Structure of the Cochliobolus sativus population variability

The genetic diversity of several local populations of the fungal pathogen Cochliobolus sativus, collected over 3 years from different regions of the Czech Republic, was examined using amplified fragment length polymorphism (AFLP). A high level of variability was found even among isolates from one lesion. Measures of multilocus linkage disequilibrium suggested that recombination has a minor impact on the genetic structure of populations. Cochliobolus sativus forms genetically divergent populations (F_ST = 0·33), indicating a low level of geneflow between populations. This was supported by a significant correlation between genetic diversity and geographical distances up to 80–100 km. The most likely explanation for the genetic variability is that the fungus forms conidia with highly variable chromosomal rearrangements. The differentiation observed among local populations implies that genetic drift, including a founder effect, combined with restricted migration generates the structure of C. sativus populations.     

Genotypic variation and population structure of Sclerotinia trifoliorum infecting chickpea in California

Sclerotinia trifoliorum, an important pathogen of cool season legumes, displays both homothallism and heterothallism in its life cycle, unique among members of the genus Sclerotinia. Very little is known about its genetic diversity and population structure. A sample of 129 isolates of S. trifoliorum from diseased chickpea in California was investigated for genetic diversity, population differentiation and reproductive mode. Genetic diversity was estimated using mycelial compatibility (MCG) phenotypes, rDNA intron variation, and allelic diversity at seven microsatellite loci. Genetic analysis revealed high levels of genotypic diversity demonstrated by high genotypic richness (0·88). Similarly, high levels of gene diversity (mean expected heterozygosity H_E = 0·68) were observed at the microsatellite loci. Geographic populations of S. trifoliorum were highly admixed as evident from low F_ST values (0–0·11), suggesting high contemporary or historical gene flow. Hierarchical analysis of molecular variance showed that more than 92% of the genetic variation occurred among isolates within populations. Bayesian clustering analysis identified four cryptic genetic populations that were not correlated to geographic location, and index of multilocus association was non‐significant in each of the four genetic populations. However, the presence of identical haplotypes within and among populations indicates clonal reproduction. The high levels of haplotype diversity and population heterogeneity, a lack of correspondence between MCG and microsatellite haplotype, and low levels of population differentiation suggest that populations of S. trifoliorum in chickpea have been undergoing extensive outcrossing and migration events probably shaped by human‐mediated dissemination, the underlying diverse cropping systems, and chickpea disease management practices.     

Genotypic diversity and migration of clonal lineages of Botrytis cinerea from chickpea fields of Bangladesh inferred by microsatellite markers

An analysis of allelic diversity at nine microsatellite loci provided an insight into the population structure of Botrytis cinerea from four fields (sampled in 2003 and 2004) that represented important regional locations for chickpea production in Bangladesh. Although three populations were limited by sample size after clone‐correction, a total of 51 alleles were amplified among 146 B. cinerea isolates from Bangladesh, which revealed a high amount of within‐population and overall genetic diversity (H_S = 0·48 and H_T = 0·54, respectively). The percentage of maximal genotypic diversity (G) ranged between populations (G = 23–40), with a total of 69 haplotypes detected (G = 25). Bayesian cluster analysis depicted two major clusters distributed among the four Bangladesh populations, indicating population admixture from two origins that have spread throughout these regions. Genotype flow between regions was detected and indicated the spread of clonal lineages, consistent with relatively low differentiation among the four populations (mean G_ST = 0·1, P < 0·05). These results highlighted the potential threat of host resistance breakdown as a result of considerable genetic diversity, genotype flow and the evolutionary potential of B. cinerea.     

Global movement and population biology of Mycosphaerella nubilosa infecting leaves of cold-tolerant Eucalyptus globulus and E. nitens

Using 10 polymorphic DNA-based microsatellite markers, the genetic diversity of eight Mycosphaerella nubilosa populations from Eucalyptus , comprising 497 isolates from five different countries, was studies using a hierarchical sampling regime. Mycosphaerella nubilosa from eastern Australia (New South Wales) had higher gene (0·506) and genotypic (76%) diversity than other populations, supporting the view that this represents the origin of the pathogen. It was also evident that M. nubilosa populations from Europe and Tanzania were clonal, with the same multilocus haplotypes occurring in South Africa, but being absent in Australia. This suggests that M. nubilosa may have been introduced into Europe via Africa, with a pathway of gene flow from Australia to South Africa, further into Africa and finally to Europe.     

Microsatellite and mating type markers reveal unexpected patterns of genetic diversity in the pine root‐infecting fungus Grosmannia alacris

Grosmannia alacris is a fungus commonly associated with root‐infesting bark beetles occurring on Pinus spp. The fungus has been recorded in South Africa, the USA, France, Portugal and Spain and importantly, has been associated with pine root diseases in South Africa and the USA. Nothing is known regarding the population genetics or origin of G. alacris, although its association with root‐infesting beetles native to Europe suggests that it is an invasive alien in South Africa. In this study, microsatellite markers together with newly developed mating type markers were used to characterize a total of 170 isolates of G. alacris from South Africa and the USA. The results showed that the genotypic diversity of the South African population of G. alacris was very high when compared to the USA populations. Two mating types were also present in South African isolates and the MAT1‐1/MAT1‐2 ratio did not differ from 1:1 (χ² = 1·39, P = 0·24). This suggests that sexual reproduction most probably occurs in the fungus in South Africa, although a sexual state has never been seen in nature. In contrast, the large collection of USA isolates harboured only a single mating type. The results suggest that multiple introductions, followed by random mating, have influenced the population structure in South Africa. In contrast, limited introductions of probably a single mating type (MAT1‐2) may best explain the clonality of USA populations.     

Genetic diversity, aggressiveness and metalaxyl sensitivity of Pythium aphanidermatum populations infecting cucumber in Oman

Seventy three isolates of Pythium aphanidermatum obtained from cucumber from four different regions of Oman and 16 isolates of muskmelon from the Batinah region in Oman were characterized for aggressiveness, sensitivity to metalaxyl and genetic diversity using AFLP fingerprinting. Twenty isolates of P. aphanidermatum from diverse hosts from different countries were also included in the study. Most isolates from Oman were found to be aggressive on cucumber seedlings and all were highly sensitive to metalaxyl (EC₅₀ < 0·80 µg mL^?1). Isolates from cucumber and muskmelon were as aggressive as each other on both hosts (P > 0·05), which implies a lack of host specialization in P. aphanidermatum on these two hosts in Oman. AFLP analysis of all isolates using four primer–pair combinations resolved 152 bands, of which 61 (~40%) were polymorphic. Isolates of P. aphanidermatum from Oman and other countries exhibited high genetic similarity (mean = 94·1%) and produced 59 different AFLP profiles. Analysis of molecular variance indicated that most AFLP variation among populations of P. aphanidermatum in Oman was associated with geographical regions (F_ST = 0·118; P < 0·0001), not hosts (F_ST = –0·004; P = 0·4323). These data were supported by the high rate of recovery (24%) of identical phenotypes between cucumber and muskmelon fields in the same region as compared to the low recovery (10%) across regions in Oman, which suggests more frequent movement of Pythium inoculum among muskmelon and cucumber fields in the same region compared to movement across geographically separated regions. However, recovering clones among regions and different countries may imply circulation of Pythium inoculum via common sources in Oman and also intercontinental spread of isolates.     

Genetic Structure and Variation in Aggressiveness in European and Australian Populations of the Grapevine Dieback Fungus, Eutypa lata

Eutypa lata is an ascomycete fungus causing a severe dieback in grapevine. The genetic structure of populations of E. lata from seven regions in Australia, France, Italy and Spain was examined using 20 random amplified polymorphic DNA (RAPD) markers. In some regions, populations were subdivided and a total of 14 samples were analysed. A total of 231 RAPD haplotypes were found among the 240 isolates. Vegetative compatibility testing further demonstrated that isolates of the same haplotype were genetically distinct. Gene diversity was the highest in the population from northern Italy and lowest in the Alsace region in France. Linkage disequilibrium between pairs of putative loci was very low and most of the multilocus analyses were consistent with the hypothesis of random association of the loci. This suggests that random mating occurred in every population and that the sexual stage shapes the genetic structure of E. lata populations in the regions sampled. Only 6% of the total variability was attributable to differences between populations. Nevertheless, significant differences in allele frequency appeared with respect to six RAPD markers indicating some genetic differentiation between populations. This differentiation appeared attributable to differences between the Italian and Spanish populations and the other populations. We thus hypothesize that a restriction of gene flow exists within Europe. The population from Australia was genetically closer to the French and Spanish populations than to that from Italy. Genetic diversity is associated with considerable variation in aggressiveness, which was assessed on cuttings in the greenhouse in six populations. All populations included a range of isolates differing in aggressiveness, but the Italian population seemed to have more isolates with low aggressiveness.     

Eutypa Canker and Dieback of Apricots

Eutypa canker and dieback of apricot trees, caused by the ascomycetous fungus Eutypa armeniacae Hansf. et Carter, has been recorded in Europe, North America, Australia and South Africa. Samples of diseased sapwood yield the imperfect Cytosporina stage in culture, whereas perithecia of E. armeniacae, immersed in a stroma, develop 2 or more years after death of a branch in high-rainfall areas. The fungus is a wound parasite. Air-borne ascospores, disseminated during and after rain, infect xylem tissues which have been freshly exposed by pruning. Cankers develop around the infected wounds; leaves on that part of the branch distal to the canker subsequently wilt and die during summer. E. armeniacae has been detected on a diverse range of host species, hence elimination of inoculum is not feasible; both biological and chemical approaches to wound protection and ultimate disease control are under investigation.     

Genetic differentiation and gene flow in Colletotrichum sublineolum in Ethiopia,the centre of origin and diversity of sorghum,as revealed by AFLP analysis

Isolates of Colletotrichum sublineolum were collected from different sorghum‐producing regions of Ethiopia and divided into five groups based on their geographic origin. The growth rate of 50 isolates showed considerable variation: 1·7–5·8 mm day^?1, mean 3·3 mm day^?1. However, the isolates displayed little variation in colony colour and colony margin, except for isolates from the north, which were different from the others. Amplified fragment length polymorphism analysis of 102 isolates revealed much greater variations among the different groups. Dice similarity coefficients ranged from 0·32 to 0·96 (mean 0·78). Cluster analysis and principal coordinate analysis revealed a differentiation of the isolates according to their geographic origin, and both methods clearly indicated a genetic separation between the southern, the eastern and the other isolates. Analysis of molecular variance (amova ) indicated a high level of genetic variation both among (42%) and within (58%) the C. sublineolum sampling sites in Ethiopia. The amova also indicated a high level of genetic differentiation (F_ST = 0·42) and limited gene flow (Nm = 0·343). The results of this study confirmed the presence of a highly diverse pathogen, which is in agreement with the existence of diverse host genotypes and widely ranging environmental conditions in sorghum‐producing regions of the country. Such diversity should be taken into account in future breeding programmes to achieve an effective and sustainable disease management strategy.     

Diversity and differentiation in two populations of Gibberella circinata in South Africa

Gibberella circinata [anamorph Fusarium circinatum (=  F. subglutinans f.sp. pini )] causes pitch canker and is an important pathogen in South African pine nurseries. The initial outbreak of the pitch canker fungus was limited to a single nursery at Ngodwana in Mpumalanga Province. Subsequently, several other pine nurseries in South Africa became infected. Most of these outbreaks were relatively small except for the outbreak in the Klipkraal nursery (Mpumalanga Province). The genetic diversity, population differentiation and relative frequencies of the sexual and asexual cycles among two South African subpopulations were determined to establish whether immigration, mutation and/or recombination contributed towards population structure. The allelic diversity of the initial population (Ngodwana) was observed to be lower (0·16) than that of the more recent Klipkraal population (0·25). Approximately 4% ( G _ST = 0·04) of total gene diversity could be attributed to differences among the subpopulations. Furthermore, six new vegetative compatibility groups (VCGs) have been identified since the initial outbreak of G. circinata in South Africa 10 years ago. The relatively low allelic diversity and low level of genetic differentiation suggest restricted gene flow among subpopulations, and indicate that the pathogen has been introduced recently. However, the amount of allelic and VCG diversity suggests that multiple genotypes have been introduced into South Africa. The increases in effective population number, allelic diversity and new VCGs over the past 10 years suggest that sexual reproduction might be occurring.     

Genetic structure of the grapevine fungal pathogen Phaeomoniella chlamydospora in southeastern Australia and southern France

In this study, 18 microsatellite loci were used to examine the genetic structure and mode of reproduction of Phaeomoniella chlamydospora, the fungus that causes Petri disease of grapevine and is involved in another grapevine disease, esca. A total of 60 southeastern Australian isolates were tested and compared with 64 isolates from southern France. The French population possessed relatively high genotypic diversity (G = 29·2) whilst the Australian population showed low genotypic diversity (G = 11·1), consistent with a limited founder population. Haplotypes from four different grapevine cultivars were not significantly differentiated (Φpt values effectively zero). Likewise, genetic differentiation of haplotypes from different regions within each country was not significant, although small but significant genetic differentiation (9%) was identified between Australia and France. Based on bootstrapped cluster analysis, there did not appear to be any genetic groups within the overall sample of isolates. Significant linkage disequilibrium identified in both countries, together with overrepresented, widespread identical haplotypes, indicated limited genetic recombination and a largely clonal structure consistent with the absence of an observed sexual cycle in this species.     

Multilocus PCR assay reveals high diversity of vegetative compatibility types in populations of Cryphonectria parasitica in Croatia

The ascomycete fungus Cryphonectria parasitica, causal agent of chestnut blight, is probably one of the best known invasive fungal pathogens in forests of Europe and North America. Mycovirus that reduces virulence of C. parasitica can be used as a biocontrol agent of the chestnut blight. However, anastomosis‐mediated virus transmission is limited by a vegetative (in)compatibility (vc) system involving at least six known diallelic vic genetic loci. This study looked at vegetative compatibility (vc) diversity in two populations of C. parasitica in Croatia. For that purpose, a PCR assay was validated and implemented using already known/published and newly designed primers for amplification of six known vic loci. The vc genotypes determined by PCR for 158 C. parasitica isolates investigated in this study were in complete agreement with the vc genotypes determined by pairwise co‐culturing of the same isolates, revealing the specificity and accuracy of the PCR‐based molecular vic genotyping assay. Twenty‐six unique vc genotypes were found among 158 isolates, and 19 vc types per population, which makes Croatian C. parasitica populations among the most diverse in Europe regarding the number of vc types and genetic diversity. Low values of multilocus linkage disequilibrium suggest sexual reproduction as a major contributor to high C. parasitica genetic diversity in studied populations.     

Phytophthora infestans populations in central,eastern and southern African countries consist of two major clonal lineages

Limited knowledge is available on Phytophthora infestans populations in Sub‐Saharan Africa (SSA). Therefore, and in response to recent severe late blight epidemics, P. infestans isolates from potato, tomato and Petunia × hybrida from eight SSA countries were characterized. Isolates were characterized with ‘old’ markers, including mating type (176 isolates), mitochondrial DNA haplotype (mtDNA) (281 isolates), glucose‐6‐phosphate isomerase (Gpi) (70 isolates), restriction fragment length polymorphism analysis with probe RG‐57 (49 isolates), and by metalaxyl sensitivity (64 isolates). Most isolates belonged to the US‐1 genotype or its variants (US‐1.10 and US‐1.11). The exceptions were genotype KE‐1 isolates (A1 mating type, mtDNA haplotype Ia, Gpi 90/100 and unique RG‐57 genotype), identified in two fields in Kenya, which are related to genotypes previously identified in Rwanda (RW‐1 and RW‐2), Ecuador and Europe. Metalaxyl‐resistant P. infestans isolates from potato were present in all the countries except Malawi, whereas all the isolates from tomato were sensitive. Genotyping of 176 isolates with seven simple sequence repeat (SSR) markers, including locus D13 that was difficult to score, revealed 79 multilocus genotypes (MLGs) in SSA. When this locus was excluded, 35 MLGs were identified. Genetic differentiation estimates between regional populations from SAA were significant when locus D13 was either excluded (P = 0·05) or included (P = 0·007), but population differentiation was only low to moderate (F_ST = 0·044 and 0·053, respectively).     

Genetic uniformity of Alternanthera philoxeroides in South China

Alternanthera philoxeroides (Mart.) Grisb is an invasive weed that is widespread in a variety of habitats around the world. It was introduced into China in the 1930s, and today occurs in 20 provinces. The level and pattern of genetic diversity of 193 individuals from 11 land‐grown A. philoxeroides populations from South China were determined using 81 intersimple sequence repeat markers. Mean Nei's gene diversity (H_E) was 0.0203 ± 0.008, and total diversity (H_T) was 0.0286, indicating that genetic diversity in A. philoxeroides in South China is very low. There was a greater proportion of diversity within populations than among (G_ST = 0.292) populations. Gene flow (Nm) among populations was 0.607. These results are in accordance with the assumption that populations in South China are genetically depauperate because of the short introduction history and the partially clonal propagation of this weed.     

Microsatellite DNA variation within and among invasive populations of Ambrosia artemisiifolia from the southern Pannonian Plain

Although the Pannonian Plain presents one of the areas in Europe most highly infested by Ambrosia artemisiifolia, previously reported population genetic studies of the invasive species have included only a few populations from this region. Our goal was to determine the level of genetic diversity and genetic structure of A. artemisiifolia populations from the southern Pannonian Plain using microsatellite DNA markers. We documented a high level of genetic diversity within the Pannonian populations, as compared with the genetic diversity parameters previously published for the other invasive populations of A. artemisiifolia in Europe. The mean number of alleles per locus (N_A) ranged between 6.8 and 9.4, allelic richness (r) between 6.59 and 8.53 and mean number of rare alleles per locus (N_R) ranged between 3.4 and 6.4 per analysed population. A low level of among‐population differentiation was detected, with percentage of variation between populations of 3.3%, generally low pairwise F_ST values (ranged from ?0.007 to 0.152) and also according to principal coordinate analysis. A Bayesian approach revealed that most individuals did not strongly associate with any single genetic cluster, confirming a lack of genetic structuring in the analysed region. Together with the results of quantification of the level of gene flow (N_m = 5.671), these observations indicated a presence of extensive gene exchange and admixture between the populations. Therefore, A. artemisiifolia in the Pannonian Plain region has the potential for rapid expansion.     

Genetic analysis of the population structure of the rice false smut fungus,Villosiclava virens,in China using microsatellite markers mined from a genome assembly

Studies on population genetics of Villosiclava virens are limited because of the lack of polymorphic markers. Based on a draft genome sequence of isolate HWD‐2 produced in this study, 20 of 403 potential simple sequence repeats (SSR) loci showed polymorphisms in preliminary screening using eight diverse V. virens isolates. Among polymorphic loci, most of them with tetra‐ to hexanucleotide unit motifs showed higher levels of polymorphism than loci with smaller motifs. After testing with 20 polymorphic SSR markers, the 87 isolates of V. virens from eight populations in China showed a high level of genetic diversity, with each as a unique haplotype. This differs from some previous findings showing little to no genetic variation based on random amplified polymorphic DNA and amplified fragment length polymorphism analyses. Among eight populations from major rice production areas of China, the population from Guangxi province in south China showed the highest levels of polymorphism, which led to the speculation that it might be closer to the centre of origin of this pathogen. The northern, central and eastern populations (Jilin, Liaoning, Hubei, Hunan, Jiangxi and Zhejiang), when considered together as a group, showed significant molecular variation compared to the southern populations (Fujian and Guangxi) (Φ_PT = 0·043, P = 0·037). A significant relationship (Mantel test, P = 0·027) but with low correlation (R² = 0·23) was also found between geographic distance and genetic distance. The 20 polymorphic SSR primer pairs designed in this study provide a tool for further research on the population diversity of this emerging fungal pathogen of rice.     

Assessing host specialization of Botrytis cinerea on lettuce and tomato by genotypic and phenotypic characterization

This study tested the hypothesis that Botyrtis cinerea shows host specialization on tomato and lettuce, using phenotypic and genotypic tools. Strains were isolated from tomato and lettuce grown together in the same greenhouse. Forty‐four lettuce strains and 42 tomato strains were investigated for their genetic diversity and their aggressiveness. Both gene diversity and allelic richness were significantly higher in lettuce strains than in tomato strains (P = 0·01). Cluster analysis revealed a clear division of the strains under study into two clusters. However, this structure did not separate the strains according to their host of origin. Tomato strains were significantly more aggressive than lettuce strains when inoculated on tomatoes (P = 0·001), but no significant differences in aggressiveness were observed when the strains were inoculated on lettuce (P = 0·17) or on apple (P = 0·87). The results suggest an absence of clear host specialization of B. cinerea on tomato and lettuce.     

Population structure and mating system of Ascochyta rabiei in Tunisia: evidence for the recent introduction of mating type 2

The population structure of Ascochyta rabiei (teleomorph: Didymella rabiei ) in Tunisia was estimated among five populations sampled from the main chickpea growing regions using simple sequence repeat markers (SSR) and a mating type ( MAT ) marker. Mating type 2 isolates ( MAT1-2 ) had reduced genetic and genotypic diversity relative to mating type 1 isolates ( MAT1-1 ). This result, coupled with previous observations of lower overall frequency and restricted geographical distribution of MAT1-2 in Tunisia, and recent (2001) observation of the sexual stage, support the hypothesis of a recent introduction of MAT1-2 . Despite the presence of both mating types in Nabeul, Kef and Jendouba, the hypothesis of random mating was rejected in these locations with multilocus gametic disequilibrium tests. Highly significant genetic differentiation ( θ  = 0·32, G _ST = 0·28, P  < 0·001) was detected among populations and genetic distance and cluster analyses based on pooled allele frequencies revealed that populations from Nabeul and Kef were distinct from those in Beja, Bizerte and Jendouba. More than 70% of total gene diversity ( H _T = 0·55) detected was attributable to variation within populations compared to 28% among populations. This result, coupled with the occurrence of private alleles in each population, suggests that gene flow is currently limited among populations, even those separated by short geographic distances. The presence of two main genetic clusters was confirmed using Bayesian model-based population structure analyses of multilocus genotypes (MLGs) without regard to geographic origin of samples. The presence of MAT1-2 isolates in both clusters suggests at least two independent introductions of MAT1-2 into Tunisia that are likely to be the result of importation and planting of infected chickpea seeds.     

Pathotypic and genetic diversity in the population of Rhizoctonia solani AG1‐IA causing rice sheath blight in China

Sheath blight, caused by Rhizoctonia solani AG1‐IA, is one of the most serious diseases of rice. In this study, a total of 175 isolates of R. solani AG1‐IA were collected from five rice‐growing regions in China. Pathogenicity tests revealed that all isolates were virulent to five cultivars with different levels of resistance at the rice seedling stage in the greenhouse. There was considerable variation in aggressiveness, and the isolates were classified into three pathotypes based on disease severity, with moderately virulent isolates prevalent in the population. Forty‐three haplotypes were identified based on ITS sequencing, and 39 haplotypes were distinct among isolates. There were high levels of haplotype diversity and nucleotide diversity within the populations of R. solani AG1‐IA. High gene flow (Nm = 1·63–5·22) was detected, consistent with relatively low differentiation between pairs of populations. Five populations were divided into two distinct clusters by the unweighted pair group method with arithmetic mean (UPGMA), and no spatial population differentiation was discernible. The majority (97·8%) of genetic diversity was distributed among isolates within populations, with only 2·2% of the genetic diversity attributed to differences among populations. The star‐like shape of the haplotype network provided evidence of signatures of population expansion in recent history. No significant relationships were found between the genetic diversity and aggressiveness or geographic origin among populations of R. solani AG1‐IA. These results highlight that the population characteristics of R. solani AG1‐IA should be taken into account in evaluating the germplasm resistance of rice cultivars to sheath blight.     

Genetic population structure and trichothecene genotypes of Fusarium graminearum isolated from wheat in southern Brazil

A sample of 140 Fusarium graminearum isolates from Rio Grande do Sul, Brazil, representing three populations at least 150 km from one another, were examined for trichothecene genotype based on PCR amplification of portions of the Tri3 and Tri12 genes and a species‐specific (Fg16F/R) primer pair. Genetic diversity was assessed in a sample of 103 F. graminearum lineage 7 (F. graminearum sensu stricto) isolates using amplified fragment length polymorphism (AFLP) markers. The 15‐ADON genotype was dominant, followed by the NIV genotype (2–18% prevalence), across all three populations. All NIV‐type isolates were in lineage 2 (F. meridionale) and all 15‐ADON‐type isolates were in lineage 7. Isolates with the same haplotype were rare and genotypic diversity was uniformly high (≥98% of the count), suggesting that recombination has played a significant role. The number of migrants (N_m) was estimated between 5 and 6 across all loci and all populations, but the high frequency of private alleles (up to 30%) suggests a historical, rather than contemporary, gene flow. Regarding linkage disequilibrium, 0·8, 1·5 and 2·2% of the locus pairs from the three populations were in disequilibrium, which is lower than values reported in other locations. Thus, Brazilian populations differ from those found in Europe, North America and most of Asia in the presence of a significant frequency (7·8%) of isolates of the NIV genotype in lineage 2.