Evaluating the Ability to ID (COVID-19) NOW: a Large Real-World Prospective Evaluation of the Abbott ID NOW COVID-19 Assay.

The Abbott ID NOW COVID-19 assay is a rapid point-of-care molecular test for SARS-CoV-2 detection. In theory, it has the potential to decrease turnaround times (TATs) and rapidly facilitate patient flow and triage. Reports for its performance have been mixed, likely due to variations in patient cohorts, preanalytical considerations, and study design. We prospectively evaluated the ID NOW performance against reference reverse transcriptase PCR (RT-PCR) tests, using dual swabs. Patients presented at a large multisite academic hospital with the highest volumes of COVID-19 admissions in Canada. From 1,968 valid swabs, 186 were true positive, 1,760 were true negative, 21 were false negatives, and 1 was false positive. At 10.5% positivity rate, the positive and negative predictive values were 99.5% and 98.8%, respectively. This led to a modest increase in the pretest probability in this cohort of individuals presenting <7 days of symptom onset. The mean times from collection to laboratory receipt and receipt to reporting were 31 and 23 min, respectively. This reduced TAT observed in our study may assist with triage of admitted patients and breaking the chain of transmission through immediate notification of status. We also observed how test performance changed with prevalence, and thus, how the test is used to "rule in" or "rule out" disease must be considered. Although the ID NOW is regarded as a rapid test, it is not high throughput and requires rapid transportation times (<1 h) that may not be plausible in large centers. The utility of this test should be considered with the observed TAT and interpreted in the context of limitations discussed. IMPORTANCE Rapid testing for COVID-19 has been recognized as one potentially important measure in managing the pandemic. However, these rapid tests vary grossly in their performance and their applicability. There have been many studies evaluating the performance of rapid tests for SARS-CoV-2 detection. However, they are frequently not prospective, and patients are not simultaneously swabbed to compare the reference standard RT-PCR. Previous ID NOW study findings are mixed, which may be due to various factors, including patient, epidemiological, and preanalytical considerations. It is critical to consider how the pretest and posttest probabilities and epidemiological factors may affect the performance as the community prevalence of disease fluctuates during this highly dynamic pandemic. We consider how the ID NOW may be utilized in different settings, with considerations of public health and infection control and prevention risk tolerance.

Virulence Genes in Heterodera glycines: Allele Frequencies and Ror Gene Groups Among Field Isolates and Inbred Lines.

ABSTRACT Genetic variation in field populations of Heterodera glycines is a key issue for both resistance gene deployment and basic understanding of virulence-gene flow in populations. In this study, we examined phenotypically defined genes for virulence under selection from host resistance. We separated the most common H. glycines genotypes in the United States into two virulence groups, based on their reproductive abilities on the resistant soybean plant introduction (PI) 88788. These groups correspond to previously identified virulence genes in the nematode, as follows: the dominant gene in H. glycines to PI88788, and the recessive genes to PI90763 and Pickett/Peking. Virulence allele frequencies and virulence genotype frequencies of selected field isolates were investigated by testing the host range of single-female-derived lines, which were developed through single-female inoculation on the standard susceptible soybean 'Lee 68'. By comparing virulence genotype frequencies between the original field isolates and their single-female-derived lines, we were able to determine allele frequencies in the field populations. The results suggest that tremendous variation in H. glycines virulence genes exists among field populations. Potential mechanisms of selection which could cause virulence genotype frequency increases are discussed as related to population genetics equilibrium theory.

Influence of poultry litter applications on nematode communities in cotton agroecosystems.

The effects of the application of poultry litter at 0.0, 6.7, 13.4, and 20.1 tons/ha on population changes during the growing season on nematode communities were evaluated in two cotton production fields in North Carolina. Numbers of bactivorous nematodes increased at midseason in response to the rate at which litter was applied but decreased with increasing litter application rates at cotton harvest. Numbers of fungivores at cotton harvest were related positively to the rate of litter applied, and this affected a positive increase in the fungivore-to-bacterivore ratio at this sampling date. The rate at which poultry litter was applied resulted in an increase in the bacterivore to plant-parasite ratio, and this corresponded with increased cotton lint yield. Trophic diversity was increased by litter application rate at cotton harvest at one location but not at another. The plant-parasite maturity index was greater consistently at one site than at a second site where the Hoplolaimus columbus population density was above the damage threshold for cotton. The population density of H. columbus was suppressed with increasing rates of poultry litter application, but other plant-parasitic nematodes were affected marginally.

Impact of Cotton Production Systems on Management of Hoplolaimus columbus.

The effectiveness of selected cultural practices in managing the Columbia lance nematode, Hoplolaimus columbus, on cotton was evaluated in experiments in growers' infested fields. The effects of planting date, cotton cultivar, treatment with the growth regulator mepiquat chloride, and destruction of cotton-root systems after harvest on cotton-lint yield and population densities of H. columbus were studied. The yield of cotton cultivar Deltapine 50 was negatively related (P = 0.054) to initial population density of H. columbus whereas the yield of Deltapine 90 was not affected by preplant density of this nematode, indicating tolerance in Deltapine 90. Reproduction of this nematode did not differ on the two cultivars. Planting date and treatment with the growth regulator mepiquat chloride did not influence cotton yield in a consistent manner. Application of mepiquat chloride suppressed (P

Effects of Rate and Time of Application of Poultry Litter on Hoplolaimus columbus on Cotton.

Field experiments were conducted to evaluate the effect of soil-incorporated poultry litter on the population dynamics of Hoplolaimus columbus and cotton lint yield. Rates of poultry litter applied varied from 0.0 to 27.0 t/ha and were applied in December, February, or March. Time of application did not influence population densities of this nematode or cotton yield. The rate of poultry litter applied was negatively related to the population density of H. columbus at midseason, but not at other sampling dates. The lower midseason levels of this nematode corresponded with increases in cotton lint yield in all experiments. Cotton yield increases generally were linear with respect to the rate of litter applied, although the highest rates of litter applied did not always result in the greatest cotton yield. Poultry litter can be used effectively to supply nutrients to the crop and suppress damaging levels of H. columbus. Optimal rates of litter application were from 6.0 to 13.4 t/ha. Application of poultry litter at these rates, however, may exceed nutrient levels required for best management practices.

Resistance as a Tactic for Management of Meloidogyne incognita on Cotton in North Carolina.

Selected cotton cultivars were evaluated for resistance to the southern root-knot nematode, Meloidogyne incognita, in greenhouse and field experiments. Cotton cultivars LA 887, Auburn 634, and NemX cotton were highly resistant to three North Carolina populations of root-knot nematode in greenhouse experiments compared to susceptible cultivars. The relative susceptibility of cultivars tested in the greenhouse from most to least susceptible were Deltapine 16 > Deltapine 50 > LA 887 or NemX > Auburn 634. The yields of resistant and susceptible cotton cultivars were increased by fumigation in fields infested with root-knot nematode. Reproduction of M. incognita in field plots on NemX, Paymaster H 1560, and Stoneville LA 887 was less than on susceptible cultivars. Diminished reproduction of the nematode on resistant cultivars may reduce the need for nematode control tactics in subsequent years.

Conversion of compatible plant-pathogen interactions into incompatible interactions by expression of the Pseudomonas syringae pv. syringae 61 hrmA gene in transgenic tobacco plants.

The hrmA gene from Pseudomonas syringae pv. syringae has previously been shown to confer avirulence on the virulent bacterium P. syringae pv. tabaci in all examined tobacco cultivars. We expressed this gene in tobacco plants under the control of the tobacco Delta0. 3 TobRB7 promoter, which is induced upon nematode infection in tobacco roots (Opperman et al. 1994, Science, 263, 221-223). A basal level of hrmA expression in leaves of transgenic plants activated the expression of pathogenesis-related genes, and the transgenic plants exhibited high levels of resistance to multiple pathogens: tobacco vein mottling virus, tobacco etch virus, black shank fungus Phytophthora parasitica, and wild fire bacterium Pseudomonas syringae pv. tabaci. However, the hrmA transgenic plants were not significantly more resistant to root-knot nematodes. Our results suggest a potential use of controlled low-level expression of bacterial avr genes, such as hrmA, in plants to generate broad-spectrum resistance to bacterial, fungal and viral pathogens.

Tolerance of Selected Cotton Lines to Rotylenchulus reniformis.

The reproductive and damage potential of the reniform nematode, Rotylenchulus reniformis, on five cotton breeding lines reported as tolerant to this nematode in Texas were compared with two standard cotton cultivars, Deltapine 50 and Stoneville LA 887, in a North Carolina field naturally infested with R. reniformis. Numbers of R. reniformis in soil were suppressed at mid-season, and cotton-lint yield was increased by preplant fumigation with 1,3-dichloropropene. Population densities of R. reniformis at cotton harvest were unaffected by fumigation in 1998, but were affected in 1999. Some of the putatively tolerant breeding lines supported lower levels of R. reniformis and had higher tolerance indices to reniform nematode than the standard cultivars, but the yields of the breeding lines were significantly lower than the standard cultivars. Fumigation resulted in a 100- to 200-kg/ha increase in cotton lint yield for cultivars LA 887 and Deltapine 50.

Identification of Sources of Resistance to Four Species of Root-knot Nematodes in Tobacco.

Resistance to the southern root-knot nematode, Meloidogyne incognita races 1 and 3, has been identified, incorporated, and deployed into commercial cultivars of tobacco, Nicotiana tabacum. Cultivars with resistance to other economically important root-knot nematode species attacking tobacco, M. arenaria, M. hapla, M. javanica, and other host-specific races of M. incognita, are not available in the United States. Twenty-eight tobacco genotypes of diverse origin and two standard cultivars, NC 2326 (susceptible) and Speight G 28 (resistant to M. incognita races 1 and 3), were screened for resistance to eight root-knot nematode populations of North Carolina origin. Based on root gall indices at 8 to 12 weeks after inoculation, all genotypes except NC 2326 and Okinawa were resistant to M. arenaria race 1, and races 1 and 3 of M. incognita. Except for slight root galling, genotypes resistant to M. arenaria race 1 responded similarly to races 1 and 3 of M. incognita. All genotypes except NC 2326, Okinawa, and Speight G 28 showed resistance to M. javanica. Okinawa, while supporting lower reproduction of M. javanica than NC 2326, was rated as moderately susceptible. Tobacco breeding lines 81-R-617A, 81-RL- 2K, SA 1213, SA 1214, SA 1223, and SA 1224 were resistant to M. arenaria race 2, and thus may be used as sources of resistance to this pathogen. No resistance to M. hapla and only moderate resistance to races 2 and 4 of M. incognita were found in any of the tobacco genotypes. Under natural field infestations of M. arenaria race 2, nematode development on resistant tobacco breeding lines 81-RL-2K, SA 1214, and SA 1215 was similar to a susceptible cultivar with some nematicide treatments; however, quantity and quality of yield were inferior compared to K 326 plus nematicides.

Aggressiveness and Damage Potential of Central American and Caribbean Populations of Radopholus spp. in Banana.

Monoxenic cultures of burrowing nematode populations extracted from banana roots from Belize, Guatemala, Honduras, and Costa Rica were established on carrot discs. Cultures of Radopholus spp. were also obtained from Florida, Puerto Rico, Dominican Republic, and Ivory Coast. The aggressiveness (defined as reproductive fitness and root necrosis) of these populations was evaluated by inoculating banana plants (Musa AAA, cv. Grande Naine) with 200 nematodes/plant. Banana plants produced by tissue culture were grown in 0.4-liter styrofoam cups, containing a 1:1 mix of a coarse and a fine sand, at ca. 27 degrees C and 80% RH. Banana plants were acclimated and allowed to grow for 4 weeks prior to inoculation. Plant height, fresh shoot and root weights, root necrosis, and nematode population densities were determined 8 weeks after inoculation. Burrowing-nematode populations varied in aggressiveness, and their reproductive fitness was generally related to damage reported in the field. Plant height and fresh shoot and root weight did not reflect damage caused by nematodes under our experimental conditions. Necrosis of primary roots was closely related to the reproductive fitness of the nematode populations. Variation in aggressiveness among nematode populations followed a similar trend in the two susceptible hosts tested, Grande Naine and Pisang mas. All nematode populations had a low reproductive factor (Rf

Resistance to Root-knot, Reniform, and Soybean Cyst Nematodes in Selected Soybean Breeding Lines.

Soybean breeding lines and reported sources of nematode resistance were evaluated in repeated greenhouse tests for resistance to North Carolina populations of the soybean cyst nematode Heterodera glycines, reniform nematode Rotylenchulus reniformis, and the root-knot nematode species Meloidogyne incognita, M. arenaria, and M. arenaria. Lines from the soybean breeding program in Missouri that had 'Hartwig' soybean as a parent were the most resistant to races 1-4 of the soybean cyst nematode and the population of reniform nematode evaluated here. Numerous cysts of an inbred soybean cyst nematode race 4 population were produced on several of these Hartwig descendants, however, and accession $92-1603 had a cyst index of 29.2%. These accessions were also susceptible to M. arenaria and M. arenaria. Soybean lines N87-539 and N91-245 from the breeding program in North Carolina had strong resistance to an inbred soybean cyst nematode race 1 population and to M. arenaria, respectively. Soybean germplasm from the Georgia breeding program demonstrated the strongest resistance to the root-knot nematode species tested. Lines from the Georgia program, including G80-1515, G83-559, G93-9106, and G93-9223, that incorporated both root-knot and soybean cyst nematode resistance had the best overall resistance to the nematode populations evaluated. Resistance reported in the soybean lines was generally upheld. In a few cases, differences in the origin and culture of the nematode populations used in this study may have led to discrepancies between reported and observed resistance.

Survey of Heterodera glycines Races and Other Plant-parasitic Nematodes on Soybean in North Carolina.

A survey of soybean-production areas in the Piedmont, Coastal Plain and Tidewater regions of North Carolina was conducted from 1994 to 1996. Heterodera glycines was detected in 55 of 77 fields sampled in 15 counties. The host race of H. glycines was determined for 39 of the populations collected. Of all populations collected, 4% were race 1, 40% race 2, 16% race 4, 7% race 5, and 4% race 9; the remaining 29% could not be accurately categorized. None of the populations evaluated had high levels of reproduction on the resistant cultivar Hartwig. The southern root-knot nematode Meloidogyne incognita was detected in 26% of the fields. Helicotylenchus spp. were detected in all fields sampled, Tylenchorhynchus spp. were found in 62%, Paratrichodorus spp. in 56%, and Pratylenchus spp. in 72% of fields sampled. Mesocriconema spp., Xiphinema spp., and Hoplolaimus spp. were detected in less than 20% of the fields sampled.

Management of Plant-parasitic Nematodes on Peanut with Selected Nematicides in North Carolina.

Field experiments were conducted to determine peanut growth and yield responses to selected fumigant and nonfumigant nemaficide treatments in 1988 and 1989. All treatments with the fumigant 1, 3-D significantly suppressed nematode reproduction (Meloidogyne arenaria, M. hapla, and Mesocriconema ornatum) and enhanced peanut yields over the other treatments in four tests in 1988. Yield increases with the fumigant ranged from about 20% to 100% over the untreated control. Test sites in 1989 had lower nematode levels than those for 1988, and fewer positive plant and nematode responses were detected. Treatments with 1,3-D improved peanut quality but not yield in one experiment with low levels of M. hapla and M. ornatum in 1988. The 1,3-D + chloropicrin treatments at another site gave higher peanut yields than 1,3-D alone.

Developing sustainable systems for nematode management.

Early researchers identified key concepts and developed tactics for multiple-option management of nematodes. Although the emphasis on integrated pest management over the past three decades has promoted strategies and tactics for nematode management, comprehensive studies on the related soil biology-ecology are relatively recent. Traditional management tactics include host resistance (where available), cultural tactics such as rotation with nonhosts, sanitation and avoidance, and destruction of residual crop roots, and the judicious use of nematicides. There have been advances in biological control of nematodes, but field-scale exploitation of this tactic remains to be realized. New technologies and resources are currently becoming central to the development of sustainable systems for nematode-pest-crop management: molecular diagnostics for nematode identification, genetic engineering for host resistance, and the elucidation and application of soil biology for general integrated cropping systems. The latter strategy includes the use of nematode-pest antagonistic cover crops, animal wastes, and limited tillage practices that favor growth-promoting rhizobacteria, earthworms, predatory mites, and other beneficial organisms while suppressing parasitic nematodes and other plant pathogens. Certain rhizobacteria may induce systemic host resistance to nematodes and, in some instances, to foliage pathogens. The systems focusing on soil biology hold great promise for sustainable crop-nematode management, but only a few research programs are currently involved in this labor-intensive endeavor.

Genetics of Soybean-Heterodera glycines Interactions.

The soybean cyst nematode, Heterodera glycines, is one of the most economically important pathogens of soybean. Effective management of the nematode is often dependent on the planting of resistant soybean cultivars. During the past 40 years, more than 60 soybean genotypes and plant introductions (PI) have been reported as resistant to H. glycines. About 130 modern soybean cultivars registered in the United States are resistant to certain races of H. glycines. Several resistance genes have been identified and genetically mapped; however, resistance levels in many soybean cultivars are not durable. Some older cultivars are no longer resistant to certain H. glycines populations in many production areas, especially if a soybean monoculture has been practiced. Past soybean registration reports show that all resistant cultivars developed in public institutions from the mid-1960s to the present have been derived from five PIs. This narrow genetic background is fragile. To further complicate the issue, soybean-H. glycines genetic interactions are complex and poorly understood. Studies to identify soybean resistance genes sometimes have overlapped, and the same genes may have been reported several times and designated by different names. Nevertheless, many potential resistance genes in existing germplasm resources have not yet been characterized. Clearly, it is necessary to identify new resistance genes, develop more precise selection methods, and integrate these resistance genes into new cultivars. Rational deployment of resistant cultivars is critical to future sustained soybean production.

Impact of Soil Texture on the Reproductive and Damage Potentials of Rotylenchulus reniformis and Meloidogyne incognita on Cotton.

The effects of soil type and initial inoculum density (Pi) on the reproductive and damage potentials of Meloidogyne incognita and Rotylenchulus reniformis on cotton were evaluated in microplot experiments from 1991 to 1993. The equilibrium nematode population density for R. reniformis on cotton was much greater than that of M. incognita, indicating that cotton is a better host for R. reniformis than M. incognita. Reproduction of M. incognita was greater in coarse-textured soils than in fine-textured soils, whereas R. reniformis reproduction was greatest in a Portsmouth loamy sand with intermediate percentages of clay plus silt. Population densities of M. incognita were inversely related to the percentage of silt and clay, but R. reniformis was favored by moderate levels of clay plus silt (ca. 28%). Both M. incognita races 3 and 4 and R. reniformis effected suppression of seed-cotton yield in all soil types evaluated. Cotton-yield suppression was greatest in response to R. reniformis at high Pi. Cotton maturity, measured as percentage of open bolls at different dates, was affected by the presence of nematodes in all 3 years.

Greenhouse Evaluation of Selected Soybean Germplasm for Resistance to North Carolina Populations of Heterodera glycines, Rotylenchulus reniformis, and Meloidogyne Species.

Selected soybean genotypes were evaluated for resistance to North Carolina populations of the soybean cyst nematode Heterodera glycines, the root-knot nematodes Meloidogyne incognita races 3 and 4, M. arenaria races 1 and 2, M. javanica, and the reniform nematode Rotylenchulus reniformis in two greenhouse tests. Populations of cyst nematode used in the first test were cultures from field samples originally classified as races 1-5, and those used in the second test included inbred cyst lines that corresponded to races 1, 3, and 4. The original race classification of some cyst populations shifted after repeated culture on susceptible 'Lee 68' soybean. Most of the cyst-resistant soybean cultivars tested were susceptible to M. arenaria and M. javanica. Exceptionally large galls were induced by M. arenaria on roots of Asgrow 5979, Hartwig, and CNS soybean. Hartwig soybean and PI 437654 were resistant to all cultured field populations of cyst nematodes in a first greenhouse test. In the second test, cyst indices of 11.3% and 19.4% were observed on roots of PI 437654 and Hartwig, respectively, when infected with an inbred line (OP50) of H. glycines corresponding to race 4. The cyst-resistant soybean germplasm tested, including Hartwig and PI 437654, supported only low numbers of reniform nematodes. The most severe soybean root necrosis observed, however, was associated with reniform nematode infection.