An accurate model for SARS-CoV-2 pooled RT-PCR test errors

Pooling is a method of simultaneously testing multiple samples for the presence of pathogens. Pooling of SARS-CoV-2 tests is increasing in popularity, due to its high testing throughput. A popular pooling scheme is Dorfman pooling: test N individuals simultaneously, if the test is positive, each individual is then tested separately; otherwise, all are declared negative. Most analyses of the error rates of pooling schemes assume that including more than a single infected sample in a pooled test does not increase the probability of a positive outcome. We challenge this assumption with experimental data and suggest a novel and parsimonious probabilistic model for the outcomes of pooled tests. As an application, we analyse the false-negative rate (i.e. the probability of a negative result for an infected individual) of Dorfman pooling. We show that the false-negative rates under Dorfman pooling increase when the prevalence of infection decreases. However, low infection prevalence is exactly the condition when Dorfman pooling achieves highest throughput efficiency. We therefore urge the cautious use of pooling and development of pooling schemes that consider correctly accounting for tests’ error rates.

Molecular Characterization of a Novel Mycovirus Infecting the Entomopathogenic Fungus Beauveria Bassiana

The entomopathogenic fungus Beauveria bassiana is used worldwide for its biological control. Seven dsRNA segments were detected from a single Beauveria bassiana strain RCEF 1446. High-throughput sequencing indicated the presence of three mycoviruses in the infected sample. Two known mycoviruses were identified as Beauveria bassiana Victorivirus 1 and Beauveria bassiana polymycovirus 1, and the novel mycovirus was designated as Beauveria bassiana bipartite mycovirus 1 (BbBV1). The complete sequence of the BbBV1 is described here. The mycovirus contains two dsRNA segments. The first dsRNA is 2,026 bp in length and encoding a RNA-dependent RNA polymerase (RdRp) (68.54 kDa), while the second segment encoding a hypothetical protein (35.55 kDa) of unknown function, was 1,810 bp in length. Moreover, the RdRp protein sequences showed the highest identity of 62.89% to Corynespora cassiicola bipartite mycovirus 1. Phylogenetic analysis of the RdRp reveals that the virus represents a distinct lineage of unassigned dsRNA mycoviruses infecting fungi.

Molecular Detections and Resistance Response of Six Rice Varieties to Tungroviruses from South Sulawesi

The suspected rice virus is found in the field, namely the tungrovirus which is transmitted by green leafhoppers (Nephotettix virescens). The study aimed to detect the tungrovirus molecularly and examine the resistance response of six rice varieties from the transmission of tungrovirus samples from South Sulawesi on a greenhouse scale. Based on the results of molecular detection with RTSV PCR of the double infected sample with DNA bands 1115 bp and RTBV of around 430 bp, Sidrap, and Maros samples were infected by 430 bp size RTBV, while Wajo sample was not detected by both viruses. The results of RTBV sequence analysis showed that the grouping of Sidrap was still one group with Maros and Pinrang samples and different from the group of samples from Malaysia, Thailand, and Philippines. While the grouping of RTSV shows that Pinrang samples are still one group with samples from Bali, Subang, and different from those of the Philippines, India, and Malaysia. The results of transmission in the greenhouse on six rice varieties (TN1, Ciherang, Mekongga, Tukad Unda, Inpari 36, Inpari 37) showed different plant resistance responses such as susceptible, moderately resistant, and resistant reactions based on the amount of disease intensity caused. Varieties that are classified as susceptible are TN1 and Ciherang varieties, moderately resistant, namely Mekongga and Tukad Unda varieties, and resistant varieties namely Inpari 36 and Inpari 37 varieties.

Biochemical Composition of Seed and Husk of Cowpea (Vigna unguiculata (L.) Walp.) Infected by Colletotrichum destructivum O’Gara in Storage

Colletotrichum destructivum was isolated from infected seeds and pods of cowpea (Var. IAR-48) with typical symptoms of anthracnose disease. The fungus during the pathogenesis, reduced the protein, fat, ash, crude fibre, carbohydrate, calcium and phosphorus, and increased the amount of iron, sodium, zinc, magnesium and potassium in the infected seed and husk. The carbohydrate, protein and phosphorus contents in the healthy husk reduced from 55.05%, 11.21% and 171.85 mg to 39.94%, 8.92% and 42.92 respectively in the infected sample whereas potassium and sodium contents in the healthy pod increased from 1.03 mg and 78.29 to 2.90 mg and 100.65 mg respectively in the infected husk. The potassium, sodium, magnesium and iron increased from 1292.25 mg, 0.19 mg, 0.09 mg and 11.00 mg in the healthy seeds to 1536.03 mg, 0.28 mg, 0.21 mg and 13.19 mg respectively in the infected seeds. The fungus caused the depletion of phosphorus from 498. 06 mg in the healthy to 430.17 mg in the infected seed, protein from 24.09% to 17.86%, carbohydrate from 57.02% to 34.35%, fat from 1.70% to 1.33% and crude fibre from 3.94% to 2.61%. The average loss of the major nutrient values; protein, carbohydrate and fat were 28.95% and 22.55% for seed and husk respectively after 8 weeks of planting.

Association between change in self-efficacy to resist drinking and drinking behaviors among an HIV-infected sample: Results from a large randomized controlled trial

Heavy drinking among HIV-infected individuals is associated with health complications. Health-behavior self-efficacy may be characteristically low among this population or negatively affected by HIV-infected status. We assessed whether self-efficacy to resist drinking increased during brief educational and motivational drinking-reduction interventions within HIV primary care and whether increases in self-efficacy predicted drinking among HIV-infected heavy drinkers. Results indicate that increases in self-efficacy from baseline to end-of-intervention inversely predicted drinking at end-of-intervention and at follow-up. Findings suggest that brief treatment interventions within HIV primary care may promote self-efficacy and that increases in self-efficacy predict initiation and maintenance of drinking reductions among HIV patients.

Keeping up with new technology: new approaches to diagnosis of Chlamydia infection

Chlamydia trachomatis infections are among the most common sexually transmitted infections in the US today. One of the keys to the prevention of C. trachomatis infection rests on the ability to make this diagnosis on the basis of accurate laboratory testing. For many years the standard for diagnosis of C. trachomatis infections has been isolation in tissue culture. Numerous nonculture methods, including enzyme immunoassay, have been used as an alternative to cell culture. The performance characteristics of these tests have all been compared with a standard, cell culture, which at best will detect 90% of positive specimens. Nucleic acid amplification techniques, including PCR and ligase chain reaction, have been recently introduced. The advantage of these tests is their ability to detect 10-20% more positive specimens when compared with culture or confirmed nonculture methods performed with a single specimen. The sensitivity of amplified tests also allows us to test specimens from multiple sites (endocervix, urethra, urine), which expands our standard from an infected sample to detection of an infected patient. Tests based on amplified nucleic acid technology have greatly improved our ability to diagnose urogenital C. trachomatis infection. The use of an expanded standard will help us accurately define the true performance and clinical utility of nonculture Chlamydia diagnostic tests.