Almost all of the 55 000 annual rabies deaths in humans result from infection with dog rabies vir... more Almost all of the 55 000 annual rabies deaths in humans result from infection with dog rabies viruses (RABV). Despite the importance of rabies for human health, little is known about the spread of RABV in dog populations, and patterns of biodiversity have only been studied in limited geographical space. To address these questions on a global scale, we sequenced 62 new isolates and performed an extensive comparative analysis of RABV gene sequence data, representing 192 isolates sampled from 55 countries. From this, we identified six clades of RABV in non-flying mammals, each of which has a distinct geographical distribution, most likely reflecting major physical barriers to gene flow. Indeed, a detailed analysis of phylogeographic structure revealed only limited viral movement among geographical localities. Using Bayesian coalescent methods we also reveal that the sampled lineages of canid RABV derive from a common ancestor that originated within the past 1500 years. Additionally, we found no evidence for either positive selection or widespread population bottlenecks during the global expansion of canid RABV. Overall, our study reveals that the stochastic processes of genetic drift and population subdivision are the most important factors shaping the global phylogeography of canid RABV.
From August 2-October 11, 2006, clusters of low pathogenicity (LP) North American lineage H5N1 an... more From August 2-October 11, 2006, clusters of low pathogenicity (LP) North American lineage H5N1 and H7N3 avian influenza A viruses (AIV), and other subtypes, were recovered from freeflying, resident, wild mallards used as sentinels at one site. The antigenic subtypes, pathogenicity potential, and Sanger sequencing of the isolates determined the H5N1 and H7N3 isolates were only recovered from samples collected on 8/2/2006 and 9/8/2006, respectively. However, subsequent efforts using next-generation sequencing (NGS) and additional Sanger sequencing found partial H7 segments in other HA-NA virus combinations on 8/2/2006, 9/8/2006 and 10/11/2006. It is well established that over larger geographic areas and years AIVs form transient genomic constellations; this sequential sampling data revealed that over a short period of time the dynamics of AIVs can be active and newer sequencing platforms increase recognition of mixed infections. Both findings provide further insight into the natural history of AIVs in natural reservoirs. §
In 1979 a lineage of avian-like H1N1 influenza A virus emerged in European swine populations inde... more In 1979 a lineage of avian-like H1N1 influenza A virus emerged in European swine populations independently from the 'classical' swine H1N1 virus lineage that had circulated in pigs since the 'Spanish' influenza pandemic of 1918. To determine whether these two distinct lineages of swine-adapted A/H1N1 viruses have evolved in similar ways, as might be expected given their common host species and origin from avian-like A/H1N1 ancestors, we compared patterns of nucleotide and amino acid change in whole genome sequences of both groups. An analysis of nucleotide compositional bias across all 8 genomic segments for the two swine lineages showed a clear lineage-specific bias, although a segment-specific effect was also apparent. As such, there only appears to be a relatively weak host-specific selection pressure.
Dengue virus (DENV) is the agent of the most widespread vector-borne viral disease of humans. To ... more Dengue virus (DENV) is the agent of the most widespread vector-borne viral disease of humans. To infer the timescale of DENV evolution with as much accuracy as possible, we compared, within a Bayesian Markov Chain Monte Carlo (MCMC) framework, estimates of phylogenetic tree length using both covarion and noncovarion models of molecular evolution, the latter also incorporating lineage-specific rate variation through a “relaxed” molecular clock. Using a data set of 32 complete genome sequences representing all four viral serotypes, we found evidence for covarion-like evolution at second codon positions in specific DENV genes, although rarely at the level of complete gene or genomes. Further, the covarion model had little effect on estimates of tree length and hence time to the Most Recent Common Ancestor (MRCA). We conclude that although covarion models can improve descriptions of the dynamics of amino acid substitution, they have little effect on estimates of the timescale of viral evolution, which in the case of DENV covers a period of no more than 2000 years.
Of the 18 trematode species that use the horn snail, Cerithidea californica, as a first intermedi... more Of the 18 trematode species that use the horn snail, Cerithidea californica, as a first intermediate host, 6 have the potential to use raccoons as a final host. The presence of raccoon latrines in Carpinteria Salt Marsh, California, allowed us to investigate associations between raccoons and trematodes in snails. Two trematode species, Problocoryphe uca and Stictodora hancocki, occurred at higher prevalences in snails near raccoon latrines than in snails away from latrines, suggesting that raccoons may serve as final hosts for these species. Fecal remains indicated that raccoons fed on shore crabs, the second intermediate host for P. uca, and fish, the second intermediate host for S. hancocki. The increase in raccoon populations in the suburban areas surrounding west coast salt marshes could increase their importance as final hosts for trematodes in this system. Upstream host communities should strongly affect the composition of parasite communities in downstream hosts. As a consequence, parasite communities in downstream hosts, should indicate the composition of upstream-host communities. We used this logic to indirectly determine whether raccoons serve as final hosts for trematodes in west coast salt marshes by studying associations between raccoon latrines and the prevalence of trematodes in snails at the Carpinteria Salt Marsh, California. Trematodes in west coast salt marshes use Cerithidea californica (and closely related snail species in more southern latitudes) as 1st intermediate hosts. Birds are common predators on 2nd intermediate hosts, e.g., polychaetes, snails, clams, crabs, and fishes, and all 18 trematode species that infect C.
Cryptic species of the digeneans, Cercaria batillariae (Heterophyidae) and an undescribed philoph... more Cryptic species of the digeneans, Cercaria batillariae (Heterophyidae) and an undescribed philophthalmid, were detected using polymerase chain reaction-based restriction fragment-length polymorphism methodology and sequence analyses. These digeneans were all collected from the same species of gastropod first intermediate host, Batillaria cumingi (ZBatillaria attramentaria). The mitochondrial cytochrome oxidase subunit 1 gene (approximately 800 bp) and nuclear internal transcribed spacer 1 gene (approximately 400 bp) were used for species level discrimination. Restriction fragment-length polymorphism analyses of cytochrome oxidase subunit 1 gene showed that C. batillariae included 10 distinguishable fragment patterns, and the philophthalmid included five patterns. On the basis of subsequent sequence analyses, the restriction fragment length polymorphism patterns of C. batillariae were grouped into eight phylogenetically distinct lineages and those of the philophthalmid into three phylogenetically distinct lineages. There was no evidence of gene flow among the different lineages due to the lack of heterozygosity within the observed internal transcribed spacer 1 gene fragment patterns. This suggests that all of these lineages are different species. Most of these species were widespread, but some exhibited restricted geographic distributions. We discuss the implications of these findings for host specificity of these trematodes. These results demonstrate the utility of genetic analysis to distinguish species of morphologically similar trematodes. Hence, trematode species diversity may often be underestimated when species identifications are limited to morphological features. q
Cryptic species of the digeneans, Cercaria batillariae (Heterophyidae) and an undescribed philoph... more Cryptic species of the digeneans, Cercaria batillariae (Heterophyidae) and an undescribed philophthalmid, were detected using polymerase chain reaction-based restriction fragment-length polymorphism methodology and sequence analyses. These digeneans were all collected from the same species of gastropod first intermediate host, Batillaria cumingi (ZBatillaria attramentaria). The mitochondrial cytochrome oxidase subunit 1 gene (approximately 800 bp) and nuclear internal transcribed spacer 1 gene (approximately 400 bp) were used for species level discrimination. Restriction fragment-length polymorphism analyses of cytochrome oxidase subunit 1 gene showed that C. batillariae included 10 distinguishable fragment patterns, and the philophthalmid included five patterns. On the basis of subsequent sequence analyses, the restriction fragment length polymorphism patterns of C. batillariae were grouped into eight phylogenetically distinct lineages and those of the philophthalmid into three phylogenetically distinct lineages. There was no evidence of gene flow among the different lineages due to the lack of heterozygosity within the observed internal transcribed spacer 1 gene fragment patterns. This suggests that all of these lineages are different species. Most of these species were widespread, but some exhibited restricted geographic distributions. We discuss the implications of these findings for host specificity of these trematodes. These results demonstrate the utility of genetic analysis to distinguish species of morphologically similar trematodes. Hence, trematode species diversity may often be underestimated when species identifications are limited to morphological features. q
Almost all of the 55 000 annual rabies deaths in humans result from infection with dog rabies vir... more Almost all of the 55 000 annual rabies deaths in humans result from infection with dog rabies viruses (RABV). Despite the importance of rabies for human health, little is known about the spread of RABV in dog populations, and patterns of biodiversity have only been studied in limited geographical space. To address these questions on a global scale, we sequenced 62 new isolates and performed an extensive comparative analysis of RABV gene sequence data, representing 192 isolates sampled from 55 countries. From this, we identified six clades of RABV in non-flying mammals, each of which has a distinct geographical distribution, most likely reflecting major physical barriers to gene flow. Indeed, a detailed analysis of phylogeographic structure revealed only limited viral movement among geographical localities. Using Bayesian coalescent methods we also reveal that the sampled lineages of canid RABV derive from a common ancestor that originated within the past 1500 years. Additionally, we found no evidence for either positive selection or widespread population bottlenecks during the global expansion of canid RABV. Overall, our study reveals that the stochastic processes of genetic drift and population subdivision are the most important factors shaping the global phylogeography of canid RABV.
From August 2-October 11, 2006, clusters of low pathogenicity (LP) North American lineage H5N1 an... more From August 2-October 11, 2006, clusters of low pathogenicity (LP) North American lineage H5N1 and H7N3 avian influenza A viruses (AIV), and other subtypes, were recovered from freeflying, resident, wild mallards used as sentinels at one site. The antigenic subtypes, pathogenicity potential, and Sanger sequencing of the isolates determined the H5N1 and H7N3 isolates were only recovered from samples collected on 8/2/2006 and 9/8/2006, respectively. However, subsequent efforts using next-generation sequencing (NGS) and additional Sanger sequencing found partial H7 segments in other HA-NA virus combinations on 8/2/2006, 9/8/2006 and 10/11/2006. It is well established that over larger geographic areas and years AIVs form transient genomic constellations; this sequential sampling data revealed that over a short period of time the dynamics of AIVs can be active and newer sequencing platforms increase recognition of mixed infections. Both findings provide further insight into the natural history of AIVs in natural reservoirs. §
In 1979 a lineage of avian-like H1N1 influenza A virus emerged in European swine populations inde... more In 1979 a lineage of avian-like H1N1 influenza A virus emerged in European swine populations independently from the 'classical' swine H1N1 virus lineage that had circulated in pigs since the 'Spanish' influenza pandemic of 1918. To determine whether these two distinct lineages of swine-adapted A/H1N1 viruses have evolved in similar ways, as might be expected given their common host species and origin from avian-like A/H1N1 ancestors, we compared patterns of nucleotide and amino acid change in whole genome sequences of both groups. An analysis of nucleotide compositional bias across all 8 genomic segments for the two swine lineages showed a clear lineage-specific bias, although a segment-specific effect was also apparent. As such, there only appears to be a relatively weak host-specific selection pressure.
Dengue virus (DENV) is the agent of the most widespread vector-borne viral disease of humans. To ... more Dengue virus (DENV) is the agent of the most widespread vector-borne viral disease of humans. To infer the timescale of DENV evolution with as much accuracy as possible, we compared, within a Bayesian Markov Chain Monte Carlo (MCMC) framework, estimates of phylogenetic tree length using both covarion and noncovarion models of molecular evolution, the latter also incorporating lineage-specific rate variation through a “relaxed” molecular clock. Using a data set of 32 complete genome sequences representing all four viral serotypes, we found evidence for covarion-like evolution at second codon positions in specific DENV genes, although rarely at the level of complete gene or genomes. Further, the covarion model had little effect on estimates of tree length and hence time to the Most Recent Common Ancestor (MRCA). We conclude that although covarion models can improve descriptions of the dynamics of amino acid substitution, they have little effect on estimates of the timescale of viral evolution, which in the case of DENV covers a period of no more than 2000 years.
Of the 18 trematode species that use the horn snail, Cerithidea californica, as a first intermedi... more Of the 18 trematode species that use the horn snail, Cerithidea californica, as a first intermediate host, 6 have the potential to use raccoons as a final host. The presence of raccoon latrines in Carpinteria Salt Marsh, California, allowed us to investigate associations between raccoons and trematodes in snails. Two trematode species, Problocoryphe uca and Stictodora hancocki, occurred at higher prevalences in snails near raccoon latrines than in snails away from latrines, suggesting that raccoons may serve as final hosts for these species. Fecal remains indicated that raccoons fed on shore crabs, the second intermediate host for P. uca, and fish, the second intermediate host for S. hancocki. The increase in raccoon populations in the suburban areas surrounding west coast salt marshes could increase their importance as final hosts for trematodes in this system. Upstream host communities should strongly affect the composition of parasite communities in downstream hosts. As a consequence, parasite communities in downstream hosts, should indicate the composition of upstream-host communities. We used this logic to indirectly determine whether raccoons serve as final hosts for trematodes in west coast salt marshes by studying associations between raccoon latrines and the prevalence of trematodes in snails at the Carpinteria Salt Marsh, California. Trematodes in west coast salt marshes use Cerithidea californica (and closely related snail species in more southern latitudes) as 1st intermediate hosts. Birds are common predators on 2nd intermediate hosts, e.g., polychaetes, snails, clams, crabs, and fishes, and all 18 trematode species that infect C.
Cryptic species of the digeneans, Cercaria batillariae (Heterophyidae) and an undescribed philoph... more Cryptic species of the digeneans, Cercaria batillariae (Heterophyidae) and an undescribed philophthalmid, were detected using polymerase chain reaction-based restriction fragment-length polymorphism methodology and sequence analyses. These digeneans were all collected from the same species of gastropod first intermediate host, Batillaria cumingi (ZBatillaria attramentaria). The mitochondrial cytochrome oxidase subunit 1 gene (approximately 800 bp) and nuclear internal transcribed spacer 1 gene (approximately 400 bp) were used for species level discrimination. Restriction fragment-length polymorphism analyses of cytochrome oxidase subunit 1 gene showed that C. batillariae included 10 distinguishable fragment patterns, and the philophthalmid included five patterns. On the basis of subsequent sequence analyses, the restriction fragment length polymorphism patterns of C. batillariae were grouped into eight phylogenetically distinct lineages and those of the philophthalmid into three phylogenetically distinct lineages. There was no evidence of gene flow among the different lineages due to the lack of heterozygosity within the observed internal transcribed spacer 1 gene fragment patterns. This suggests that all of these lineages are different species. Most of these species were widespread, but some exhibited restricted geographic distributions. We discuss the implications of these findings for host specificity of these trematodes. These results demonstrate the utility of genetic analysis to distinguish species of morphologically similar trematodes. Hence, trematode species diversity may often be underestimated when species identifications are limited to morphological features. q
Cryptic species of the digeneans, Cercaria batillariae (Heterophyidae) and an undescribed philoph... more Cryptic species of the digeneans, Cercaria batillariae (Heterophyidae) and an undescribed philophthalmid, were detected using polymerase chain reaction-based restriction fragment-length polymorphism methodology and sequence analyses. These digeneans were all collected from the same species of gastropod first intermediate host, Batillaria cumingi (ZBatillaria attramentaria). The mitochondrial cytochrome oxidase subunit 1 gene (approximately 800 bp) and nuclear internal transcribed spacer 1 gene (approximately 400 bp) were used for species level discrimination. Restriction fragment-length polymorphism analyses of cytochrome oxidase subunit 1 gene showed that C. batillariae included 10 distinguishable fragment patterns, and the philophthalmid included five patterns. On the basis of subsequent sequence analyses, the restriction fragment length polymorphism patterns of C. batillariae were grouped into eight phylogenetically distinct lineages and those of the philophthalmid into three phylogenetically distinct lineages. There was no evidence of gene flow among the different lineages due to the lack of heterozygosity within the observed internal transcribed spacer 1 gene fragment patterns. This suggests that all of these lineages are different species. Most of these species were widespread, but some exhibited restricted geographic distributions. We discuss the implications of these findings for host specificity of these trematodes. These results demonstrate the utility of genetic analysis to distinguish species of morphologically similar trematodes. Hence, trematode species diversity may often be underestimated when species identifications are limited to morphological features. q
Uploads
Papers by Eleca Dunham