Estimating infectiousness throughout SARS-CoV-2 infection course

Two elementary parameters for quantifying viral infection and shedding are viral load and whether samples yield a replicating virus isolate in cell culture. We examined 25,381 German SARS-CoV-2 cases, including 6110 from test centres attended by pre-symptomatic, asymptomatic, and mildly-symptomatic (PAMS) subjects, 9519 who were hospitalised, and 1533 B.1.1.7 lineage infections. The youngest had mean log10 viral load 0.5 (or less) lower than older subjects and an estimated ~78% of the peak cell culture replication probability, due in part to smaller swab sizes and unlikely to be clinically relevant. Viral loads above 109 copies per swab were found in 8% of subjects, one-third of whom were PAMS, with mean age 37.6. We estimate 4.3 days from onset of shedding to peak viral load (8.1) and cell culture isolation probability (0.75). B.1.1.7 subjects had mean log10 viral load 1.05 higher than non-B.1.1.7, with estimated cell culture replication probability 2.6 times higher.

Influence of soybean tissue and oomicide seed treatments on oomycete isolation

Soybean seedlings are vulnerable to different oomycete pathogens. Seed treatments containing the two anti-oomycete (oomicide) chemicals, metalaxyl-M (mefenoxam), and ethaboxam are used for the protection against oomycete pathogens. This study aimed to evaluate the influence of these two oomicides on the isolation probability of oomycetes from soybean taproot or lateral root sections. Soybean plants were collected between the first and third trifoliate growth stages from five Midwest field locations in 2016 and four of the same fields in 2017. Oomycetes were isolated from taproot and lateral root. In 2016, 369 isolation attempts were completed resulting in 121 isolates from the taproot and 154 isolates from the lateral root. In 2017, 468 isolation attempts were completed, with 44 isolates from the taproot and 120 isolates from the lateral roots. In three of nine site-years, the probability of isolating an oomycete from a taproot or lateral root section was significantly different. Seed treatments containing a mixture of ethaboxam and metalaxyl significantly reduced the probability of oomycete isolation from lateral roots in Illinois in 2016 and 2017, but not in other locations, which may have been related to the heavy soil type (clay loam). Among the 439 isolates collected from the two years sampled, 24 oomycete species were identified, and community compositions differed depending on location and year. The five most abundant species were Pythium sylvaticum (28.9%), Pythium heterothallicum (14.3%), Pythium ultimum var. ultimum (11.8%), Pythium attrantheridium (7.9%), and Pythium irregulare (6.6%) which accounted for 61.7% of the isolates collected. Oomicide sensitivity to ethaboxam and mefenoxam was assessed for more than 300 isolates. There were large differences in ethaboxam sensitivity among oomycete species with EC50 ranging from < 0.01 to > 100 μg ml-1, and a median of 0.65 μg ml-1. Isolates with insensitivity to ethaboxam (> 12 μg ml-1) belonging to the species Pythium torulosum and Pythium rostratifingens but were sensitive to mefenoxam. Oomicide sensitivity to mefenoxam ranged from < 0.01 to 0.62 μg ml-1 with a median of 0.03 μg ml-1. The mean EC50 of the five most abundant species to ethaboxam ranged from 0.35 to 0.97 μg ml-1 of ethaboxam and from 0.02 to 0.04 μg ml-1 of mefenoxam. No shift in sensitivity to mefenoxam or ethaboxam was observed due to soybean seed treatment or year relative to the non-treated seed controls. In summary, this study contributed to the understanding of the composition of oomycete populations from different soybean root tissues, locations, years, and seed treatments. Finally, the effectiveness of seed treatments containing mefenoxam or metalaxyl plus ethaboxam can be effective in reducing the probability of oomycete isolation from soybean roots.

Cost-effectiveness analysis of pneumococcal conjugate vaccines in preventing pneumonia in Peruvian children

Introduction: Pneumococcal pneumonia (PP) has a high burden of morbimortality in children. Use of pneumococcal conjugate vaccines (PCVs) is an effective preventive measure. After PCV 7-valent (PCV7) withdrawal, PCV 10-valent (PCV10) and PCV 13-valent (PCV13) are the alternatives in Peru. This study aimed to evaluate cost effectiveness of these vaccines in preventing PP in Peruvian children <5 years-old. Methodology: A cost-effectiveness analysis was developed in three phases: a systematic evidence search for calculating effectiveness; a cost analysis for vaccine strategies and outcome management; and an economic model based on decision tree analysis, including deterministic and probabilistic sensitivity analysis using acceptability curves, tornado diagram, and Monte Carlo simulation. A hypothetic 100 vaccinated children/vaccine cohort was built. An incremental cost-effectiveness ratio (ICER) was calculated. Results: The isolation probability for all serotypes in each vaccine was estimated: 38% for PCV7, 41% PCV10, and 17% PCV13. Avoided hospitalization was found to be the best effectiveness model measure. Estimated costs for PCV7, PCV10, and PCV13 cohorts were USD13,761, 11,895, and 12,499, respectively. Costs per avoided hospitalization were USD718 for PCV7, USD333 for PCV10, andUSD 162 for PCV13. At ICER, PCV7 was dominated by the other PCVs. Eliminating PCV7, PCV13 was more cost effective than PCV10 (confirmed in sensitivity analysis). Conclusions: PCV10 and PCV13 are more cost effective than PCV7 in prevention of pneumonia in children <5 years-old in Peru. PCV13 prevents more hospitalizations and is more cost-effective than PCV10. These results should be considered when making decisions about the Peruvian National Inmunizations Schedule.