. The KSA methodology underwent a proof of concept in six medical treatment facilities.

Results: The KSA metric feasibly quantifies the combat relevance of surgical practice. Orthopedic surgeons are more likely than general surgeons to meet the threshold. Medical treatment facilities do not provide enough demand for general surgery services to achieve readiness.

Conclusion: The Clinical Readiness Program identifies imbalances between the health care delivery and readiness missions. To close the readiness gap, the Military Health System needs to recapture high KSA value procedures, expand access to care, and/or partner with civilian institutions.
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http://dx.doi.org/10.1093/milmed/usaa385DOI Listing
January 2021

Selection of Cytochrome Mutants Is Rare among Plasmodium falciparum Patients Failing Treatment with Atovaquone-Proguanil in Cambodia.

Antimicrob Agents Chemother 2021 02 17;65(3). Epub 2021 Feb 17.

Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.

Atovaquone-proguanil remains effective against multidrug-resistant in Southeast Asia, but resistance is mediated by a single point mutation in cytochrome () that can arise during treatment. Among 14 atovaquone-proguanil treatment failures in a clinical trial in Cambodia, only one recrudescence harbored the mutation Y268C. Deep sequencing did not detect the mutation at baseline or in the first 3 days of treatment, suggesting that it arose Further sequencing across similarly found no low-frequency mutations that were up-selected from baseline to recrudescence. Copy number amplification in dihydroorotate dehydrogenase (DHODH) and cytb as markers of atovaquone tolerance was also absent. mutation played a minor role in atovaquone-proguanil treatment failures in an active comparator clinical trial.
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http://dx.doi.org/10.1128/AAC.01249-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8092515PMC
February 2021

DHFR and DHPS Mutations Are Associated With HIV-1 Co-Infection and a Novel DHPS Mutation I504T Is Identified in Western Kenya.

Front Cell Infect Microbiol 2020 26;10:600112. Epub 2020 Nov 26.

Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID, United States.

Antifolate resistance is significant in Kenya and presumed to result from extensive use and cross-resistance between antifolate antimalarials and antibiotics, including cotrimoxazole/Bactrim used for HIV-1 chemotherapy. However, little is known about antifolate-resistant malaria in the context of newly diagnosed HIV-1 co-infection prior to administration of HIV-1 chemotherapy. Blood samples from a cross-sectional study of asymptomatic adult Kenyans enrolled during voluntary HIV testing were analyzed by PCR for spp. More than 95% of volunteers with identifiable parasite species (132 HIV-1 co-infected) were infected with alone or with and/or . Deep sequencing was used to screen for mutations in (N51I, C59R, S108N, I164L) and (S436H, A437G, K540E, A581G) from 1133 volunteers. Individual mutations in DHPS but not DHFR correlated with HIV-1 status. DHFR haplotype diversity was significantly different among volunteers by gender and HIV-1 status. DHPS haplotype diversity by HIV-1 status was significantly different between volunteers paired by age and gender, indicating that patterns of resistance were independent of these variables. Molecular simulations for a novel DHPS mutation (I504T) suggested that the mutated protein has increased affinity for the endogenous ligand DHPPP and decreased affinity for drug binding. A sub-group of monoclonal infections revealed that age and parasitemia were not correlated and enabled identification of a rare septuple-mutant haplotype (IRNL-HGEA). In our study, adult Kenyans newly diagnosed with HIV-1 infection were predominantly infected with moderately resistant , with patterns of infecting parasite genotypes significantly associated with HIV-1 status. Together with the discovery of DHPS I504T, these data indicate that antifolate resistance continues to evolve in Kenya. Further, they highlight the need to understand the effects of associated mutations on both fitness and resistance of in the context of HIV-1 co-infection to better inform treatment for asymptomatic malaria.
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http://dx.doi.org/10.3389/fcimb.2020.600112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7725689PMC
November 2020

Airflows inside passenger cars and implications for airborne disease transmission.

Sci Adv 2021 01 1;7(1). Epub 2021 Jan 1.

Center for Fluid Mechanics, Brown University, Providence, RI 02912, USA.

Transmission of highly infectious respiratory diseases, including SARS-CoV-2, is facilitated by the transport of exhaled droplets and aerosols that can remain suspended in air for extended periods of time. A passenger car cabin represents one such situation with an elevated risk of pathogen transmission. Here, we present results from numerical simulations to assess how the in-cabin microclimate of a car can potentially spread pathogenic species between occupants for a variety of open and closed window configurations. We estimate relative concentrations and residence times of a noninteracting, passive scalar-a proxy for infectious particles-being advected and diffused by turbulent airflows inside the cabin. An airflow pattern that travels across the cabin, farthest from the occupants, can potentially reduce the transmission risk. Our findings reveal the complex fluid dynamics during everyday commutes and nonintuitive ways in which open windows can either increase or suppress airborne transmission.
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http://dx.doi.org/10.1126/sciadv.abe0166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7775778PMC
January 2021

Deep Gene Sequence Cluster Analyses of Multi-Virus-Infected Mucosal Tissue Reveal Enhanced Transmission of Acute HIV-1.

J Virol 2021 01 13;95(3). Epub 2021 Jan 13.

Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada

Exposure of the genital mucosa to a genetically diverse viral swarm from the donor HIV-1 can result in breakthrough and systemic infection by a single transmitted/founder (TF) virus in the recipient. The highly diverse HIV-1 envelope (Env) in this inoculating viral swarm may have a critical role in transmission and subsequent immune response. Thus, chronic (Env) and acute (Env) Env chimeric HIV-1 were tested using multivirus competition assays in human mucosal penile and cervical tissues. Viral competition analysis revealed that Env viruses resided and replicated mainly in the tissue, while Env viruses penetrated the human tissue and established infection of CD4 T cells more efficiently. Analysis of the replication fitness, as tested in peripheral blood mononuclear cells (PBMCs), showed similar replication fitness of Env and Env viruses, which did not correlate with transmission fitness in penile tissue. Further, we observed that chimeric Env viruses with higher replication in genital mucosal tissue (chronic Env viruses) had higher binding affinity to C-type lectins. Data presented herein suggest that the inoculating HIV-1 may be sequestered in the genital mucosal tissue (represented by chronic Env HIV-1) but that a single HIV-1 clone (e.g., acute Env HIV-1) can escape this trapped replication for systemic infection. During heterosexual HIV-1 transmission, a genetic bottleneck occurs in the newly infected individual as the virus passes from the mucosa, leading to systemic infection with a single transmitted HIV-1 clone in the recipient. This bottleneck in the recipient has just been described (K. Klein et al., PLoS Pathog 14:e1006754, https://doi.org/10.1371/journal.ppat.1006754), and the mechanisms involved in this selection process have not been elucidated. However, understanding mucosal restriction is of the utmost importance for understanding dynamics of infections and for designing focused vaccines. Using our human penile and cervical mucosal tissue models for mixed HIV infections, we provide evidence that HIV-1 from acute/early infection, compared to that from chronic infection, can more efficiently traverse the mucosal epithelium and be transmitted to T cells, suggesting higher transmission fitness. This study focused on the role of the HIV-1 envelope in transmission and provides strong evidence that HIV transmission may involve breaking the mucosal lectin trap.
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http://dx.doi.org/10.1128/JVI.01737-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7925087PMC
January 2021

Describing the current status of Plasmodium falciparum population structure and drug resistance within mainland Tanzania using molecular inversion probes.

Mol Ecol 2021 01 29;30(1):100-113. Epub 2020 Nov 29.

National Institute for Medical Research, Dar es Salaam, Tanzania.

High-throughput Plasmodium genomic data is increasingly useful in assessing prevalence of clinically important mutations and malaria transmission patterns. Understanding parasite diversity is important for identification of specific human or parasite populations that can be targeted by control programmes, and to monitor the spread of mutations associated with drug resistance. An up-to-date understanding of regional parasite population dynamics is also critical to monitor the impact of control efforts. However, this data is largely absent from high-burden nations in Africa, and to date, no such analysis has been conducted for malaria parasites in Tanzania countrywide. To this end, over 1,000 P. falciparum clinical isolates were collected in 2017 from 13 sites in seven administrative regions across Tanzania, and parasites were genotyped at 1,800 variable positions genome-wide using molecular inversion probes. Population structure was detectable among Tanzanian P. falciparum parasites, approximately separating parasites from the northern and southern districts and identifying genetically admixed populations in the north. Isolates from nearby districts were more likely to be genetically related compared to parasites sampled from more distant districts. Known drug resistance mutations were seen at increased frequency in northern districts (including two infections carrying pfk13-R561H), and additional variants with undetermined significance for antimalarial resistance also varied by geography. Malaria Indicator Survey (2017) data corresponded with genetic findings, including average region-level complexity-of-infection and malaria prevalence estimates. The parasite populations identified here provide important information on extant spatial patterns of genetic diversity of Tanzanian parasites, to which future surveys of genetic relatedness can be compared.
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http://dx.doi.org/10.1111/mec.15706DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8088766PMC
January 2021

Therapeutic Efficacy of Artemether-Lumefantrine for Uncomplicated Falciparum Malaria in Northern Zambia.

Am J Trop Med Hyg 2020 12 15;103(6):2224-2232. Epub 2020 Oct 15.

Macha Research Trust, Macha, Zambia.

Artemether-lumefantrine (AL) is a first-line agent for uncomplicated malaria caused by . The WHO recommends periodic therapeutic efficacy studies of antimalarial drugs for the detection of malaria parasite drug resistance and to inform national malaria treatment policies. We conducted a therapeutic efficacy study of AL in a high malaria transmission region of northern Zambia from December 2014 to July 2015. One hundred children of ages 6 to 59 months presenting to a rural health clinic with uncomplicated falciparum malaria were admitted for treatment with AL (standard 6-dose regimen) and followed weekly for 5 weeks. Parasite counts were taken every 6 hours during treatment to assess parasite clearance. Recurrent episodes during follow-up ( = 14) were genotyped to distinguish recrudescence from reinfection and to identify drug resistance single nucleotide polymorphisms (SNPs) and multidrug resistance protein 1 () copy number variation. Day 7 lumefantrine concentrations were measured for correspondence with posttreatment reinfection. All children who completed the parasite clearance portion of the study ( = 94) were microscopy-negative by 72 hours. The median parasite elimination half-life was 2.7 hours (interquartile range: 2.1-3.3). Genotype-corrected therapeutic efficacy was 98.8% (95% CI: 97.6-100). Purported artemisinin and lumefantrine drug resistance SNPs in , , and were detected but did not correlate with parasite recurrence, nor did day 7 lumefantrine concentrations. In summary, AL was highly effective for the treatment of uncomplicated falciparum malaria in northern Zambia during the study period. The high incidence of recurrent parasitemia was consistent with reinfection due to high, perennial malaria transmission.
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http://dx.doi.org/10.4269/ajtmh.20-0852DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7695049PMC
December 2020

Convalescent plasma for patients with severe COVID-19: a matched cohort study.

Clin Infect Dis 2020 Oct 10. Epub 2020 Oct 10.

Division of Infectious Diseases, Warren Alpert Medical School of Brown University, Providence, RI, USA.

Background: The efficacy of convalescent plasma (CP) for the treatment of COVID-19 remains unclear.

Methods: In a matched cohort analysis of hospitalized patients with severe COVID-19, the impact of CP treatment on in-hospital mortality was evaluated using univariate and multivariate Cox proportional-hazards models, and the impact of CP treatment on time to hospital discharge was assessed using a stratified log-rank analysis.

Results: 64 patients who received CP a median of 7 days after symptom onset were compared to a matched control group of 177 patients. The incidence of in-hospital mortality was 12.5% and 15.8% in the CP and control groups, respectively (p = 0.52). There was no significant difference in the risk of in-hospital mortality between the two groups (adjusted hazard ratio [aHR] 0.93, 95% confidence interval [CI] 0.39 - 2.20). The overall rate of hospital discharge was not significantly different between the two groups (rate ratio [RR] 1.28, 95% CI 0.91 - 1.81), although there was a significantly increased rate of hospital discharge among patients 65-years-old or greater who received CP (RR 1.86, 95% CI 1.03 - 3.36). There was a greater than expected frequency of transfusion reactions in the CP group (2.8% reaction rate observed per unit transfused).

Conclusions: We did not demonstrate a significant difference in risk of mortality or rate of hospital discharge between the CP and control groups. There was a signal for improved outcomes among the elderly, and further adequately powered randomized studies should target this subgroup when assessing the efficacy of CP treatment.
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http://dx.doi.org/10.1093/cid/ciaa1548DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7665324PMC
October 2020

Sensitive, highly multiplexed sequencing of microhaplotypes from the Plasmodium falciparum heterozygome.

J Infect Dis 2020 Aug 25. Epub 2020 Aug 25.

EPPIcenter research program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA.

Background: Targeted next generation sequencing offers the potential for consistent, deep coverage of information rich genomic regions to characterize polyclonal Plasmodium falciparum infections. However, methods to identify and sequence these genomic regions are currently limited.

Methods: A bioinformatic pipeline and multiplex methods were developed to identify and simultaneously sequence 100 targets and applied to dried blood spot (DBS) controls and field isolates from Mozambique. For comparison, WGS data were generated for the same controls.

Results: Using publicly available genomes, 4465 high diversity genomic regions suited for targeted sequencing were identified, representing the P. falciparum heterozygome. For this study, 93 microhaplotypes with high diversity (median HE = 0.7) were selected along with 7 drug resistance loci. The sequencing method achieved very high coverage (median 99%), specificity (99.8%) and sensitivity (90% for haplotypes with 5% within sample frequency in DBS with 100 parasites/µL). In silico analyses revealed that microhaplotypes provided much higher resolution to discriminate related from unrelated polyclonal infections than biallelic SNP barcodes.

Discussion: The bioinformatic and laboratory methods outlined here provide a flexible tool for efficient, low-cost, high throughput interrogation of the P. falciparum genome, and can be tailored to simultaneously address multiple questions of interest in various epidemiological settings.
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http://dx.doi.org/10.1093/infdis/jiaa527DOI Listing
August 2020

Successful recovery from COVID-19 in three kidney transplant recipients who received convalescent plasma therapy.

Transpl Infect Dis 2021 Feb 3;23(1):e13451. Epub 2020 Sep 3.

Division of Infectious Diseases, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA.

Novel coronavirus disease 2019 (COVID-19) is a highly infectious, rapidly spreading viral disease that typically presents with greater severity in patients with underlying medical conditions or those who are immunosuppressed. We present a novel case series of three kidney transplant recipients with COVID-19 who recovered after receiving COVID-19 convalescent plasma (CCP) therapy. Physicians should be aware of this potentially useful treatment option. Larger clinical registries and randomized clinical trials should be conducted to further explore the clinical and allograft outcomes associated with CCP use in this population.
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http://dx.doi.org/10.1111/tid.13451DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7460867PMC
February 2021

Spatial and epidemiological drivers of malaria among adults in the Democratic Republic of the Congo.

BMJ Glob Health 2020 06;5(6)

Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.

Background: Adults are frequently infected with malaria and may serve as a reservoir for further transmission, yet we know relatively little about risk factors for adult infections. In this study, we assessed malaria risk factors among adults using samples from the nationally representative, cross-sectional 2013-2014 Demographic and Health Survey (DHS) conducted in the Democratic Republic of the Congo (DRC). We further explored differences in risk factors by urbanicity.

Methods: infection was determined by PCR. Covariates were drawn from the DHS to model individual, community and environmental-level risk factors for infection. Additionally, we used deep sequencing data to estimate the community-level proportions of drug-resistant infections and included these estimates as potential risk factors. All identified factors were assessed for differences in associations by urbanicity.

Results: A total of 16 126 adults were included. Overall prevalence of malaria was 30.3% (SE=1.1) by PCR; province-level prevalence ranged from 6.7% to 58.3%. Only 17% of individuals lived in households with at least one bed-net for every two people, as recommended by the WHO. Protective factors included increasing within-household bed-net coverage (Prevalence Ratio=0.85, 95% CI=0.76-0.95) and modern housing (PR=0.58, 95% CI=0.49-0.69). Community-level protective factors included increased median wealth (PR=0.87, 95% CI=0.83-0.92). Education, wealth, and modern housing showed protective associations in cities but not in rural areas.

Conclusions: The DRC continues to suffer from a high burden of malaria; interventions that target high-risk groups and sustained investment in malaria control are sorely needed. Areas of high prevalence should be prioritised for interventions to target the largest reservoirs for further transmission.
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http://dx.doi.org/10.1136/bmjgh-2020-002316DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7326263PMC
June 2020

Epstein-Barr Virus Genomes Reveal Population Structure and Type 1 Association with Endemic Burkitt Lymphoma.

J Virol 2020 08 17;94(17). Epub 2020 Aug 17.

Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA

Endemic Burkitt lymphoma (eBL), the most prevalent pediatric cancer in sub-Saharan Africa, is distinguished by its inclusion of Epstein-Barr virus (EBV). In order to better understand the impact of EBV variation in eBL tumorigenesis, we improved viral DNA enrichment methods and generated a total of 98 new EBV genomes from both eBL cases ( = 58) and healthy controls ( = 40) residing in the same geographic region in Kenya. Using our unbiased methods, we found that EBV type 1 was significantly more prevalent in eBL patients (74.5%) than in healthy children (47.5%) (odds ratio = 3.24, 95% confidence interval = 1.36 to 7.71, = 0.007), as opposed to similar proportions in both groups. Controlling for EBV type, we also performed a genome-wide association study identifying six nonsynonymous variants in the genes EBNA1, EBNA2, BcLF1, and BARF1 that were enriched in eBL patients. In addition, viruses isolated from plasma of eBL patients were identical to their tumor counterparts consistent with circulating viral DNA originating from the tumor. We also detected three intertypic recombinants carrying type 1 EBNA2 and type 2 EBNA3 regions, as well as one novel genome with a 20-kb deletion, resulting in the loss of multiple lytic and virion genes. Comparing EBV types, viral genes displayed differential variation rates as type 1 appeared to be more divergent, while type 2 demonstrated novel substructures. Overall, our findings highlight the complexities of the EBV population structure and provide new insight into viral variation, potentially deepening our understanding of eBL oncogenesis. Improved viral enrichment methods conclusively demonstrate EBV type 1 to be more prevalent in eBL patients than in geographically matched healthy controls, which previously underrepresented the prevalence of EBV type 2. Genome-wide association analysis between cases and controls identifies six eBL-associated nonsynonymous variants in EBNA1, EBNA2, BcLF1, and BARF1 genes. Analysis of population structure reveals that EBV type 2 exists as two genomic subgroups and was more commonly found in female than in male eBL patients.
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http://dx.doi.org/10.1128/JVI.02007-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7431785PMC
August 2020

A New Hope for CD56CD16 NK Cells as Unconventional Cytotoxic Mediators: An Adaptation to Chronic Diseases.

Front Cell Infect Microbiol 2020 21;10:162. Epub 2020 Apr 21.

Division of Infectious Diseases, Department of Medicine, University of Massachusetts, Worcester, MA, United States.

Natural Killer (NK) cells play an essential role in antiviral and anti-tumoral immune responses. In peripheral blood, NK cells are commonly classified into two major subsets: CD56CD16 and CD56CD16 despite the characterization of a CD56CD16 subset 25 years ago. Since then, several studies have described the prevalence of an CD56CD16 NK cell subset in viral non-controllers as the basis for their NK cell dysfunction. However, the mechanistic basis for their cytotoxic impairment is unclear. Recently, using a strict flow cytometry gating strategy to exclude monocytes, we reported an accumulation of CD56CD16 NK cells in malaria-exposed children and pediatric cancer patients diagnosed with endemic Burkitt lymphoma (eBL). Here, we use live-sorted cells, histological staining, bulk RNA-sequencing and flow cytometry to confirm that this CD56CD16 NK cell subset has the same morphological features as the other NK cell subsets and a similar transcriptional profile compared to CD56CD16 NK cells with only 120 genes differentially expressed (fold change of 1.5, < 0.01 and FDR<0.05) out of 9235 transcripts. CD56CD16 NK cells have a distinct profile with significantly higher expression of (perforin 2), (CD16b), , and (CD32A and B) as well as , and (PD-1), whereas Interleukin 18 (IL18) receptor genes ( and ), cytotoxic genes such as (NKp80) and (NKp46), and inhibitory (TIM-3) are significantly down-regulated compared to CD56CD16 NK cells. Together, these data confirm that CD56CD16 cells are legitimate NK cells, yet their transcriptional and protein expression profiles suggest their cytotoxic potential is mediated by pathways reliant on antibodies such as antibody-dependent cell cytotoxicity (ADCC), antibody-dependent respiratory burst (ADRB), and enhanced by complement receptor 3 (CR3) and FAS/FASL interaction. Our findings support the premise that chronic diseases induce NK cell modifications that circumvent proinflammatory mediators involved in direct cytotoxicity. Therefore, individuals with such altered NK cell profiles may respond differently to NK-mediated immunotherapies, infections or vaccines depending on which cytotoxic mechanisms are being engaged.
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http://dx.doi.org/10.3389/fcimb.2020.00162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7186373PMC
April 2020

Case reduction and cost-effectiveness of the RTS,S/AS01 malaria vaccine alongside bed nets in Lilongwe, Malawi.

Vaccine 2020 05 30;38(25):4079-4087. Epub 2020 Apr 30.

Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA. Electronic address:

Background: RTS,S/AS01, the most advanced vaccine against malaria, is now undergoing pilot implementation in Malawi, Ghana, and Kenya where an estimated 360,000 children will be vaccinated each year. In this study we evaluate RTS,S/AS01 alongside bed net use and estimate cost-effectiveness.

Methods: RTS,S/AS01 phase III trial and bed net prevalence data were used to determine the effect of vaccination in the urban/periurban and rural areas of Lilongwe, Malawi. Cost data were used to calculate the cost-effectiveness of various interventions over three years.

Findings: Since bed nets reduce malaria incidence and homogeneous vaccine efficacy was assumed, participants without bed nets received greater relative benefit from vaccination with RTS,S/AS01 than participants with bed nets. Similarly, since malaria incidence in rural Lilongwe is higher than in urban Lilongwe, the impact and cost-effectiveness of vaccine interventions is increased in rural areas. In rural Lilongwe, we estimated that vaccinating one child without a bed net would prevent 2·59 (1·62 to 3·38) cases of malaria over three years, corresponding to a cost of $10·08 (7·71 to 16·13) per case averted. Alternatively, vaccinating one child with a bed net would prevent 1·59 (0·87 to 2·57) cases, corresponding to $16·43 (10·16 to 30·06) per case averted. Providing RTS,S/AS01 to 30,000 children in rural Lilongwe was estimated to cost $782,400 and to prevent 58,611 (35,778 to 82,932) cases of malaria over a three-year period. Joint interventions providing both vaccination and bed nets (to those without them) were estimated to prevent additional cases of malaria and to be similarly cost-effective, compared to vaccine-only interventions.

Interpretation: To maximize malaria prevention, vaccination and bed net distribution programs could be integrated.

Funding: Impacts of Environment, Host Genetics and Antigen Diversity on Malaria Vaccine Efficacy (1R01AI137410-01).
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http://dx.doi.org/10.1016/j.vaccine.2020.04.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7282487PMC
May 2020

The impact of antimalarial resistance on the genetic structure of Plasmodium falciparum in the DRC.

Nat Commun 2020 04 30;11(1):2107. Epub 2020 Apr 30.

Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, USA.

The Democratic Republic of the Congo (DRC) harbors 11% of global malaria cases, yet little is known about the spatial and genetic structure of the parasite population in that country. We sequence 2537 Plasmodium falciparum infections, including a nationally representative population sample from DRC and samples from surrounding countries, using molecular inversion probes - a high-throughput genotyping tool. We identify an east-west divide in haplotypes known to confer resistance to chloroquine and sulfadoxine-pyrimethamine. Furthermore, we identify highly related parasites over large geographic distances, indicative of gene flow and migration. Our results are consistent with a background of isolation by distance combined with the effects of selection for antimalarial drug resistance. This study provides a high-resolution view of parasite genetic structure across a large country in Africa and provides a baseline to study how implementation programs may impact parasite populations.
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http://dx.doi.org/10.1038/s41467-020-15779-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7192906PMC
April 2020

Deployment of convalescent plasma for the prevention and treatment of COVID-19.

J Clin Invest 2020 06;130(6):2757-2765

Division of Transfusion Medicine, Department of Pathology.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), has spurred a global health crisis. To date, there are no proven options for prophylaxis for those who have been exposed to SARS-CoV-2, nor therapy for those who develop COVID-19. Immune (i.e., "convalescent") plasma refers to plasma that is collected from individuals following resolution of infection and development of antibodies. Passive antibody administration through transfusion of convalescent plasma may offer the only short-term strategy for conferring immediate immunity to susceptible individuals. There are numerous examples in which convalescent plasma has been used successfully as postexposure prophylaxis and/or treatment of infectious diseases, including other outbreaks of coronaviruses (e.g., SARS-1, Middle East respiratory syndrome [MERS]). Convalescent plasma has also been used in the COVID-19 pandemic; limited data from China suggest clinical benefit, including radiological resolution, reduction in viral loads, and improved survival. Globally, blood centers have robust infrastructure for undertaking collections and constructing inventories of convalescent plasma to meet the growing demand. Nonetheless, there are nuanced challenges, both regulatory and logistical, spanning donor eligibility, donor recruitment, collections, and transfusion itself. Data from rigorously controlled clinical trials of convalescent plasma are also few, underscoring the need to evaluate its use objectively for a range of indications (e.g., prevention vs. treatment) and patient populations (e.g., age, comorbid disease). We provide an overview of convalescent plasma, including evidence of benefit, regulatory considerations, logistical work flow, and proposed clinical trials, as scale-up is brought underway to mobilize this critical resource.
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http://dx.doi.org/10.1172/JCI138745DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7259988PMC
June 2020

Kaposi Sarcoma-Associated Herpesvirus Infection and Endemic Burkitt Lymphoma.

J Infect Dis 2020 06;222(1):111-120

Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA.

Background: Endemic Burkitt lymphoma (eBL) is associated with Epstein-Barr virus (EBV) and Plasmodium falciparum malaria coinfections. However, the role of Kaposi sarcoma-associated herpesvirus (KSHV), also endemic in Africa, has not been evaluated as a cofactor in eBL pathogenesis.

Methods: Multiplexed seroprofiles for EBV, malaria, and KSHV were generated for 266 eBL patients, 78 non-eBL cancers, and 202 healthy children. KSHV and EBV loads were quantified by PCR.

Results: KSHV seroprevalence did not differ by study group but was associated with age. Seropositivity, defined by K8.1/LANA or in combination with 5 other KSHV antigens (ORF59, ORF65, ORF61, ORF38, and K5) was associated with antimalarial antibody levels to AMA1 (odds ratio [OR], 2.41, P < .001; OR, 2.07, P < .001) and MSP1 (OR, 2.41, P = .0006; OR, 5.78, P < .001), respectively. KSHV loads did not correlate with antibody levels nor differ across groups but were significantly lower in children with detectable EBV viremia (P = .014).

Conclusions: Although KSHV-EBV dual infection does not increase eBL risk, EBV appears to suppress reactivation of KSHV while malaria exposure is associated with KSHV infection and/or reactivation. Both EBV and malaria should, therefore, be considered as potential effect modifiers for KSHV-associated cancers in sub-Saharan Africa.
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http://dx.doi.org/10.1093/infdis/jiaa060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7296861PMC
June 2020

Combining Citizen Science and Genomics to Investigate Tick, Pathogen, and Commensal Microbiome at Single-Tick Resolution.

Front Genet 2019 21;10:1322. Epub 2020 Jan 21.

Bioinformatics and Integrative Biology Program, University of Massachusetts Medical School, Worcester, MA, United States.

The prevalence of tickborne diseases worldwide is increasing virtually unchecked due to the lack of effective control strategies. The transmission dynamics of tickborne pathogens are influenced by the tick microbiome, tick co-infection with other pathogens, and environmental features. Understanding this complex system could lead to new strategies for pathogen control, but will require large-scale, high-resolution data. Here, we introduce Project Acari, a citizen science-based project to assay, at single-tick resolution, species, pathogen infection status, microbiome profile, and environmental conditions of tens of thousands of ticks collected from numerous sites across the United States. In the first phase of the project, we collected more than 2,400 ticks wild-caught by citizen scientists and developed high-throughput methods to process and sequence them individually. Applying these methods to 192 ticks collected in a region with a high incidence of Lyme disease, we found that 62% were colonized by , the Lyme disease pathogen. In contrast to previous reports, we did not find an association between the microbiome diversity of a tick and its probability of carrying . However, we did find undescribed associations between carriage and the presence of specific microbial taxa within individual ticks. Our findings underscore the power of coupling citizen science with high-throughput processing to reveal pathogen dynamics. Our approach can be extended for massively parallel screening of individual ticks, offering a powerful tool to elucidate the ecology of tickborne disease and to guide pathogen-control initiatives.
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http://dx.doi.org/10.3389/fgene.2019.01322DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6985576PMC
January 2020

Falciparum malaria from coastal Tanzania and Zanzibar remains highly connected despite effective control efforts on the archipelago.

Malar J 2020 Jan 28;19(1):47. Epub 2020 Jan 28.

Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.

Background: Tanzania's Zanzibar archipelago has made significant gains in malaria control over the last decade and is a target for malaria elimination. Despite consistent implementation of effective tools since 2002, elimination has not been achieved. Importation of parasites from outside of the archipelago is thought to be an important cause of malaria's persistence, but this paradigm has not been studied using modern genetic tools.

Methods: Whole-genome sequencing (WGS) was used to investigate the impact of importation, employing population genetic analyses of Plasmodium falciparum isolates from both the archipelago and mainland Tanzania. Ancestry, levels of genetic diversity and differentiation, patterns of relatedness, and patterns of selection between these two populations were assessed by leveraging recent advances in deconvolution of genomes from polyclonal malaria infections.

Results: Significant decreases in the effective population sizes were inferred in both populations that coincide with a period of decreasing malaria transmission in Tanzania. Identity by descent analysis showed that parasites in the two populations shared long segments of their genomes, on the order of 5 cM, suggesting shared ancestry within the last 10 generations. Even with limited sampling, two of isolates between the mainland and Zanzibar were identified that are related at the expected level of half-siblings, consistent with recent importation.

Conclusions: These findings suggest that importation plays an important role for malaria incidence on Zanzibar and demonstrate the value of genomic approaches for identifying corridors of parasite movement to the island.
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http://dx.doi.org/10.1186/s12936-020-3137-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6988337PMC
January 2020

Sensitive detection of EBV microRNAs across cancer spectrum reveals association with decreased survival in adult acute myelocytic leukemia.

Sci Rep 2019 12 30;9(1):20321. Epub 2019 Dec 30.

Department of Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA.

Epstein Barr virus (EBV) is the etiologic agent involved in numerous human cancers. After infecting the host, EBV establishes a latent infection, with low levels of messenger RNA (mRNA) and protein expression, evolved to evade immune recognition. Conversely, EBV microRNAs (miRNA) are expressed ubiquitously and abundantly within infected cells. Their role in tumor biology and clinical outcomes across the spectrum of cancer is not fully explained. Here, we applied our bioinformatics pipeline for quantitative EBV miRNA detection to examine sequencing data of 8,955 individual tumor samples across 27 tumor types representing the breadth of cancer. We uncover an association of intermediate levels of viral miRNA with decreased survival in adult acute myeloid leukemia (AML) patients (P = 0.00013). Prognostic modeling of this association suggests that increased EBV miRNA levels represent an independent risk factor for poor patient outcomes. Furthermore, we explore differences in expression between elevated and absent viral miRNA loads in adult AML tumors finding that EBV positivity was associated with proinflammatory signals. Together, given no associations were found for pediatric AML, our analyses suggests EBV positivity has the potential for being a prognostic biomarker and might represent a surrogate measure related to immune impairment in adult patients.
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http://dx.doi.org/10.1038/s41598-019-56472-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6937232PMC
December 2019

The changing landscape of Plasmodium falciparum drug resistance in the Democratic Republic of Congo.

BMC Infect Dis 2019 Oct 22;19(1):872. Epub 2019 Oct 22.

Medical Research Council Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK.

Background: Drug resistant malaria is a growing concern in the Democratic Republic of the Congo (DRC), where previous studies indicate that parasites resistant to sulfadoxine/pyrimethamine or chloroquine are spatially clustered. This study explores longitudinal changes in spatial patterns to understand how resistant malaria may be spreading within the DRC, using samples from nation-wide population-representative surveys.

Methods: We selected 552 children with PCR-detectable Plasmodium falciparum infection and identified known variants in the pfdhps and pfcrt genes associated with resistance. We compared the proportion of mutant parasites in 2013 to those previously reported from adults in 2007, and identified risk factors for carrying a resistant allele using multivariate mixed-effects modeling. Finally, we fit a spatial-temporal model to the observed data, providing smooth allele frequency estimates over space and time.

Results: The proportion of co-occurring pfdhps K540E/A581G mutations increased by 16% between 2007 and 2013. The spatial-temporal model suggests that the spatial range of the pfdhps double mutants expanded over time, while the prevalence and range of pfcrt mutations remained steady.

Conclusions: This study uses population-representative samples to describe the changing landscape of SP resistance within the DRC, and the persistence of chloroquine resistance. Vigilant molecular surveillance is critical for controlling the spread of resistance.
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http://dx.doi.org/10.1186/s12879-019-4523-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6805465PMC
October 2019

The whole-genome landscape of Burkitt lymphoma subtypes.

Blood 2019 11;134(19):1598-1607

Department of Immunology and.

Burkitt lymphoma (BL) is an aggressive, MYC-driven lymphoma comprising 3 distinct clinical subtypes: sporadic BLs that occur worldwide, endemic BLs that occur predominantly in sub-Saharan Africa, and immunodeficiency-associated BLs that occur primarily in the setting of HIV. In this study, we comprehensively delineated the genomic basis of BL through whole-genome sequencing (WGS) of 101 tumors representing all 3 subtypes of BL to identify 72 driver genes. These data were additionally informed by CRISPR screens in BL cell lines to functionally annotate the role of oncogenic drivers. Nearly every driver gene was found to have both coding and non-coding mutations, highlighting the importance of WGS for identifying driver events. Our data implicate coding and non-coding mutations in IGLL5, BACH2, SIN3A, and DNMT1. Epstein-Barr virus (EBV) infection was associated with higher mutation load, with type 1 EBV showing a higher mutational burden than type 2 EBV. Although sporadic and immunodeficiency-associated BLs had similar genetic profiles, endemic BLs manifested more frequent mutations in BCL7A and BCL6 and fewer genetic alterations in DNMT1, SNTB2, and CTCF. Silencing mutations in ID3 were a common feature of all 3 subtypes of BL. In vitro, mass spectrometry-based proteomics demonstrated that the ID3 protein binds primarily to TCF3 and TCF4. In vivo knockout of ID3 potentiated the effects of MYC, leading to rapid tumorigenesis and tumor phenotypes consistent with those observed in the human disease.
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http://dx.doi.org/10.1182/blood.2019001880DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6871305PMC
November 2019

Plasmodium vivax chloroquine resistance links to pvcrt transcription in a genetic cross.

Nat Commun 2019 09 20;10(1):4300. Epub 2019 Sep 20.

Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Campbell University, Buies Creek, NC, 27506, USA.

Mainstay treatment for Plasmodium vivax malaria has long relied on chloroquine (CQ) against blood-stage parasites plus primaquine against dormant liver-stage forms (hypnozoites), however drug resistance confronts this regimen and threatens malaria control programs. Understanding the basis of P. vivax chloroquine resistance (CQR) will inform drug discovery and malaria control. Here we investigate the genetics of P. vivax CQR by a cross of parasites differing in drug response. Gametocytogenesis, mosquito infection, and progeny production are performed with mixed parasite populations in nonhuman primates, as methods for P. vivax cloning and in vitro cultivation remain unavailable. Linkage mapping of progeny surviving >15 mg/kg CQ identifies a 76 kb region in chromosome 1 including pvcrt, an ortholog of the Plasmodium falciparum CQR transporter gene. Transcriptional analysis supports upregulated pvcrt expression as a mechanism of CQR.
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http://dx.doi.org/10.1038/s41467-019-12256-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6754410PMC
September 2019

Pooled Deep Sequencing of Drug Resistance Loci from Parasites across Ethiopia.

Am J Trop Med Hyg 2019 11;101(5):1139-1143

Ethiopian Public Health Institute, Addis Ababa, Ethiopia.

Although Ethiopia has an overall lower prevalence of among countries in Africa, the emergence of drug resistance could seriously hinder elimination efforts. Using samples collected from five therapeutic efficacy studies conducted in 2007-11, we evaluated the prevalence of putative drug resistance mutations in the , , and genes at the time of those studies, as well as the gene for genetic relatedness using a pooled amplicon deep sequencing approach. Among all sites, the gene showed no mutations, whereas the CVIET genotype was fixed in all populations. By contrast, the gene demonstrated frequencies of resistant genotypes ranging from 10 to 100% at amino acid position 86 and from 0% to 57.8% at amino acid position 1246. Although we observed a low degree of haplotype sharing between sites, we did observe considerable haplotype sharing within sites over time. This suggests that populations in Ethiopia are isolated and able to persist through time.
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http://dx.doi.org/10.4269/ajtmh.19-0142DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6838589PMC
November 2019

Genetic Variation Within the Gene Modulates Susceptibility to Type 1 Diabetes in HLA-DR3 Homozygotes.

Diabetes 2019 07 8;68(7):1523-1527. Epub 2019 Apr 8.

Division of Endocrinology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA

Type 1 diabetes (T1D) involves the interaction of multiple gene variants, environmental factors, and immunoregulatory dysfunction. Major T1D genetic risk loci encode HLA-DR and -DQ. Genetic heterogeneity and linkage disequilibrium in the highly polymorphic HLA region confound attempts to identify additional T1D susceptibility loci. To minimize HLA heterogeneity, T1D patients ( = 365) and control subjects ( = 668) homozygous for the HLA-DR3 high-risk haplotype were selected from multiple large T1D studies and examined to identify new T1D susceptibility loci using molecular inversion probe sequencing technology. We report that risk for T1D in HLA-DR3 homozygotes is increased significantly by a previously unreported haplotype of three single nucleotide polymorphisms (SNPs) within the first intron of The homozygous risk haplotype has an odds ratio of 4.65 relative to the protective homozygous haplotype in our sample. Individually, these SNPs reportedly function as "expression quantitative trait loci," modulating and - expression. From our analysis of available data, we conclude that the tri-SNP haplotype within may modulate class II expression, suggesting that increased T1D risk could be attributable to regulated expression of class II genes. These findings could help clarify the role of HLA in T1D susceptibility and improve diabetes risk assessment, particularly in high-risk HLA-DR3 homozygous individuals.
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http://dx.doi.org/10.2337/db18-1128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6609989PMC
July 2019

Correction to: Mapping malaria by combining parasite genomic and epidemiologic data.

BMC Med 2018 12 28;16(1):241. Epub 2018 Dec 28.

Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA.

The original article [1] contained an error in the presentation of Figure 1; this error has now been rectified and Figure 1 is now presented correctly.
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http://dx.doi.org/10.1186/s12916-018-1232-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6309057PMC
December 2018

Advanced Resuscitative Care in Tactical Combat Casualty Care: TCCC Guidelines Change 18-01:14 October 2018.

J Spec Oper Med Winter 2018;18(4):37-55

TCCC has previously recommended interventions that can effectively prevent 4 of the top 5 causes of prehospital preventable death in combat casualties-extremity hemorrhage, junctional hemorrhage, airway obstruction, and tension pneumothorax- and deaths from these causes have been markedly reduced in US combat casualties. Noncompressible torso hemorrhage (NCTH) is the last remaining major cause of preventable death on the battlefield and often causes death within 30 minutes of wounding. Increased use of whole blood, including the capability for massive transfusion, if indicated, has the potential to increase survival in casualties with either thoracic and/or abdominopelvic hemorrhage. Additionally, Zone 1 Resuscitative Endovascular Balloon Occlusion of the Aorta (REBOA) can provide temporary control of bleeding in the abdomen and pelvis and improve hemodynamics in casualties who may be approaching traumatic cardiac arrest as a result of hemorrhagic shock. Together, these two interventions are designated Advanced Resuscitative Care (ARC) and may enable casualties with severe NCTH to survive long enough to reach the care of a surgeon. Although Special Operations units are now using whole blood far-forward, this capability is not routinely present in other US combat units at this point in time. REBOA is not envisioned as care that could be accomplished by a unit medic working out of his or her aid bag. This intervention should be undertaken only by designated teams of advanced combat medical personnel with special training and equipment.
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June 2019

Mapping malaria by combining parasite genomic and epidemiologic data.

BMC Med 2018 10 18;16(1):190. Epub 2018 Oct 18.

Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA.

Background: Recent global progress in scaling up malaria control interventions has revived the goal of complete elimination in many countries. Decreasing transmission intensity generally leads to increasingly patchy spatial patterns of malaria transmission in elimination settings, with control programs having to accurately identify remaining foci in order to efficiently target interventions.

Findings: The role of connectivity between different pockets of local transmission is of increasing importance as programs near elimination since humans are able to transfer parasites beyond the limits of mosquito dispersal, thus re-introducing parasites to previously malaria-free regions. Here, we discuss recent advances in the quantification of spatial epidemiology of malaria, particularly Plasmodium falciparum, in the context of transmission reduction interventions. Further, we highlight the challenges and promising directions for the development of integrated mapping, modeling, and genomic approaches that leverage disparate datasets to measure both connectivity and transmission.

Conclusion: A more comprehensive understanding of the spatial transmission of malaria can be gained using a combination of parasite genetics and epidemiological modeling and mapping. However, additional molecular and quantitative methods are necessary to answer these public health-related questions.
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http://dx.doi.org/10.1186/s12916-018-1181-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6193293PMC
October 2018