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  • 1.

    【2hr】Evolutionary dynamics and molecular epidemiology of West Nile virus in New York State: 1999–2015

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    机译 纽约州西尼罗河病毒的进化动力学和分子流行病学：1999–2015年
    摘要：
  • 2.

    【2hr】A complex evolutionary relationship between HHV-6A and HHV-6B

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    机译 HHV-6A和HHV-6B之间的复杂进化关系
    摘要：Human betaherpesviruses 6A and 6B (HHV-6A and HHV-6B) are highly prevalent in human populations. The genomes of these viruses can be stably integrated at the telomeres of human chromosomes and be vertically transmitted (inherited chromosomally integrated HHV-6, iciHHV6). We reconstructed the population structure of HHV-6 and we show that HHV-6A genomes diverged less than HHV-6B genomes from the ancestral common HHV-6A/B population. Analysis of ancestry proportions indicated that HHV-6A exogenous viruses and iciHHV-6A derived most of their genomes from distinct ancestral sources. Conversely, exogenous viral and iciHHV-6B populations were similar in terms of ancestry components, with no evident geographic structuring. Most HHV-6B genomes sampled to date derive from viral populations that experienced considerable drift. However, a population of HHV-6 exogenous viruses, currently classified as HHV-6B and sampled in New York state, formed a separate cluster (NY cluster) and harbored a considerable portion of HHV-6A-like ancestry. Recombination detection methods identified these viruses as interspecies recombinants, but phylogenetic reconstruction indicated that the recombination signals are due to shared ancestry. In analogy to iciHHV-6A, NY cluster viruses have high nucleotide diversity and constant population size. We propose that HHV-6A sequences and the NY cluster population diverged from an ancestral HHV-6A-like population. A relatively recent bottleneck of the NY (or a related) population with subsequent expansion originated most HHV-6B genomes currently sampled. Our findings indicate that the distinction between HHV-6A and -6B is not as clear-cut as previously thought. More generally, epidemiological and clinical surveys would benefit from taking HHV-6 genetic diversity into account.
  • 3.

    【2hr】Modular nature of simian foamy virus genomes and their evolutionary history

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    机译 猿猴泡沫病毒基因组的模块性质及其进化史
    摘要：Among all known retroviruses, foamy viruses (FVs) have the most stable virus–host co-speciation history, co-diverging in concert with their vertebrate hosts for hundreds of millions of years. However, detailed molecular analyses indicate that different parts of their genome might have different evolutionary histories. While their polymerase gene displays a robust and straightforward virus–host co-speciation pattern, the evolutionary history of their envelope (env) gene, is much more complicated. Here, we report eleven new FV env sequences in two mandrill populations in Central Africa, geographically separated by the Ogooué River into the North and the South populations. Phylogenetic reconstruction of the polymerase gene shows that the two virus populations are distinct, and each contains two variants of env genes co-existing with one another. The distinction between the two env variants can be mapped to the surface domain, flanked by two recombination hotspots, as previously reported for chimpanzee and gorilla FVs. Our analyses suggest that the two env variants originated during the diversification of Old World monkeys and apes, ∼30 million years ago. We also show that this env gene region forms two phylogenetically distinct clades, each displaying a host co-divergence and geographical separation pattern, while the rest of the genome of the two strains is phylogenetically indistinguishable in each of the host-specific groups. We propose possible evolutionary mechanisms to explain the modular nature of the FV genome.
  • 4.

    【2hr】Inferring putative transmission clusters with Phydelity

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    机译 用Phydelity推断推定的传输簇
    摘要：Current phylogenetic clustering approaches for identifying pathogen transmission clusters are limited by their dependency on arbitrarily defined genetic distance thresholds for within-cluster divergence. Incomplete knowledge of a pathogen’s underlying dynamics often reduces the choice of distance threshold to an exploratory, ad hoc exercise that is difficult to standardise across studies. Phydelity is a new tool for the identification of transmission clusters in pathogen phylogenies. It identifies groups of sequences that are more closely related than the ensemble distribution of the phylogeny under a statistically principled and phylogeny-informed framework, without the introduction of arbitrary distance thresholds. Relative to other distance threshold- and model-based methods, Phydelity outputs clusters with higher purity and lower probability of misclassification in simulated phylogenies. Applying Phydelity to empirical datasets of hepatitis B and C virus infections showed that Phydelity identified clusters with better correspondence to individuals that are more likely to be linked by transmission events relative to other widely used non-parametric phylogenetic clustering methods without the need for parameter calibration. Phydelity is generalisable to any pathogen and can be used to identify putative direct transmission events. Phydelity is freely available at .
  • 5.

    【2hr】Hepatitis C virus genotype 1 and 2 recombinant genomes and the phylogeographic history of the 2k/1b lineage

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    机译 丙型肝炎病毒基因型1和2的重组基因组和2k / 1b谱系的系统地理记录
    摘要：Recombination is an important driver of genetic diversity, though it is relatively uncommon in hepatitis C virus (HCV). Recent investigation of sequence data acquired from HCV clinical trials produced twenty-one full-genome recombinant viruses belonging to three putative inter-subtype forms 2b/1a, 2b/1b, and 2k/1b. The 2k/1b chimera is the only known HCV circulating recombinant form (CRF), provoking interest in its genetic structure and origin. Discovered in Russia in 1999, 2k/1b cases have since been detected throughout the former Soviet Union, Western Europe, and North America. Although 2k/1b prevalence is highest in the Caucasus mountain region (i.e., Armenia, Azerbaijan, and Georgia), the origin and migration patterns of CRF 2k/1b have remained obscure due to a paucity of available sequences. We assembled an alignment which spans the entire coding region of the HCV genome containing all available 2k/1b sequences (>500 nucleotides; n = 109) sampled in ninteen countries from public databases (102 individuals), additional newly sequenced genomic regions (from 48 of these 102 individuals), unpublished isolates with newly sequenced regions (5 additional individuals), and novel complete genomes (2 additional individuals) generated in this study. Analysis of this expanded dataset reconfirmed the monophyletic origin of 2k/1b with a recombination breakpoint at position 3,187 (95% confidence interval: 3,172–3,202; HCV GT1a reference strain H77). Phylogeography is a valuable tool used to reveal viral migration dynamics. Inference of the timed history of spread in a Bayesian framework identified Russia as the ancestral source of the CRF 2k/1b clade. Further, we found evidence for migration routes leading out of Russia to other former Soviet Republics or countries under the Soviet sphere of influence. These findings suggest an interplay between geopolitics and the historical spread of CRF 2k/1b.
  • 6.

    【2hr】The multifurcating skyline plot

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    机译 多分支天际线图
    摘要：
  • 7.

    【2hr】Potato virus Y; the Andean connection

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    机译 马铃薯Y病毒；安第斯山脉
    摘要：Potato virus Y (PVY) causes disease in potatoes and other solanaceous crops. The appearance of its necrogenic strains in the 1980s made it the most economically important virus of potatoes. We report the isolation and genomic sequences of 32 Peruvian isolates of PVY which, together with 428 published PVY genomic sequences, gave an alignment of 460 sequences. Of these 190 (41%) were non-recombinant, and 162 of these provided a dated phylogeny, that corresponds well with the likely history of PVY, and show that PVY originated in South America which is where potatoes were first domesticated. The most basal divergences of the PVY population produced the N and C: O phylogroups; the origin of the N phylogroup is clearly Andean, but that of the O and C phylogroups is unknown, although they may have been first to establish in European crops. The current PVY population originated around 156 CE. PVY was probably first taken from South America to Europe in the 16th century in tubers. Most of the present PVY diversity emerged in the second half of the 19th century, after the Phytophthora infestans epidemics of the mid-19th century destroyed the European crop and stimulated potato breeding. Imported breeding lines were shared, and there was no quarantine. The early O population was joined later by N phylogroup isolates and their recombinants generated the R1 and R2 populations of damaging necrogenic strains. Our dating study has confirmed that human activity has dominated the phylodynamics of PVY for the last two millennia.
  • 8.

    【2hr】The multifurcating skyline plot

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    机译 多分支天际线图
    摘要：A variety of methods based on coalescent theory have been developed to infer demographic history from gene sequences sampled from natural populations. The ‘skyline plot’ and related approaches are commonly employed as flexible prior distributions for phylogenetic trees in the Bayesian analysis of pathogen gene sequences. In this work we extend the classic and generalized skyline plot methods to phylogenies that contain one or more multifurcations (i.e. hard polytomies). We use the theory of Λ-coalescents (specifically, Beta(2-α,α)-coalescents) to develop the ‘multifurcating skyline plot’, which estimates a piecewise constant function of effective population size through time, conditional on a time-scaled multifurcating phylogeny. We implement a smoothing procedure and extend the method to serially sampled (heterochronous) data, but we do not address here the problem of estimating trees with multifurcations from gene sequence alignments. We validate our estimator on simulated data using maximum likelihood and find that parameters of the Beta(2-α,α) -coalescent process can be estimated accurately. Furthermore, we apply the multifurcating skyline plot to simulated trees generated by tracking transmissions in an individual-based model of epidemic superspreading. We find that high levels of superspreading are consistent with the high-variance assumptions underlying Λ-coalescents and that the estimated parameters of the Λ-coalescent model contain information about the degree of superspreading.
  • 9.

    【2hr】DisCVR: Rapid viral diagnosis from high-throughput sequencing data

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    机译 DisCVR：根据高通量测序数据进行快速病毒诊断
    摘要：High-throughput sequencing (HTS) enables most pathogens in a clinical sample to be detected from a single analysis, thereby providing novel opportunities for diagnosis, surveillance, and epidemiology. However, this powerful technology is difficult to apply in diagnostic laboratories because of its computational and bioinformatic demands. We have developed DisCVR, which detects known human viruses in clinical samples by matching sample k-mers (twenty-two nucleotide sequences) to k-mers from taxonomically labeled viral genomes. DisCVR was validated using published HTS data for eighty-nine clinical samples from adults with upper respiratory tract infections. These samples had been tested for viruses metagenomically and also by real-time polymerase chain reaction assay, which is the standard diagnostic method. DisCVR detected human viruses with high sensitivity (79%) and specificity (100%), and was able to detect mixed infections. Moreover, it produced results comparable to those in a published metagenomic analysis of 177 blood samples from patients in Nigeria. DisCVR has been designed as a user-friendly tool for detecting human viruses from HTS data using computers with limited RAM and processing power, and includes a graphical user interface to help users interpret and validate the output. It is written in Java and is publicly available from .
  • 10.

    【2hr】A22 Phylogenetic clustering of hepatitis C virus infection among people who inject drugs in Baltimore

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    机译 A22巴尔的摩注射毒品者中丙型肝炎病毒感染的系统发生聚类
    摘要：The availability of effective, oral direct acting antivirals for hepatitis C virus (HCV) treatment has fueled optimism for HCV elimination through treatment as prevention (TasP) among people who inject drugs (PWID). Identifying characteristics of individuals in transmission networks would provide critical information for the development and implementation of effective, targeted HCV TasP strategies. The AIDS linked to the IntraVenous Experience (ALIVE) cohort has followed PWID in Baltimore since 1988. Sequencing of the HCV core/E1 region (342 nucleotides) was performed on HCV viremic samples from the most recent study visit attended by ALIVE participants between August, 2005 and December, 2016. Outgroup sequences were retrieved from GenBank through a BLAST search for HCV sequences similar to study sequences to support identification of ‘local clusters’ and were aligned to study sequences using Clustal O. Phylogenetic trees were inferred for each of HCV subtype 1a and 1b separately through maximum likelihood analysis implemented in the MEGA X software using the Tamura-Nei model with gamma distribution and invariant sites. Nucleotide substitution model selection was based on the corrected Akaike information criterion scores of various models in MEGA. Robustness of the resulting tree was assessed by bootstrapping with 1,000 replicates. Clusters were identified using ClusterPicker software (70% bootstrap threshold and 0.05 maximum genetic distance threshold). Sensitivity analyses were performed by varying the genetic distance threshold between 0.025 and 0.05 to determine the effect on identification of factors associated with clustering. HCV infection clustering was defined as > 2 participants with HCV genome sequences satisfying 70 per cent bootstrap and 0.05 genetic threshold distance requirement for sequence similarity. Logistic regression was used to assess sociodemographic factors associated with being in an HCV cluster. Among 512 HCV genotype 1 viremic PWID, HCV subtype prevalence was 83 per cent genotype 1a and 17 per cent genotype 1b. The median age of participants was 54 years, 68 per cent male, 87 per cent Black, and 38 per cent HIV infected. Overall, 9 per cent (n = 44) were grouped into 21 clusters, consisting of 20 pairs and 1 triad. Of the 425 genotype 1a and 87 genotype 1b samples evaluated, 8 per cent (n = 33) and 13 per cent (n = 11) respectively, were in clusters. In unadjusted analyses, membership in a cluster, was associated with younger age (odds ratio (OR) 1.5 [95% confidence interval (CI) 1.1–2.1] per 10 year age decrease); female sex (OR 2.8 [95% CI 1.5–5.3]), HIV infection (OR 4.9 [95% CI 2.5–9.9]), and living in East Baltimore (versus outside East Baltimore, OR 2.0 [95% CI 1.0–3.9]). In adjusted analyses, female sex (OR 2.0 [95% CI 1.0–3.9] and HIV infection (OR 5.4 [95% CI 2.6–11.1] remained independently associated with being in an HCV infection cluster. HIV-infected PWID and their networks should be prioritized for HCV treatment and prevention interventions given an increased likelihood of transmission in these groups.
  • 11.

    【2hr】A50 Whole-genome sequencing of African swine fever isolates from Sardinia

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    机译 A50撒丁岛非洲猪瘟分离株的全基因组测序
    摘要：In order to assess the molecular epidemiology of African swine fever (ASF) in Sardinia, we analyzed a wide range of isolates from wild and domestic pigs over a 31-year period (1978–2009) by genotyping sequence data from the genes encoding the p54 and the p72 proteins and the CVR. On this basis, the analysis of the B602L gene revealed a minor difference, placing the Sardinian isolates into two clusters according to their temporal distribution. As an extension of this study, in order to achieve a higher level of discrimination, three further variable genome regions, namely p30, CD2v, and I73R/I329L, of a large number of isolates collected from outbreaks in the years 2002–14 have been investigated. Sequence analysis of the CD2v region revealed a temporal subdivision of the viruses into two subgroups. These data, together with those from the B602L gene analysis, demonstrated that the viruses circulating in Sardinia belong to p72/genotype I, but since 1990 have undergone minor genetic variations in respect to its ancestor, thus making it impossible to trace isolates, enabling a more accurate assessment of the origin of outbreaks, and extending knowledge of virus evolution. To solve this problem, we have sequenced and annotated the complete genome of nine ASF isolates collected in Sardinia between 1978 and 2012. This was achieved using sequence data determined by next-generation sequencing. The results showed a very high identity with range of nucleotide similarity among isolates of 99.5 per cent to 99.9 per cent. The ASF virus (ASFV) genomes were composed of terminal inverted repeats and conserved and non-conserved ORFs. Among the conserved ORFs, B385R, H339R, and O61R-p12 showed 100 per cent amino acid identity. The same was true for the hypervariable ORFs, with regard to X69R, DP96R, DP60R, EP153R, B407L, I10L, and L60L genes. The EP402R and B602L genes showed, as expected, an amino acid identity range of 98.5 per cent to 100 per cent and 91 per cent to 100 per cent, respectively. In addition, all of the isolates displayed variable intergenic sequences. As a whole, the results from our studies confirmed a remarkable genetic stability of the ASFV/p72 genotype I viruses circulating in Sardinia.
  • 12.

    【2hr】A4 An amplicon-based approach for universal amplification, sequencing, and assembly of full-length HIV-1 samples from the DRC

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    机译 A4一种基于扩增子的方法，用于对刚果民主共和国的全长HIV-1样本进行通用扩增，测序和组装
    摘要：Phylogenetic studies have contributed to our understanding of the early epidemic onset of HIV-1 in the Democratic Republic of Congo (DRC); however, the factors driving its early emergence and establishment in human populations still remain unresolved. In order to determine the key aspects of its successful epidemic spread, complete genome data are required from samples representative of the viral diversity in the DRC. In this study, we have established a universal PCR-assay that uses seven different panels of primers to produce overlapping amplicons covering the complete HIV genome. To circumvent the limitations of purifying these fragments and sequencing them with traditional approaches, we have developed a massive parallel sequencing method and a protocol for efficiently assembling HIV-1 genomes. A total of thirty-six samples, collected between 1997 and 2001 from different locations across the DRC, have been obtained, and, at this stage, we are focusing on complementing our dataset with more archival samples that can be used as HIV ‘molecular fossils’. By generating complete genome phylogeographic data from the DRC, we aim to create a genomic window into the past evolutionary and epidemiological dynamics of HIV-1 in Central Africa and understand the natural history of this devastating pandemic.
  • 13.

    【2hr】A39 Reconstruction of Ebola chains of transmission using sequence and epidemiological data

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    机译 A39利用序列和流行病学数据重建埃博拉传播链
    摘要：Transmission trees can be established through detailed contact histories, statistical inference, phylogenetic inference, or a combination of methods. Each method has its limitations, and the extent to which they succeed in revealing a ‘true’ transmission history remains unclear. Moreover, the net value of pathogen sequencing in transmission tree reconstruction is yet to be assessed. We explored the accuracy and sensitivity to biases of a range of methods for transmission chain inference. We studied eight transmission chains determined by contact tracing, each one having more than a third of its cases sequenced (87 samples over 199 cases in total). We compared three inference methods on the selected transmission chains: (i) phylogenetic inference: the Ebola virus (EBOV) sequences derived from patients were mapped onto a dated EBOV phylogeny tree including 398 EBOV sequences sampled in Guinea between March 2014 and October 2015; (ii) statistical inference: we used the maximum likelihood framework developed by Wallinga and Teunis to infer the most likely transmitter-recipient relationships from the onset dates; (iii) combined method: we inferred probabilistic transmission events using both pathogen sequences and collection dates with the R package Outbreaker2. The cases coming from each transmission chain were mostly clustered together in the phylogenetic tree. The few misclassified cases were most likely allocated to the wrong chains of transmission because of the timing of their symptom onsets. Probabilistic transmission tree using only onset dates broadly matched the contact tracing data, but multiple potential infectors were identified for each case. The combined method showed that an a priori knowledge of the number of independent imports had an important impact on the outcome. Although cases were allocated to the correct transmission chains, discrepancies were found in identifying direct case linkage and transmission generations within a chain. Phylogenetic, epidemiological, and combined approaches for transmission chain reconstructions globally concurred in their output. Sequence data proved useful (if not necessary) to place the sampled cases in a wider context, identify transmission clusters, and misclassified cases when epidemiological chains are inferred from date of symptom onset only, and to identify links between supposedly independent chains of transmission.
  • 14.

    【2hr】A49 Emerging rodent-borne viral pathogens in Italy: Overview of seroprevalence and genomic investigations

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    机译 A49意大利新出现的啮齿动物传播的病毒病原体：血清阳性率和基因组研究概述
    摘要：Rodents play a key role as reservoirs of many zoonotic pathogens which represent an emerging public health threat worldwide. Among these, Dobrava-Belgrade virus (DOBV) is the most pathogenic hantavirus in Europe with a case-fatality rate of up to 12 per cent, while Lymphocytic choriomeningitis virus (LCMV) has a mortality rate below 1 per cent. Both viruses are predominantly transmitted to humans through the inhalation of infected particles in aerosolized urine, feces, or saliva that are shed in the environment by chronically infected hosts, such as the yellow-necked mouse Apodemus flavicollis. Although no human cases of DOBV or LCMV have been reported in the Province of Trento (northeastern Italy) thus far, in order to evaluate the human hazard for these viruses, the prevalence of antibodies to DOBV and LCMV has been monitored using a specific immunofluorescence assay test in a wild population of A. flavicollis since 2000. These investigations have shown that the two RNA viruses circulate silently in this species in the study area. In particular, a sudden increase (up to 12.5%) in DOBV seroprevalence was observed in this rodent species between 2010 and 2012. Several efforts have been undertaken to isolate these viruses and characterize their genomes, but it has not yet been possible to detect viral RNA from seropositive mice using traditional methods such as RT-PCR. Since RNA viruses are very diverse and often difficult to isolate, innovative molecular methods based on viral targeted enrichment and high-throughput sequencing have been applied. We intend to report on this long-term seroprevalence study and provide an overview of the molecular approaches adopted in the attempt to confirm the presence of these viruses, and identify which variants are circulating in the region, as well as their pathogenicity.
  • 15.

    【2hr】A59 A strategy to studying zoonotic infectious diseases

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    机译 A59研究人畜共患传染病的策略
    摘要：An increasing number of zoonotic viruses have been detected in animals, especially in poultry species. Understanding the diversity of zoonotic infections and the local behavior helps to characterize the pathogen diversity in human and animals and predict the risk of pathogen spill-over from animals to human. Vietnam is considered, along with other countries in Southeast Asia, as a hotspot for zoonotic viruses. In Vietnam, domestic animals are typically farmed in close proximity to humans, which may increase the risk of transmission of zoonotic pathogens. Our previous studies found the presence of some zoonotic viruses (e.g. rotavirus group A, hepatitis E virus) in domestic pigs. However, the risk of pathogenic transmission from domestic animals to humans has not been determined. Detailed genomic sequence data may help to track the origin and evolution of zoonotic pathogens. To understand the origins and emergence of zoonotic infections in people, who have regular contact with animals, we will investigate the viral diversity in farmers and domestic animals in their farm, using high-throughput sequencing technique. Viral RNA was extracted from pooled fecal samples of 30 farmers and 50 pigs, and used as input for SureSelect target enrichment and Illumina MiSeq sequencing.
  • 16.

    【2hr】A23 Population level diversification of hepatitis C viral strains over time among people who inject drugs in Baltimore, MD

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    机译 A23马里兰州巴尔的摩市注射毒品的人群中丙型肝炎病毒株的人群水平随时间推移而多样化
    摘要：Hepatitis C virus (HCV) infection occurs in 30–90 per cent of people who inject drugs (PWID). Although cure rates can exceed 95 per cent, treatment access is limited and approximately 400,000 people die each year due to complications of chronic infection. A temporal analysis of cluster networks among PWID can be used to inform strategies to interdict transmission. In Baltimore, PWID have been recruited for The AIDS Linked to the IntraVenous Experience (ALIVE) cohort. A demographic questionnaire was administered and recorded for baseline and recent participants. Viral RNA underwent PCR with primers targeting the core and envelope-1 protein (CE1) and sequenced via Sanger sequencing. Sequences with > 400 bp reads and Q-scores >370 were used for downstream analysis resulting in 322 ALIVE baseline participants (1988–9) and 548 recently diagnosed subjects enrolled approximately two decades later (2005–16). Cluster networks were rendered with a threshold of 4 per cent in MicrobeTRACE, and statistical analyses were performed in R Studio. Of the 1988–9 subjects, the majority (259/317, 81.7%) were a part of cluster. There were nine clusters and fifty-eight singletons, with two large clusters containing most sequences of genotype 1a (73.5%). Two decades later, a minority of recently diagnosed individuals (235/512, 44.1%) were part of a cluster. There were seventeen clusters with 286 singletons with two large clusters containing 1a genotype individuals (21.5%). Additional clustering was done by parsing the two datasets by subtype 1a (n = 714) and 1b (n = 151). The genotype 1a network demonstrates a majority, 65.8 per cent, of participants in clusters. Moreover, two large clusters can be observed with baseline participants towards the center and recent participants on the outskirts indicative of high linkage at baseline. The genotype 1b network produced a single large cluster but subclusters were observed. The sequences between the two time points co-mingled but subclusters were also observed. Interestingly, the two large clusters from 1988 to 1989 were still evident in the 2005–16 viral sequences. We observed greater cluster diversity in more recently diagnosed individuals, indicative of a less connected network of individuals sharing transmission risk, though major viral strains did persist over time in this cohort.
  • 17.

    【2hr】A54 Genomic analysis of camel-HKU23 in Nigeria dromedary camels reveals strain-specific cross-species recombination

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    机译 A54在尼日利亚单峰骆驼中骆驼-HKU23的基因组分析揭示了菌株特异性的跨物种重组
    摘要：Coronaviruses (CoVs) are enveloped, single stranded, positive-sense RNA viruses with a large genomic size of 26–32 kilobases. The first human CoV identified in the 1960s was isolated from patients presenting with common cold symptoms. Subsequent epidemic outbreaks of novel zoonotic CoV transmission were reported, examples including HCoV-229E (229E), HCoV-OC43 (OC43), severe acute respiratory syndrome, and Middle East respiratory syndrome (MERS). The ongoing outbreak of MERS in the Middle East is originating from a zoonotic source of dromedary camels. Surveillance later revealed that three CoV species—HCoV-229E (229E), camel-HKU23, and MERS-CoV—were co-circulating in Saudi Arabia dromedary camels. Camel-HKU23 belongs to Group 2a CoV, which also includes human coronavirus OC43, bovine coronavirus, and porcine hemagglutinating encephalomyelitis virus. Recombination, resulting in the generation of different novel genotypes, has been reported previously among these CoVs. Our surveillance of dromedary camels slaughtered in a major abattoir in Nigeria identified camel-HKU23 from nasal swab samples with a prevalence of 2.2 per cent. Phylogenetic analysis showed Nigeria camel-HKU23 is distinct from those previously identified in Saudi Arabia, while still genetically similar, as they share a monophyletic origin. Recombination analysis of Nigeria camel-HKU23 revealed two recombination breakpoints at positions of 22774–24100 base pairs (bp) and 28224–29362 bp. Recombination breakpoint at position 22774, encoding the Group 2a CoV-specific hemagglutinin esterase gene, exhibited high bootstrap support for clustering with RbCoV HKU14, which was previously detected in domestic rabbits in China. The recombination signal is only observed in Nigeria camel-HKU23, suggesting a regional varied evolutionary history of camel-HKU23. Our findings extended the knowledge of the evolutionary relationship among Group 2a CoVs. Further surveillance in other African camels will be important to elucidate the evolution of camel-HKU23.
  • 18.

    【2hr】A11 Evaluation of phylogenetic inference methods to determine direction of HIV transmission

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    机译 A11系统发育推断方法的评估，以确定艾滋病毒的传播方向
    摘要：It has been postulated that the direction of HIV transmission between two individuals can be determined by phylogenetic analysis of HIV sequences. This approach may be problematic, since HIV sequences from newly infected individuals are often more similar to index sequences from samples collected years before transmission, compared to those from samples collected at the time of transmission. We evaluated the accuracy of phylogenetic methods for determining the direction of HIV transmission by analyzing next-generation sequencing (NGS) data from index–partner pairs enrolled in the HIV Prevention Trials Network (HPTN) 052 trial. HIV-infected index and HIV-uninfected partner participants were enrolled as serodiscordant couples; samples were analyzed from couples with index-to-partner HIV transmission that was confirmed by genetic linkage studies. NGS for HIV gp41 (HXB2 coordinates: 7691–8374) was performed using plasma samples from thirty-nine index–partner pairs (seventy-eight samples collected within 3 months of partner seroconversion). Maximum likelihood trees were generated using the entire dataset using FastTree v.2. Topological patterns of HIV from each index–partner pair were analyzed. The analysis included 9,368 consensus sequences and 521,145 total sequence reads for the seventy-eight samples analyzed. In 10 per cent (four out of thirty-nine) of couples, the phylogeny was inconsistent with the known direction of transmission. In 26 per cent (ten out of thirty-nine) of couples, the phylogeny results could not discern directionality. In 64 per cent (twenty-five out of thirty-nine) of couples, the results correctly indicated index-to-partner transmission; in two of these twenty-five cases, only one index sequence was closest to the most recent common ancestor. Phylogenetic analysis of NGS data obtained from samples collected within 3 months of transmission correctly determined the direction of transmission in 64 per cent of the cases analyzed. In 36 per cent of the cases, the phylogenetic topology did not support the known direction of infection, and in one-third of these cases the observed topology was opposite to the known direction of transmission. This demonstrates that phylogenetic topology alone may not be sufficient to accurately determine the direction of HIV transmission.
  • 19.

    【2hr】A40 Estimation of Lassa virus emergence in Upper Guinea through a time-calibrated phylogeny

    包量

    机译 A40通过时间校准的系统发育对上几内亚拉萨病毒的出现进行估计
    摘要：Lassa fever is a hemorrhagic fever caused by an arenavirus, the Lassa virus (LASV), and can affect 150–200,000 persons per year in West Africa. The virus is hosted by several rodents, Mastomys natalensis and M. erythroleucus, Hylomyscus pamfi, and Mus baoulei. People can be contaminated at home or in the farms, by touching contaminated surfaces, eating contaminated food, or breathing aerosolized viral particles. Human-to-human transmission is occurring as well through infected bodily fluids. In Upper Guinea in particular, M. natalensis is the main host, with LASV prevalence of 14 per cent and IgG prevalence of 27 per cent. In humans, IgG prevalence is 40 per cent. This is, therefore, a hot spot for LASV transmission. In a previous phylogenetic study including 132 partial nucleoprotein (NP) sequences isolated from rodents, we showed that LASV could have emerged 90 years ago in the area. Here, we aim to revise the time of emergence upon analyzing the complete NP and polymerase genes of two strains coming from Upper Guinea: ‘Bantou 366’, a strain isolated from M. natalensis in 2003, and ‘Faranah’, a strain isolated from a human in 1996. They were aligned with 22 other LASV sequences belonging to all lineages and dated by their day of collection. In BEAST (v1.10) tree reconstruction, the following settings were used: GTR+gamma distributed rate variation (four discrete categories) across each codon position and constant population size demographic model. Four clock models were tested: strict, uncorrelated relaxed, random local, and fixed local. The best model was determined by comparing the resulting likelihoods using AICM model testing. Markov chain Monte Carlo (MCMC) sampling was performed for a total of 20 million states (sampling every 10,000 states) to obtain an effective sample size above 200 for all parameters. Results of MCMC sampling were examined in Tracer 1.6. The results showed that the Upper Guinea clade emerged 153 years ago when the phylogeny was reconstructed for partial NP (nt = 754, better model fit with strict clock), 208 years ago with complete NP (nt = 1,707, better model fit with random local clock), and 350 years ago with complete polymerase (nt = 6,681, better model fit with strict clock). The difference of emergence 1, 2, or 3 centuries ago, can be explained by the inclusion of some parts of the genome evolving slower than the partial NP. Therefore, the longer the sequence, the greater the divergence time. In order to have an accurate time of divergence, we suggest to use complete genes to perform a time-calibrated phylogeny.
  • 20.

    【2hr】A18 HIV-2 molecular epidemiology in Spain: 30 years since the first case

    包量

    机译 西班牙的A18 HIV-2分子流行病学：自第一例病例以来已有30多年的历史
    摘要：HIV-2 is a retrovirus that mainly infects West Africans. In Europe, HIV-2 has been circulating since the 1980s, and more recent immigration has contributed to its spread. Excluding HIV-2 in all HIV seropositive individuals precludes misinterpretation of viral loads (VL) and antiretroviral (ART) choices. Surveillance registers enables tracking of epidemic spread and identification of major contributors, allowing the establishment of convenient preventive measures. The HIV-2 Spanish study group was founded in 1989. Since then, blood specimens from HIV-2 carriers have been collected. More than 40 Spanish hospitals are part of the group and provide clinical and epidemiological data. Records for each HIV-2 patient include country of origin, gender, age, transmission category, monitoring of HIV-2 VL, CD4 counts, drug resistance, and HIV-2 subtype. Up to December 2017, 354 HIV-2+ individuals were identified in Spain and incidence (15–20/year) has been stable within the last decade. At diagnosis, mean age was 44.6 years and 63 per cent were male. The majority were Africans (78%), whereas 16.5 per cent were native Spaniards. 78.2 per cent acquired HIV-2 by heterosexual contact. HIV-2 subtyping using the HIV2EU tool was performed in 126 subjects: 86 Africans and 27 native Spaniards. The subtype distribution was as follows: 108 (85.7%) HIV-2 subtype A and 18 (14.3%) B. Africans and Spaniards were mostly infected with subtype A (87.2% and 77.8%, respectively). HIV-2 subtype B was found in six native Spaniards (22.2%; 6/27), five patients from Equatorial Guinea (71.4%; 5/7), four from Senegal (18.1%; 4/22), two from Ivory Coast (100%; 2/2), and one from Burkina Faso (50%; 1/2). Using phylogenetic analyses, two clusters were identified among homosexual Spanish men (subtype A: 8 men and subtype B: 2 men with viral isolates related to Malian and Senegalese isolates). Before starting ART, CD4 count mean values for subtype A and B were 378 and 357, respectively. Corresponding VL values were 2.63 and 2.32 HIV-2 RNA log copies/ml, respectively.
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