David J. D. Earn

A draft genome of Yersinia pestis from victims of the Black Death

Technological advances in DNA recovery and sequencing have drastically expanded the scope of genetic analyses of ancient specimens to the extent that full genomic investigations are now feasible and are quickly becoming standard. This trend has important implications for infectious disease research because genomic data from ancient microbes may help to elucidate mechanisms of pathogen evolution and adaptation for emerging and re-emerging infections. Here we report a reconstructed ancient genome of Yersinia pestis at 30-fold average coverage from Black Death victims securely dated to episodes of pestilence-associated mortality in London, England, 1348–1350. Genetic architecture and phylogenetic analysis indicate that the ancient organism is ancestral to most extant strains and sits very close to the ancestral node of all Y. pestis commonly associated with human infection. Temporal estimates suggest that the Black Death of 1347–1351 was the main historical event responsible for the introduction and widespread dissemination of the ancestor to all currently circulating Y. pestis strains pathogenic to humans, and further indicates that contemporary Y. pestis epidemics have their origins in the medieval era. Comparisons against modern genomes reveal no unique derived positions in the medieval organism, indicating that the perceived increased virulence of the disease during the Black Death may not have been due to bacterial phenotype. These findings support the notion that factors other than microbial genetics, such as environment, vector dynamics and host susceptibility, should be at the forefront of epidemiological discussions regarding emerging Y. pestis infections.

Effect of Influenza Vaccination of Children on Infection Rates in Hutterite Communities: A Randomized Trial

CONTEXT Children and adolescents appear to play an important role in the transmission of influenza. Selectively vaccinating youngsters against influenza may interrupt virus transmission and protect those not immunized. OBJECTIVE To assess whether vaccinating children and adolescents with inactivated influenza vaccine could prevent influenza in other community members. DESIGN, SETTING, AND PARTICIPANTS A cluster randomized trial involving 947 Canadian children and adolescents aged 36 months to 15 years who received study vaccine and 2326 community members who did not receive the study vaccine in 49 Hutterite colonies in Alberta, Saskatchewan, and Manitoba. Follow-up began December 28, 2008, and ended June 23, 2009. INTERVENTION Children were randomly assigned according to community and in a blinded manner to receive standard dosing of either inactivated trivalent influenza vaccine or hepatitis A vaccine, which was used as a control. MAIN OUTCOME MEASURES Confirmed influenza A and B infection using a real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay and by measuring serum hemagglutination inhibition titers. RESULTS The mean rate of study vaccine coverage among eligible participants was 83% (range, 53%-100%) for the influenza vaccine colonies and 79% (range, 50%-100%) for the hepatitis A vaccine colonies. Among nonrecipients, 39 of 1271 (3.1%) in the influenza vaccine colonies and 80 of 1055 (7.6%) in the hepatitis A vaccine colonies had influenza illness confirmed by RT-PCR, for a protective effectiveness of 61% (95% confidence interval [CI], 8%-83%; P = .03). Among all study participants (those who were and those who were not vaccinated), 80 of 1773 (4.5%) in the influenza vaccine colonies and 159 of 1500 (10.6%) in the hepatitis A vaccine colonies had influenza illness confirmed by RT-PCR for an overall protective effectiveness of 59% (95% CI, 5%-82%; P = .04). No serious vaccine adverse events were observed. CONCLUSION Immunizing children and adolescents with inactivated influenza vaccine significantly protected unimmunized residents of rural communities against influenza. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00877396.

Ecology and evolution of the flu

Influenza (flu) is a common infectious disease, but it is unusual in that the primary timescales for disease dynamics (epidemics) and viral evolution (new variants) are roughly the same. Recently, extraordinarily reliable phylogenetic reconstructions of flu virus evolution have been made using samples from both extant and extinct strains. In addition, because of their public health importance, flu epidemics have been monitored throughout the period over which the phylogenetic trees extend. In parallel with this empirical work, theoretical ecologists have developed mathematical and computational models that elucidate many properties of multistrain systems. In the future, to unravel and interpret the complex interactions between ecological and evolutionary forces on flu dynamics, the documented evolution of the virus must be related to the observed population dynamics of the disease. New theoretical insights are also required to simplify model structures and facilitate predictions that can be tested with accessible data.

Surgical Mask vs N95 Respirator for Preventing Influenza Among Health Care Workers: A Randomized Trial

CONTEXT Data about the effectiveness of the surgical mask compared with the N95 respirator for protecting health care workers against influenza are sparse. Given the likelihood that N95 respirators will be in short supply during a pandemic and not available in many countries, knowing the effectiveness of the surgical mask is of public health importance. OBJECTIVE To compare the surgical mask with the N95 respirator in protecting health care workers against influenza. DESIGN, SETTING, AND PARTICIPANTS Noninferiority randomized controlled trial of 446 nurses in emergency departments, medical units, and pediatric units in 8 tertiary care Ontario hospitals. INTERVENTION Assignment to either a fit-tested N95 respirator or a surgical mask when providing care to patients with febrile respiratory illness during the 2008-2009 influenza season. MAIN OUTCOME MEASURES The primary outcome was laboratory-confirmed influenza measured by polymerase chain reaction or a 4-fold rise in hemagglutinin titers. Effectiveness of the surgical mask was assessed as noninferiority of the surgical mask compared with the N95 respirator. The criterion for noninferiority was met if the lower limit of the 95% confidence interval (CI) for the reduction in incidence (N95 respirator minus surgical group) was greater than -9%. RESULTS Between September 23, 2008, and December 8, 2008, 478 nurses were assessed for eligibility and 446 nurses were enrolled and randomly assigned the intervention; 225 were allocated to receive surgical masks and 221 to N95 respirators. Influenza infection occurred in 50 nurses (23.6%) in the surgical mask group and in 48 (22.9%) in the N95 respirator group (absolute risk difference, -0.73%; 95% CI, -8.8% to 7.3%; P = .86), the lower confidence limit being inside the noninferiority limit of -9%. CONCLUSION Among nurses in Ontario tertiary care hospitals, use of a surgical mask compared with an N95 respirator resulted in noninferior rates of laboratory-confirmed influenza. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00756574

Group interest versus self-interest in smallpox vaccination policy

The recent threat of bioterrorism has fueled debate on smallpox vaccination policy for the United States. Certain policy proposals call for voluntary mass vaccination; however, if individuals decide whether to vaccinate according to self-interest, the level of herd immunity achieved may differ from what is best for the population as a whole. We present a synthesis of game theory and epidemic modeling that formalizes this conflict between self-interest and group interest and shows that voluntary vaccination is unlikely to reach the group-optimal level. This shortfall results in a substantial increase in expected mortality after an attack.

Interactions Between the Immune System and Cancer: A Brief Review of Non-spatial Mathematical Models

We briefly review spatially homogeneous mechanistic mathematical models describing the interactions between a malignant tumor and the immune system. We begin with the simplest (single equation) models for tumor growth and proceed to consider greater immunological detail (and correspondingly more equations) in steps. This approach allows us to clarify the necessity for expanding the complexity of models in order to capture the biological mechanisms we wish to understand. We conclude by discussing some unsolved problems in the mathematical modeling of cancer-immune system interactions.

Yersinia pestis and the Plague of Justinian 541–543 AD: a genomic analysis

BACKGROUND Yersinia pestis has caused at least three human plague pandemics. The second (Black Death, 14-17th centuries) and third (19-20th centuries) have been genetically characterised, but there is only a limited understanding of the first pandemic, the Plague of Justinian (6-8th centuries). To address this gap, we sequenced and analysed draft genomes of Y pestis obtained from two individuals who died in the first pandemic. METHODS Teeth were removed from two individuals (known as A120 and A76) from the early medieval Aschheim-Bajuwarenring cemetery (Aschheim, Bavaria, Germany). We isolated DNA from the teeth using a modified phenol-chloroform method. We screened DNA extracts for the presence of the Y pestis-specific pla gene on the pPCP1 plasmid using primers and standards from an established assay, enriched the DNA, and then sequenced it. We reconstructed draft genomes of the infectious Y pestis strains, compared them with a database of genomes from 131 Y pestis strains from the second and third pandemics, and constructed a maximum likelihood phylogenetic tree. FINDINGS Radiocarbon dating of both individuals (A120 to 533 AD [plus or minus 98 years]; A76 to 504 AD [plus or minus 61 years]) places them in the timeframe of the first pandemic. Our phylogeny contains a novel branch (100% bootstrap at all relevant nodes) leading to the two Justinian samples. This branch has no known contemporary representatives, and thus is either extinct or unsampled in wild rodent reservoirs. The Justinian branch is interleaved between two extant groups, 0.ANT1 and 0.ANT2, and is distant from strains associated with the second and third pandemics. INTERPRETATION We conclude that the Y pestis lineages that caused the Plague of Justinian and the Black Death 800 years later were independent emergences from rodents into human beings. These results show that rodent species worldwide represent important reservoirs for the repeated emergence of diverse lineages of Y pestis into human populations. FUNDING McMaster University, Northern Arizona University, Social Sciences and Humanities Research Council of Canada, Canada Research Chairs Program, US Department of Homeland Security, US National Institutes of Health, Australian National Health and Medical Research Council.

Persistence, chaos and synchrony in ecology and epidemiology

The decline of species in natural habitats concerns ecologists, who view extinction as a danger and conservation of biological diversity as a goal. In contrast, the proliferation of ‘undesirable’ species is the principal concern of epidemiologists, who view persistence as a problem and eradication as an achievement. While ecologists and epidemiologists have essentially opposite goals, the mathematical structure of the population dynamics that they study is very similar. We briefly review the similarities and differences between these two fields, emphasizing recent work in both areas on the effects of spatial synchrony and dynamical chaos. We hope to stimulate further cross–fertilization of ideas between the disciplines.

Initial human transmission dynamics of the pandemic (H1N1) 2009 virus in North America.

Background  Between 5 and 25 April 2009, pandemic (H1N1) 2009 caused a substantial, severe outbreak in Mexico, and subsequently developed into the first global pandemic in 41 years. We determined the reproduction number of pandemic (H1N1) 2009 by analyzing the dynamics of the complete case series in Mexico City during this early period.

Generality of the Final Size Formula for an Epidemic of a Newly Invading Infectious Disease

The well-known formula for the final size of an epidemic was published by Kermack and McKendrick in 1927. Their analysis was based on a simple susceptible-infected-recovered (SIR) model that assumes exponentially distributed infectious periods. More recent analyses have established that the standard final size formula is valid regardless of the distribution of infectious periods, but that it fails to be correct in the presence of certain kinds of heterogeneous mixing (e.g., if there is a core group, as for sexually transmitted diseases). We review previous work and establish more general conditions under which Kermack and McKendricks formula is valid. We show that the final size formula is unchanged if there is a latent stage, any number of distinct infectious stages and/or a stage during which infectives are isolated (the durations of each stage can be drawn from any integrable distribution). We also consider the possibility that the transmission rates of infectious individuals are arbitrarily distributed—allowing, in particular, for the existence of super-spreaders—and prove that this potential complexity has no impact on the final size formula. Finally, we show that the final size formula is unchanged even for a general class of spatial contact structures. We conclude that whenever a new respiratory pathogen emerges, an estimate of the expected magnitude of the epidemic can be made as soon the basic reproduction number ℝ0 can be approximated, and this estimate is likely to be improved only by more accurate estimates of ℝ0, not by knowledge of any other epidemiological details.