Recommendations for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples.

OBJECTIVES: Genotyping of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been instrumental in monitoring viral evolution and transmission during the pandemic. The quality of the sequence data obtained from these genotyping efforts depends on several factors, including the quantity/integrity of the input material, the technology, and laboratory-specific implementation. The current lack of guidelines for SARS-CoV-2 genotyping leads to inclusion of error-containing genome sequences in genomic epidemiology studies. We aimed to establish clear and broadly applicable recommendations for reliable virus genotyping. METHODS: We established and used a sequencing data analysis workflow that reliably identifies and removes technical artefacts; such artefacts can result in miscalls when using alternative pipelines to process clinical samples and synthetic viral genomes with an amplicon-based genotyping approach. We evaluated the impact of experimental factors, including viral load and sequencing depth, on correct sequence determination. RESULTS: We found that at least 1000 viral genomes are necessary to confidently detect variants in the SARS-CoV-2 genome at frequencies of ≥10%. The broad applicability of our recommendations was validated in over 200 clinical samples from six independent laboratories. The genotypes we determined for clinical isolates with sufficient quality cluster by sampling location and period. Our analysis also supports the rise in frequencies of 20A.EU1 and 20A.EU2, two recently reported European strains whose dissemination was facilitated by travel during the summer of 2020. CONCLUSIONS: We present much-needed recommendations for the reliable determination of SARS-CoV-2 genome sequences and demonstrate their broad applicability in a large cohort of clinical samples.

Epigenome-wide association study in whole blood on type 2 diabetes among sub-Saharan African individuals: findings from the RODAM study.

BACKGROUND: Type 2 diabetes (T2D) results from a complex interplay between genetics and the environment. Several epigenome-wide association studies (EWAS) have found DNA methylation loci associated with T2D in European populations. However, data from African populations are lacking. We undertook the first EWAS for T2D among sub-Saharan Africans, aiming at identifying ubiquitous and novel DNA methylation loci associated with T2D. METHODS: The Illumina 450k DNA-methylation array was used on whole blood samples of 713 Ghanaian participants (256 with T2D, 457 controls) from the cross-sectional Research on Obesity and Diabetes among African Migrants (RODAM) study. Differentially methylated positions (DMPs) for T2D and HbA1c were identified through linear regression analysis adjusted for age, sex, estimated cell counts, hybridization batch, array position and body mass index (BMI). We also did a candidate analysis of previously reported EWAS loci for T2D in non-African populations, identified through a systematic literature search. RESULTS: Four DMPs [cg19693031 (TXNIP), cg04816311 (C7orf50), cg00574958 (CPT1A), cg07988171 (TPM4)] were associated with T2D after correction for inflation by possible systematic biases. The most strongly associated DMP-cg19693031, TXNIP (P = 2.6E-19) -showed hypomethylation in T2D cases compared with controls. Two out of the four DMPs [cg19693031 (TXNIP), cg04816311 (C7orf50)] remained associated with T2D after adjustment for BMI, and one locus [cg07988171 (TPM4)] that has not been reported previously. CONCLUSIONS: In this first EWAS for T2D in sub-Saharan Africans, we have identified four DMPs at epigenome-wide level, one of which is novel. These findings provide insight into the epigenetic loci that underlie the burden of T2D in sub-Saharan Africans.

An epigenome-wide association study in whole blood of measures of adiposity among Ghanaians: the RODAM study.

BACKGROUND: Epigenome-wide association studies (EWAS) have identified DNA methylation loci involved in adiposity. However, EWAS on adiposity in sub-Saharan Africans are lacking despite the high burden of adiposity among African populations. We undertook an EWAS for anthropometric indices of adiposity among Ghanaians aiming to identify DNA methylation loci that are significantly associated. METHODS: The Illumina 450k DNA methylation array was used to profile DNA methylation in whole blood samples of 547 Ghanaians from the Research on Obesity and Diabetes among African Migrants (RODAM) study. Differentially methylated positions (DMPs) and differentially methylation regions (DMRs) were identified for BMI and obesity (BMI ≥ 30 kg/m2), as well as for waist circumference (WC) and abdominal obesity (WC ≥ 102 cm in men, ≥88 cm in women). All analyses were adjusted for age, sex, blood cell distribution estimates, technical covariates, recruitment site and population stratification. We also did a replication study of previously reported EWAS loci for anthropometric indices in other populations. RESULTS: We identified 18 DMPs for BMI and 23 for WC. For obesity and abdominal obesity, we identified three and one DMP, respectively. Fourteen DMPs overlapped between BMI and WC. DMP cg00574958 annotated to gene CPT1A was the only DMP associated with all outcomes analysed, attributing to 6.1 and 5.6% of variance in obesity and abdominal obesity, respectively. DMP cg07839457 (NLRC5) and cg20399616 (BCAT1) were significantly associated with BMI, obesity and with WC and had not been reported by previous EWAS on adiposity. CONCLUSIONS: This first EWAS for adiposity in Africans identified three epigenome-wide significant loci (CPT1A, NLRC5 and BCAT1) for both general adiposity and abdominal adiposity. The findings are a first step in understanding the role of DNA methylation in adiposity among sub-Saharan Africans. Studies on other sub-Saharan African populations as well as translational studies are needed to determine the role of these DNA methylation variants in the high burden of adiposity among sub-Saharan Africans.

Obesity and type 2 diabetes in sub-Saharan Africans - Is the burden in today's Africa similar to African migrants in Europe? The RODAM study.

BACKGROUND: Rising rates of obesity and type 2 diabetes (T2D) are impending major threats to the health of African populations, but the extent to which they differ between rural and urban settings in Africa and upon migration to Europe is unknown. We assessed the burden of obesity and T2D among Ghanaians living in rural and urban Ghana and Ghanaian migrants living in different European countries. METHODS: A multi-centre cross-sectional study was conducted among Ghanaian adults (n = 5659) aged 25-70 years residing in rural and urban Ghana and three European cities (Amsterdam, London and Berlin). Comparisons between groups were made using prevalence ratios (PRs) with adjustments for age and education. RESULTS: In rural Ghana, the prevalence of obesity was 1.3 % in men and 8.3 % in women. The prevalence was considerably higher in urban Ghana (men, 6.9 %; PR: 5.26, 95 % CI, 2.04-13.57; women, 33.9 %; PR: 4.11, 3.13-5.40) and even more so in Europe, especially in London (men, 21.4 %; PR: 15.04, 5.98-37.84; women, 54.2 %; PR: 6.63, 5.04-8.72). The prevalence of T2D was low at 3.6 % and 5.5 % in rural Ghanaian men and women, and increased in urban Ghanaians (men, 10.3 %; PR: 3.06; 1.73-5.40; women, 9.2 %; PR: 1.81, 1.25-2.64) and highest in Berlin (men, 15.3 %; PR: 4.47; 2.50-7.98; women, 10.2 %; PR: 2.21, 1.30-3.75). Impaired fasting glycaemia prevalence was comparatively higher only in Amsterdam, and in London, men compared with rural Ghana. CONCLUSION: Our study shows high risks of obesity and T2D among sub-Saharan African populations living in Europe. In Ghana, similarly high prevalence rates were seen in an urban environment, whereas in rural areas, the prevalence of obesity among women is already remarkable. Similar processes underlying the high burden of obesity and T2D following migration may also be at play in sub-Saharan Africa as a consequence of urbanisation.

Development of forensic assay signatures for ebolaviruses.

Ebolaviruses are a diverse group of RNA viruses comprising five different species, four of which cause fatal hemorrhagic fever in humans. Because of their high infectivity and lethality, ebolaviruses are considered major biothreat agents. Although detection assays exist, no forensic assays are currently available. Here, we report the development of forensic assays that differentiate ebolaviruses. We performed phylogenetic analyses and identified canonical SNPs for all species, major clades and isolates. TaqMan-MGB allelic discrimination assays based on these SNPs were designed, screened against synthetic RNA templates, and validated against ebolavirus genomic RNAs. A total of 45 assays were validated to provide 100% coverage of the species and variants with additional resolution at the isolate level. These assays enabled accurate forensic analysis on 4 "unknown" ebolaviruses. Unknowns were correctly classified to species and variant. A goal of providing resolution below the isolate level was not successful. These high-resolution forensic assays allow rapid and accurate genotyping of ebolaviruses for forensic investigations.

Rationale and cross-sectional study design of the Research on Obesity and type 2 Diabetes among African Migrants: the RODAM study.

INTRODUCTION: Obesity and type 2 diabetes (T2D) are highly prevalent among African migrants compared with European descent populations. The underlying reasons still remain a puzzle. Gene-environmental interaction is now seen as a potential plausible factor contributing to the high prevalence of obesity and T2D, but has not yet been investigated. The overall aim of the Research on Obesity and Diabetes among African Migrants (RODAM) project is to understand the reasons for the high prevalence of obesity and T2D among sub-Saharan Africans in diaspora by (1) studying the complex interplay between environment (eg, lifestyle), healthcare, biochemical and (epi)genetic factors, and their relative contributions to the high prevalence of obesity and T2D; (2) to identify specific risk factors within these broad categories to guide intervention programmes and (3) to provide a basic knowledge for improving diagnosis and treatment. METHODS AND ANALYSIS: RODAM is a multicentre cross-sectional study among homogenous sub-Saharan African participants (ie, Ghanaians) aged >25 years living in rural and urban Ghana, the Netherlands, Germany and the UK (http://rod-am.eu/). Standardised data on the main outcomes, genetic and non-genetic factors are collected in all locations. The aim is to recruit 6250 individuals comprising five subgroups of 1250 individuals from each site. In Ghana, Kumasi and Obuasi (urban stratum) and villages in the Ashanti region (rural stratum) are served as recruitment sites. In Europe, Ghanaian migrants are selected through the municipality or Ghanaian organisations registers. ETHICS AND DISSEMINATION: Ethical approval has been obtained in all sites. This paper gives an overview of the rationale, conceptual framework and methods of the study. The differences across locations will allow us to gain insight into genetic and non-genetic factors contributing to the occurrence of obesity and T2D and will inform targeted intervention and prevention programmes, and provide the basis for improving diagnosis and treatment in these populations and beyond.

Forensic signatures for Marburgviruses.

Marburgvirus is one of the most important hemorrhagic fever viruses with extremely high infectivity and fatality rate (~90%). It is transmitted easily in human populations through a respiratory route and therefore considered as a major biothreat agent. Although detection assays have been developed, no assay is available for forensic analysis. Here we report development of forensic assays for Marburgvirus. We performed detailed phylogenetic analysis of strains and isolates from all known Marburg virus outbreaks as well as from several laboratory strains and identified canonical SNPs for all major clades (outbreaks) and strains. TaqMan-MGB allelic discrimination assays targeting these SNPs were designed and experimentally screened against synthetic RNA templates and genomic RNAs. A total of 45 assays were validated to provide 100% coverage of the clades (outbreaks) and 91% at the strain level (21 out of the 23 targeted Marburgvirus strains) with built-in redundancy for increased robustness. Using these validated assays, we were able to provide accurate forensic analysis on 3 "unknown" Marburgviruses. These high-resolution forensic assays allow rapid and accurate genotyping of Marburgviruses for forensic investigations.

Selecting summary statistics in approximate Bayesian computation for calibrating stochastic models.

Approximate Bayesian computation (ABC) is an approach for using measurement data to calibrate stochastic computer models, which are common in biology applications. ABC is becoming the "go-to" option when the data and/or parameter dimension is large because it relies on user-chosen summary statistics rather than the full data and is therefore computationally feasible. One technical challenge with ABC is that the quality of the approximation to the posterior distribution of model parameters depends on the user-chosen summary statistics. In this paper, the user requirement to choose effective summary statistics in order to accurately estimate the posterior distribution of model parameters is investigated and illustrated by example, using a model and corresponding real data of mitochondrial DNA population dynamics. We show that for some choices of summary statistics, the posterior distribution of model parameters is closely approximated and for other choices of summary statistics, the posterior distribution is not closely approximated. A strategy to choose effective summary statistics is suggested in cases where the stochastic computer model can be run at many trial parameter settings, as in the example.

Identification of genes in the VirR regulon of Pectobacterium atrosepticum and characterization of their roles in quorum sensing-dependent virulence.

In the economically important phytopathogen, Pectobacterium atrosepticum, expression of plant cell wall degrading enzymes and other virulence determinants is controlled in a cell density-dependent fashion, termed quorum sensing (QS). Canonical QS systems in Gram-negative bacteria contain a LuxI-type protein, synthesizing a signalling molecule, and a LuxR-type regulator, responding to the signalling molecule above threshold concentrations. In P. atrosepticum, the central LuxR-type repressor of virulence, VirR, has been identified and its impacts on virulence characterized. Here we define the broader VirR regulon using chromatin immunoprecipitation (ChIP) and in planta microarrays. Ninety-four direct VirR targets were identified by ChIP microarrays and a consensus VirR binding site was determined. Purified VirR was used in DNA gel shift assays on target promoters and VirR : promoter binding was disrupted by exogenous addition of the signalling molecule, N-(3-oxohexanoyl)-l-homoserine lactone (OHHL). VirR autorepressed, and directly activated the transcription of rsmA in the absence of OHHL. Finally, we showed that VirR directly regulated the production of siderophores and controlled swimming motility. This is the first report characterizing the direct targets of VirR and provides clear evidence that this LuxR-type protein can act in vivo as both an activator and repressor of transcription in the absence of its cognate signalling molecule.

Effects of background suppression of gamma counts on signal estimation.

Gamma detectors at border crossings are intended to detect illicit nuclear material. One of their performance challenges is the fact that vehicles suppress the natural background and, thus, potentially reduce probability of detection of threat items. Here we test several methods to adjust the detection to background suppression in the context of signal estimation. We show that, for the small-to-moderate suppression magnitudes, suppression adjustment leads to higher detection probability. However, for signals triggering alarm without an adjustment, adjustment does not improve estimation of the signal location, only moderately improves estimation of the signal magnitude, and does not improve estimation of the signal width.

The reproduction number R(t) in structured and nonstructured populations.

Using daily counts of newly infected individuals, Wallinga and Teunis (WT) introduced a conceptually simple method to estimate the number of secondary cases per primary case (R(t)) for a given day. The method requires an estimate of the generation interval probability density function (pdf), which specifies the probabilities for the times between symptom onset in a primary case and symptom onset in a corresponding secondary case. Other methods to estimate R(t) are based on explicit models such as the SIR model; therefore, one might expect the WT method to be more robust to departures from SIR- type behavior. This paper uses simulated data to compare the quality of daily R(t) estimates based on a SIR model to those using the WT method for both structured (classical SIR assumptions are violated) and nonstructured (classical SIR assumptions hold) populations. By using detailed simulations that record the infection day of each new infection and the donor-recipient identities, the true R(t) and the generation interval pdf is known with negligible error. We find that the generation interval pdf is time dependent in all cases, which agrees with recent results reported elsewhere. We also find that the WT method performs essentially the same in the structured populations (except for a spatial network) as it does in the nonstructured population. And, the WT method does as well or better than a SIR-model based method in three of the four structured populations. Therefore, even if the contact patterns are heterogeneous as in the structured populations evaluated here, the WT method provides reasonable estimates of R(t), as does the SIR method.

Quorum sensing coordinates brute force and stealth modes of infection in the plant pathogen Pectobacterium atrosepticum.

Quorum sensing (QS) in vitro controls production of plant cell wall degrading enzymes (PCWDEs) and other virulence factors in the soft rotting enterobacterial plant pathogen Pectobacterium atrosepticum (Pba). Here, we demonstrate the genome-wide regulatory role of QS in vivo during the Pba-potato interaction, using a Pba-specific microarray. We show that 26% of the Pba genome exhibited differential transcription in a QS (expI-) mutant, compared to the wild-type, suggesting that QS may make a greater contribution to pathogenesis than previously thought. We identify novel components of the QS regulon, including the Type I and II secretion systems, which are involved in the secretion of PCWDEs; a novel Type VI secretion system (T6SS) and its predicted substrates Hcp and VgrG; more than 70 known or putative regulators, some of which have been demonstrated to control pathogenesis and, remarkably, the Type III secretion system and associated effector proteins, and coronafacoyl-amide conjugates, both of which play roles in the manipulation of plant defences. We show that the T6SS and a novel potential regulator, VirS, are required for full virulence in Pba, and propose a model placing QS at the apex of a regulatory hierarchy controlling the later stages of disease progression in Pba. Our findings indicate that QS is a master regulator of phytopathogenesis, controlling multiple other regulators that, in turn, co-ordinately regulate genes associated with manipulation of host defences in concert with the destructive arsenal of PCWDEs that manifest the soft rot disease phenotype.

Signatures for several types of naturally occurring radioactive materials.

Detectors to scan for illicit nuclear material began to be installed at various screening locations in 2002. On the sites considered, each vehicle drives slowly by radiation detectors that scan for neutron and gamma radiation, resulting in a time series profile. One performance limitation is that naturally occurring radioactive materials (NORM), such as cat litter, are routinely shipped across borders, leading to nuisance alarms. One strategy for nuisance alarms is to define and recognize "signatures" of certain types of NORM so that many nuisance alarms can be quickly resolved as being innocent. Here, we consider candidate profile features, such as the peak width and the maximum energy ratio, and use pattern recognition methods to illustrate the extent to which several common types of NORM can be distinguished.

RelA-dependent (p)ppGpp production controls exoenzyme synthesis in Erwinia carotovora subsp. atroseptica.

In this report, we investigate the link between nutrient limitation, RelA-mediated (p)ppGpp production, and virulence in the phytopathogen Erwinia carotovora subsp. atroseptica. A relA null mutant (JWC7) was constructed by allelic exchange, and we confirmed that, unlike the wild-type progenitor, this mutant did not produce elevated levels of (p)ppGpp upon nutrient downshift. However, (p)ppGpp production could be restored in strain JWC7 during nutrient limitation by supplying relA in trans. During growth on exoenzyme-inducing minimal medium, the relA mutant showed a diminution in secreted pectate lyase and protease activities and a severe defect in motility. The relA mutant was also impaired in its ability to cause rot in potato tubers. In the presence of serine hydroxamate (a competitive inhibitor of seryl tRNA synthase and a potent inducer of the stringent response in wild-type E. carotovora subsp. atroseptica), exoenzyme production was essentially abolished in JWC7 but could be restored in the presence of plasmid-borne relA. The inhibition of exoenzyme production in JWC7 caused by serine hydroxamate could not be overcome by addition of the quorum-sensing signal molecule, N-3-oxohexanoyl-l-homoserine lactone. Quantitative reverse transcription-PCR analysis of selected RNA species confirmed that the effects of relA on secreted pectate lyase activity and motility could be attributed to a reduction in transcription of the corresponding genes. We conclude that nutrient limitation is a potent environmental cue that triggers (p)ppGpp-dependent exoenzyme production in E. carotovora subsp. atroseptica. Furthermore, our data suggest that nutrient limitation [or rather, (p)ppGpp accumulation] is a prerequisite for effective quorum-sensing-dependent activation of exoenzyme production.

Quorum sensing, virulence and secondary metabolite production in plant soft-rotting bacteria.

Quorum sensing describes the ability of bacteria to sense their population density and respond by modulating gene expression. In the plant soft-rotting bacteria, such as Erwinia, an arsenal of plant cell wall-degrading enzymes is produced in a cell density-dependent manner, which causes maceration of plant tissue. However, quorum sensing is central not only to controlling the production of such destructive enzymes, but also to the control of a number of other virulence determinants and secondary metabolites. Erwinia synthesizes both N-acylhomoserine lactone (AHL) and autoinducer-2 types of quorum sensing signal, which both play a role in regulating gene expression in the phytopathogen. We review the models for AHL-based regulation of carbapenem antibiotic production in Erwinia. We also discuss the importance of quorum sensing in the production and secretion of virulence determinants by Erwinia, and its interplay with other regulatory systems.

Alarm criteria in radiation portal monitoring.

Gamma detectors at border crossings are intended to detect illicit nuclear material. These detectors collect counts that are used to determine whether to trigger an alarm. Several candidate alarm rules are evaluated, with attention to background suppression caused by the vehicle. Because the count criterion leads to many nuisance alarms and because background suppression by the vehicle is smaller for ratios of counts, analysis of a ratio criterion is included. Detection probability results that consider the effects of 5 factors are given for 2 signal-injection studies, 1 for counts, and 1 for count ratios.

Computer-aided diagnosis with potential application to rapid detection of disease outbreaks.

Our objectives are to quickly interpret symptoms of emergency patients to identify likely syndromes and to improve population-wide disease outbreak detection. We constructed a database of 248 syndromes, each syndrome having an estimated probability of producing any of 85 symptoms, with some two-way, three-way, and five-way probabilities reflecting correlations among symptoms. Using these multi-way probabilities in conjunction with an iterative proportional fitting algorithm allows estimation of full conditional probabilities. Combining these conditional probabilities with misdiagnosis error rates and incidence rates via Bayes theorem, the probability of each syndrome is estimated. We tested a prototype of computer-aided differential diagnosis (CADDY) on simulated data and on more than 100 real cases, including West Nile Virus, Q fever, SARS, anthrax, plague, tularaemia and toxic shock cases. We conclude that: (1) it is important to determine whether the unrecorded positive status of a symptom means that the status is negative or that the status is unknown; (2) inclusion of misdiagnosis error rates produces more realistic results; (3) the naive Bayes classifier, which assumes all symptoms behave independently, is slightly outperformed by CADDY, which includes available multi-symptom information on correlations; as more information regarding symptom correlations becomes available, the advantage of CADDY over the naive Bayes classifier should increase; (4) overlooking low-probability, high-consequence events is less likely if the standard output summary is augmented with a list of rare syndromes that are consistent with observed symptoms, and (5) accumulating patient-level probabilities across a larger population can aid in biosurveillance for disease outbreaks.

Accounting for seasonal patterns in syndromic surveillance data for outbreak detection.

BACKGROUND: Syndromic surveillance (SS) can potentially contribute to outbreak detection capability by providing timely, novel data sources. One SS challenge is that some syndrome counts vary with season in a manner that is not identical from year to year. Our goal is to evaluate the impact of inconsistent seasonal effects on performance assessments (false and true positive rates) in the context of detecting anomalous counts in data that exhibit seasonal variation. METHODS: To evaluate the impact of inconsistent seasonal effects, we injected synthetic outbreaks into real data and into data simulated from each of two models fit to the same real data. Using real respiratory syndrome counts collected in an emergency department from 2/1/94-5/31/03, we varied the length of training data from one to eight years, applied a sequential test to the forecast errors arising from each of eight forecasting methods, and evaluated their detection probabilities (DP) on the basis of 1000 injected synthetic outbreaks. We did the same for each of two corresponding simulated data sets. The less realistic, nonhierarchical model's simulated data set assumed that "one season fits all," meaning that each year's seasonal peak has the same onset, duration, and magnitude. The more realistic simulated data set used a hierarchical model to capture violation of the "one season fits all" assumption. RESULTS: This experiment demonstrated optimistic bias in DP estimates for some of the methods when data simulated from the nonhierarchical model was used for DP estimation, thus suggesting that at least for some real data sets and methods, it is not adequate to assume that "one season fits all." CONCLUSION: For the data we analyze, the "one season fits all " assumption is violated, and DP performance claims based on simulated data that assume "one season fits all," for the forecast methods considered, except for moving average methods, tend to be optimistic. Moving average methods based on relatively short amounts of training data are competitive on all three data sets, but are particularly competitive on the real data and on data from the hierarchical model, which are the two data sets that violate the "one season fits all" assumption.

The structural basis of cooperative regulation at an alternate genetic switch.

Bacteriophage lambda is a paradigm for understanding the role of cooperativity in gene regulation. Comparison of the regulatory regions of lambda and the unrelated temperate bacteriophage 186 provides insight into alternate ways to assemble functional genetic switches. The structure of the C-terminal domain of the 186 repressor, determined at 2.7 A resolution, reveals an unusual heptamer of dimers, consistent with presented genetic studies. In addition, the structure of a cooperativity mutant of the full-length 186 repressor, identified by genetic screens, was solved to 1.95 A resolution. These structures provide a molecular basis for understanding lysogenic regulation in 186. Whereas the overall fold of the 186 and lambda repressor monomers is remarkably similar, the way the two repressors cooperatively assemble is quite different and explains in part the differences in their regulatory activity.

Identification of the central quorum sensing regulator of virulence in the enteric phytopathogen, Erwinia carotovora: the VirR repressor.

In the Gram-negative phytopathogen, Erwinia carotovora ssp. atroseptica (Eca) virulence depends on the production of a N-(3-oxohexanoyl)-L-homoserine lactone (OHHL) quorum sensing (QS) signal. This work identifies the elusive 'missing link' between QS and virulence in Erwinia. We have identified and characterized a novel regulator of virulence, VirR, in Eca and show that a virR mutation completely restores virulence factor production to an Eca mutant unable to synthesize OHHL. This effect of the virR mutation translates to a restoration of virulence to wild-type levels and thus provides evidence that VirR acts to prevent the production of virulence factors at low cell density. We also show that, in Eca, transcription of virulence genes is controlled by OHHL and that this control is effected through the action of VirR. We also demonstrate that the VirR regulatory pathway is present and functional in both blackleg and soft rotting species of Erwinia.