Unifying the spatial population dynamics and molecular evolution of epidemic rabies virus

Infectious disease emergence is under the simultaneous influence of both genetic and ecological factors. Yet, we lack a general framework for linking ecological dynamics of infectious disease with underlying molecular and evolutionary change. As a model, we illustrate the linkage between ecological and evolutionary dynamics in rabies virus during its epidemic expansion into eastern and southern Ontario. We characterized the phylogeographic relationships among 83 isolates of fox rabies virus variant using nucleotide sequences from the glycoprotein-encoding glycoprotein gene. The fox rabies virus variant descended as an irregular wave with two arms invading from northern Ontario into southern Ontario over the 1980s and 1990s. Correlations between genetic and geographic distance suggest an isolation by distance population structure for the virus. The divergence among viral lineages since the most recent common ancestor correlates with position along the advancing wave front with more divergent lineages near the origin of the epidemic. Based on divergence from the most recent common ancestor, the regional population can be partitioned into two subpopulations, each corresponding to an arm of the advancing wave. Subpopulation A (southern Ontario) showed reduced isolation by distance relative to subpopulation B (eastern Ontario). The temporal dynamics of subpopulation A suggests that the subregional viral population may have undergone several smaller waves that reduced isolation by distance. The use of integrated approaches, such as the geographical analysis of sequence variants, coupled with information on spatial dynamics will become indispensable aids in understanding patterns of disease emergence.     

The Algerian Chapter of SARS-CoV-2 Pandemic: An Evolutionary,Genetic, and Epidemiological Prospect

To explore the SARS-CoV-2 pandemic in Algeria, a dataset comprising ninety-five genomes originating from SARS-CoV-2 sampled from Algeria and other countries worldwide, from 24 December 2019, through 4 March 2021, was thoroughly examined. While performing a multi-component analysis regarding the Algerian outbreak, the toolkit of phylogenetic, phylogeographic, haplotype, and genomic analysis were effectively implemented. We estimated the Time to the Most Recent Common Ancestor (TMRCA) in reference to the Algerian pandemic and highlighted the multiple introductions of the disease and the missing data depicted in the transmission loop. In addition, we emphasized the significant role played by local and international travels in disease dissemination. Most importantly, we unveiled mutational patterns, the effect of unique mutations on corresponding proteins, and the relatedness regarding the Algerian sequences to other sequences worldwide. Our results revealed individual amino-acid replacements such as the deleterious replacement A23T in the orf3a gene in Algeria_EPI_ISL_418241. Additionally, a connection between Algeria_EPI_ISL_420037 and sequences originating from the USA was observed through a USA characteristic amino-acid replacement T1004I in the nsp3 gene, found in the aforementioned Algerian sequence. Similarly, successful tracing could be established, such as Algeria/G37318-8849/2020|EPI_ISL_766863, which was imported from Saudi Arabia during the pilgrimage. Lastly, we assessed the Algerian mitigation measures regarding disease containment using statistical analyses.     

Predicting the spatial dynamics of rabies epidemics on heterogeneous landscapes

Often as an epidemic spreads, the leading front is irregular, reflecting spatial variation in local transmission rates. We developed a methodology for quantifying spatial variation in rates of disease spread across heterogeneous landscapes. Based on data for epidemic raccoon rabies in Connecticut, we developed a stochastic spatial model of rabies spread through the state's 169 townships. We quantified spatial variation in transmission rates associated with human demography and key habitat features. We found that large rivers act as semipermeable barriers, leading to a 7-fold reduction in the local rates of propagation. By combining the spatial distribution of major rivers with long-distance dispersal we were able to account for the observed irregular pattern of disease spread across the state without recourse to direct assessment of host-pathogen populations.     

Nosocomial transmission of parainfluenza 3 virus in hematological patients characterized by molecular epidemiology

A.V. Lee, D.F. Bibby, H. Oakervee, A. Rohatiner, I. Ushiro‐Lumb, D.A. Clark, F.M. Mattes. Nosocomial transmission of parainfluenza 3 virus in hematological patients characterized by molecular epidemiology.
Transpl Infect Dis 2011: 13: 433–437. All rights reserved Abstract: We report an outbreak of parainfluenza 3 virus involving 17 hematology–oncology patients on 2 hospital wards. Sequence analysis of clinical samples confirmed homology of strains for 16/17 patients and 1 healthcare worker. Epidemiological analysis of the outbreak supported the molecular data with nosocomial transmission of the same genetic strain as the cause of the outbreak.     

Origin and Spread of the Dengue Virus Type 1, Genotype V in Senegal, 2015–2019

Dengue virus (DENV) is the most widespread arthropod-borne virus, with the number and severity of outbreaks increasing worldwide in recent decades. Dengue is caused by genetically distinct serotypes, DENV-1–4. Here, we present data on DENV-1, isolated from patients with dengue fever during an outbreak in Senegal and Mali (Western Africa) in 2015–2019, that were analyzed by sequencing the envelope (E) gene. The emergence and the dynamics of DENV-1 in Western Africa were inferred by using maximum likelihood and Bayesian methods. The DENV-1 grouped into a monophyletic cluster that was closely related to those from Southeast Asia. The virus appears to have been introduced directly into Medina Gounass (Suburb of Dakar), Senegal (location probability = 0.301, posterior = 0.76). The introduction of the virus in Senegal occurred around 2014 (95% HPD = 2012.88–2014.84), and subsequently, the virus moved to regions within Senegal (e.g., Louga and Fatick), causing intense outbreaks in the subsequent years. The virus appears to have been introduced in Mali (a neighboring country) after its introduction in Senegal. In conclusion, we present evidence that the outbreak caused by DENV-1 in urban environments in Senegal and Mali after 2015 was caused by a single viral introduction from Asia.     

From the Cover: The origin and early spread of SARS-CoV-2 in Europe

The investigation of migratory patterns during the SARS-CoV-2 pandemic before spring 2020 border closures in Europe is a crucial first step toward an in-depth evaluation of border closure policies. Here we analyze viral genome sequences using a phylodynamic model with geographic structure to estimate the origin and spread of SARS-CoV-2 in Europe prior to border closures. Based on SARS-CoV-2 genomes, we reconstruct a partial transmission tree of the early pandemic and coinfer the geographic location of ancestral lineages as well as the number of migration events into and between European regions. We find that the predominant lineage spreading in Europe during this time has a most recent common ancestor in Italy and was probably seeded by a transmission event in either Hubei, China or Germany. We do not find evidence for preferential migration paths from Hubei into different European regions or from each European region to the others. Sustained local transmission is first evident in Italy and then shortly thereafter in the other European regions considered. Before the first border closures in Europe, we estimate that the rate of occurrence of new cases from within-country transmission was within the bounds of the estimated rate of new cases from migration. In summary, our analysis offers a view on the early state of the epidemic in Europe and on migration patterns of the virus before border closures. This information will enable further study of the necessity and timeliness of border closures.

In response to the pandemic potential of the SARS-CoV-2 virus, many nations closed their borders in spring 2020 to curb the virus’ spread (1). These closures incurred high economic and social costs. To weigh the relative costs and benefits of border closures, it will be important to understand the efficacy of these policies. At the early stages of an outbreak, border closures can delay a pathogen’s arrival, thereby giving countries additional time to prepare (2). However, the success of this strategy depends on timely implementation and a good knowledge of where the pathogen is already circulating. To evaluate the efficacy of border closures in limiting the spread of SARS-CoV-2, it is important to reconstruct the timeline of the early international spread of the virus, before such policies were implemented.In this analysis, we aim to estimate the early patterns of SARS-CoV-2 transmission into and across Europe. We also address the more specific question of where the predominant SARS-CoV-2 lineage circulating in Europe originated. We hope that by addressing these questions we can inform further analysis of the efficacy of border closures as a strategy to combat SARS-CoV-2.The SARS-CoV-2 virus was identified as the cause of an epidemic in Wuhan, China in late 2019 (3). The epidemic in Wuhan was reported to the World Health Organization (WHO) on 31 December 2019 and within 1 mo, SARS-CoV-2 was confirmed to have spread to 19 additional countries (4). By the end of February 2020, the virus was detected in all WHO regions (https://covid19.who.int/). By late spring 2020, several lineages of the SARS-CoV-2 virus were circulating across the globe. The intermixing of these lineages in different countries and regions suggests that the virus was transmitted across borders many times (https://nextstrain.org/ncov/global).Here we focus on estimating the early introductions of SARS-CoV-2 into Europe and the virus’ migration across European borders. Through national surveillance efforts, the first COVID-19 cases in Europe were detected in France on 24 January 2020 and in Germany on 28 January 2020 (5, 6). Of the 47 cases detected in Europe by 21 February 2020, 14 were infected in China, 14 were linked to the initial cases in Germany, 7 were linked to the initial cases in France, and 12 were of unknown origin (5). In addition to the unknown sources of transmission, some early introductions may not have been detected. This is especially probable given that a significant proportion of infected individuals are likely to be asymptomatic (7). In summary, it is difficult to draw firm conclusions about the source, number, and timing of SARS-CoV-2 introductions into Europe based on confirmed case data alone.Viral genomes are an important secondary source of information on outbreak dynamics. If viruses acquire mutations on the same timescale as an outbreak, these mutations can provide information about past transmission events. Phylodynamic methods couple a model of viral evolution describing the mutational process to an epidemiological model describing the transmission process. By fitting the combined model to viral genomes sampled from a cohort of infected individuals, we can infer the evolutionary and epidemiological model parameters. Here we fit a phylodynamic model with geographic structure to SARS-CoV-2 genomes from Hubei, China and 19 European countries before the first borders were closed in these regions. We coinfer the transmission tree linking these sequences, the geographic location of ancestral lineages, migration rates of infected individuals between regions, the effective reproductive number, and the proportion of no-longer infectious cases sequenced in each region.In addition to these inferences, we specifically focus on estimating the geographic origin of the predominant SARS-CoV-2 lineage in Europe. This lineage is defined by a characteristic amino acid substitution at position 314 in the ORF1b gene from proline to leucine and was provisionally named the A2a lineage by the Nextstrain team, later renamed to 20A. In the more dynamic, tree-based “pangolin” nomenclature suggested by Rambaut et al. (8), this lineage corresponds to the B.1 lineage described as “A large European lineage that corresponds to the Italian outbreak.” (9). As of 1 April 2020, two-thirds of the SARS-CoV-2 sequences collected in Europe belonged to this lineage and just 10% of sequences from the lineage were collected outside Europe [data from https://www.gisaid.org/; lineages assigned using Nextstrain (10)]. Here, we use the name A2a to refer to the group of SARS-CoV-2 viruses defined by the ORF1b:P314L mutation.The origin of the A2a lineage was initially controversial, with conflicting reports in the academic and media press (11–14). Its characteristic ORF1b:P314L mutation was found in some of the earliest confirmed COVID-19 cases in Italy, Switzerland, Germany, Finland, Mexico, and Brazil in late February (11, 12). Intriguingly, a late-January sample from a cluster of infections in Bavaria, Germany linked to business travel from Shanghai, China (15, 16) shares a mutation at site 614 in the S gene with the A2a lineage, but does not have the A2a lineage-defining ORF1b:P314L mutation. This German sample is part of a smaller clade that is closely related to the larger clade of A2a sequences and which was originally named the A2 lineage but was later included in the larger 19A (Nextstrain nomenclature) or B (pangolin nomenclature) lineage (https://nextstrain.org/ncov/global). As a result, it was hypothesized that a German transmission cluster may have seeded the larger European outbreak (11–13). However, it was quickly pointed out that incomplete and biased sampling must be taken into account before this hypothesis can be rigorously addressed (12, 14, 17).Phylodynamic models with geographic structure aim to account for such biases. First, parameter estimates are generated by integrating over a distribution of potential phylogenies, which acknowledges that we cannot reconstruct the true transmission tree with certainty. Second, sampling parameters are allowed to differ between regions, which acknowledges that testing and sequencing resources vary across regions. Here, we fit a phylodynamic model with geographic structure to full-length SARS-CoV-2 genomes collected before 8 March 2020 to: 1) Estimate the early patterns of SARS-CoV-2 spread into and across Europe, 2) weigh genomic evidence for competing hypotheses about the geographic origin of the predominant A2a lineage in Europe, 3) report on the epidemiological parameters, and 4) compare the rate of new cases arising from within-region transmission versus migration during the early epidemic.     

长春地区人与猪戊型肝炎病毒分子流行病学及部分基因序列分析

目的分析长春地区猪和人群流行的戊型肝炎病毒的系统进化关系。方法参照文献设计引物,对长春地区猪和人群流行的8株HEV(其中3株来源于人,5株来源于猪)进行RT-PCR,并将RT-PCR产物克隆到p MD18-T载体,筛选阳性重组质粒测序,测序结果采用Clustal X v.1.8进行多重比对分析,并与基因1~4型HEV代表株的核苷酸及氨基酸进行同源性比较,绘制遗传进化树。结果本研究获得的8株HEV核苷酸同源性在91.2%~99.1%,推导氨基酸同源性在97.4%~100%之间;基因1~4型内各株序列间同源性分别为:87.9%~100%,100%,85.9%~96.6%,84.8%~100%。结论研究表明获得的长春各株病毒均属基因4型,由进化关系看长春地区猪HEV与人HEV可能由同一毒株进化而来。     

Genetic diversity and molecular epidemiology of the G protein of subgroups A and B of respiratory syncytial viruses isolated over 9 consecutive epidemics in Korea

To study genetic variation and molecular epidemiology of the G protein of respiratory syncytial virus (RSV), 253 strains from a children's hospital in Korea over 9 consecutive epidemics were analyzed. Restriction analysis of the entire G protein gene demonstrated 24 genotypes among 188 subgroup A and 6 among 65 subgroup B isolates. Two to 4 dominant genotypes of subgroup A cocirculated, and different genotypes predominated in each epidemic. Predominant genotypes were replaced with new genotypes during consecutive epidemics. One of 2 dominant genotypes among subgroup B predominated alternately or concurrently. Phylogenetic analysis revealed that there were multiple lineages, with clustering related to their location and time of isolation among strains from Korea and worldwide. Geographic and temporal distinction have been shown more clearly for subgroup B than subgroup A. These results suggest that the G protein of RSV is continuously evolving, with a distinct pattern presumably due to immune selection in a localized region over time.     

Smoking and the molecular epidemiology of lung cancer

Lung carcinogenesis in humans requires exposure to environmental agents, including the inhalation of tobacco smoke, radioactive compounds, asbestos, heavy metals, and petrochemicals. Tobacco smoking is the risk factor with the highest attributable lung cancer risk worldwide. This article discusses occupational carcinogen exposure and exposure from tobacco use, and the lung-cancer risk associated with these types of exposure.     

Characterization of severe acute respiratory syndrome coronavirus genomes in Taiwan: molecular epidemiology and genome evolution

Since early March 2003, the severe acute respiratory syndrome (SARS) coronavirus (CoV) infection has claimed 346 cases and 37 deaths in Taiwan. The epidemic occurred in two stages. The first stage caused limited familial or hospital infections and lasted from early March to mid-April. All cases had clear contact histories, primarily from Guangdong or Hong Kong. The second stage resulted in a large outbreak in a municipal hospital, and quickly spread to northern and southern Taiwan from late April to mid-June. During this stage, there were some sporadic cases with untraceable contact histories. To investigate the origin and transmission route of SARS-CoV in Taiwan's epidemic, we conducted a systematic viral lineage study by sequencing the entire viral genome from ten SARS patients. SARS-CoV viruses isolated from Taiwan were found closely related to those from Guangdong and Hong Kong. In addition, all cases from the second stage belonged to the same lineage after the municipal hospital outbreak, including the patients without an apparent contact history. Analyses of these full-length sequences showed a positive selection occurring during SARS-CoV virus evolution. The mismatch distribution indicated that SARS viral genomes did not reach equilibrium and suggested a recent introduction of the viruses into human populations. The estimated genome mutation rate was approximately 0.1 per genome, demonstrating possibly one of the lowest rates among known RNA viruses.     

Anatomical enablers and the evolution of C4 photosynthesis in grasses

C₄ photosynthesis is a series of anatomical and biochemical modifications to the typical C₃ pathway that increases the productivity of plants in warm, sunny, and dry conditions. Despite its complexity, it evolved more than 62 times independently in flowering plants. However, C₄ origins are absent from most plant lineages and clustered in others, suggesting that some characteristics increase C₄ evolvability in certain phylogenetic groups. The C₄ trait has evolved 22–24 times in grasses, and all origins occurred within the PACMAD clade, whereas the similarly sized BEP clade contains only C₃ taxa. Here, multiple foliar anatomy traits of 157 species from both BEP and PACMAD clades are quantified and analyzed in a phylogenetic framework. Statistical modeling indicates that C₄ evolvability strongly increases when the proportion of vascular bundle sheath (BS) tissue is higher than 15%, which results from a combination of short distance between BS and large BS cells. A reduction in the distance between BS occurred before the split of the BEP and PACMAD clades, but a decrease in BS cell size later occurred in BEP taxa. Therefore, when environmental changes promoted C₄ evolution, suitable anatomy was present only in members of the PACMAD clade, explaining the clustering of C₄ origins in this lineage. These results show that key alterations of foliar anatomy occurring in a C₃ context and preceding the emergence of the C₄ syndrome by millions of years facilitated the repeated evolution of one of the most successful physiological innovations in angiosperm history.     

Present status of studies on epidemiology and molecular epidemiology of Mycobacterium kansasii, in special reference to its molecular epidemiology

There appears to be some genetic diversity among Mycobacterium kansasii (M. kansasii) isolates recovered throughout the world. Restriction analysis of heat shock protein 65-polymerase chain reaction-restriction analysis (hsp65PRA) showed that M. kansasii contains seven subspecies genetically distinct from M. kansasii isolates. M. kansasii genotype I is predominant in Japan and shows a very tight clonal structure. Different molecular typing methods including the 16S-23S rRNA spacer (ITS) region, RFLP, and PFGE analysis have been applied to isolates worldwide, and M. kansasii genotype I, as defined by hsp65PRA, appears to be highly clonal and the most common genotype associated with human disease. However, the identification of M. kansasii at the subtype level may possibly be more than just an interesting epidemiological tool; it may be relevant to determining the infectious pathway and clinical management of individual cases, as it allows the differentiation of potentially pathogenic subtypes from nonpathogenic subtypes. This review has been followed by the first review of the epidemiology of M. kansasii, and summarizes the evidence of molecular epidemiology and establishes the validity and importance of studies of M. kansasii. Further, the more precise definition of various M. kansasii isolates herein should provide a significant contribution to the understanding of key aspects of its biology, genotype, and molecular epidemiology.     

Resetting the evolution of marine reptiles at the Triassic-Jurassic boundary

Ichthyosaurs were important marine predators in the Early Jurassic, and an abundant and diverse component of Mesozoic marine ecosystems. Despite their ecological importance, however, the Early Jurassic species represent a reduced remnant of their former significance in the Triassic. Ichthyosaurs passed through an evolutionary bottleneck at, or close to, the Triassic-Jurassic boundary, which reduced their diversity to as few as three or four lineages. Diversity bounced back to some extent in the aftermath of the end-Triassic mass extinction, but disparity remained at less than one-tenth of pre-extinction levels, and never recovered. The group remained at low diversity and disparity for its final 100 Myr. The end-Triassic mass extinction had a previously unsuspected profound effect in resetting the evolution of apex marine predators of the Mesozoic.     

The molecular epidemiology of malaria

This review discusses how the use of molecular genetic techniques such as the polymerase chain reaction are helping in the management and prevention of malaria.     

Innovations in the molecular epidemiology of tuberculosis

The application of genotyping tools to the analysis of tuberculosis (TB) has allowed us to identify clinical isolates of Mycobacterium tuberculosis to strain level. M. tuberculosis fingerprinting has been applied at different levels: a) in the laboratory, to optimize identification of cross-contamination events which can lead to a false diagnosis; b) in the patient, to determine whether recurrences are due to reactivations or exogenous reinfections or to identify cases coinfected by more than one strain; c) at the micropopulation level, to identify clusters of cases infected by the same strains (recent transmission) and to differentiate them from orphan cases that are most probably due to reactivations; and d) at the macropopulation level, to define the global distribution of M. tuberculosis lineages, to monitor the international spread of high-risk strains, and to explore the evolutionary features of M. tuberculosis. In recent years, important methodological and strategic advances have been applied at these different levels of analysis. Rather than provide an exhaustive review, the present study focuses on specific advances in micropopulation and macropopulation analysis.     

The transmission dynamics and diversity of human metapneumovirus in Peru

Background

The transmission dynamics of human metapneumovirus (HMPV) in tropical countries remain unclear. Further understanding of the genetic diversity of the virus could aid in HMPV vaccine design and improve our understanding of respiratory virus transmission dynamics in low‐ and middle‐income countries.

Materials & Methods

We examined the evolution of HMPV in Peru through phylogenetic analysis of 61 full genome HMPV sequences collected in three ecologically diverse regions of Peru (Lima, Piura, and Iquitos) during 2008‐2012, comprising the largest data set of HMPV whole genomes sequenced from any tropical country to date.

Results

We revealed extensive genetic diversity generated by frequent viral introductions, with little evidence of local persistence. While considerable viral traffic between non‐Peruvian countries and Peru was observed, HMPV epidemics in Peruvian locales were more frequently epidemiologically linked with other sites within Peru. We showed that Iquitos experienced greater HMPV traffic than the similar sized city of Piura by both Bayesian and maximum likelihood methods.

Conclusions

There is extensive HMPV genetic diversity even within smaller and relatively less connected cities of Peru and this virus is spatially fluid. Greater diversity of HMPV in Iquitos compared to Piura may relate to higher volumes of human movement, including air traffic to this location.     

加拿大棘球绦虫的基因分型与分子流行病学研究进展

通过比较加拿大棘球绦虫不同基因型的线粒体基因组,尤其是其中的cox1和nad1基因核苷酸序列的差异性,了解加拿大棘球绦虫各基因型的分子遗传标记特征与变异情况,阐明加拿大棘球绦虫基因型在棘球属中的分类地位、命名和进化关系。另外,本文通过对加拿大棘球绦虫各基因型的分子流行病学特征、研究意义、未来研究方向等进行综述,为从事该领域研究的学者和临床工作者提供丰富的分子流行病学信息或资料,并为棘球蚴病分子流行病学调查、预警预报和综合防治策略的制定等提供理论依据和指导。     

Heterogeneity in tuberculosis transmission and the role of geographic hotspots in propagating epidemics

The importance of high-incidence "hotspots" to population-level tuberculosis (TB) incidence remains poorly understood. TB incidence varies widely across countries, but within smaller geographic areas (e.g., cities), TB transmission may be more homogeneous than other infectious diseases. We constructed a steady-state compartmental model of TB in Rio de Janeiro, replicating nine epidemiological variables (e.g., TB incidence) within 1% of their observed values. We estimated the proportion of TB transmission originating from a high-incidence hotspot (6.0% of the city's population, 16.5% of TB incidence) and the relative impact of TB control measures targeting the hotspot vs. the general community. If each case of active TB in the hotspot caused 0.5 secondary transmissions in the general community for each within-hotspot transmission, the 6.0% of people living in the hotspot accounted for 35.3% of city-wide TB transmission. Reducing the TB transmission rate (i.e., number of secondary infections per infectious case) in the hotspot to that in the general community reduced city-wide TB incidence by 9.8% in year 5, and 29.7% in year 50-an effect similar to halving time to diagnosis for the remaining 94% of the community. The importance of the hotspot to city-wide TB control depended strongly on the extent of TB transmission from the hotspot to the general community. High-incidence hotspots may play an important role in propagating TB epidemics. Achieving TB control targets in a hotspot containing 6% of a city's population can have similar impact on city-wide TB incidence as achieving the same targets throughout the remaining community.