Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes

Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries. Rabies is an almost invariably fatal viral disease that causes a large public health and economic burden in Asia and Africa, despite being entirely vaccine preventable. With policy efforts now directed towards achieving a global goal of zero dog-mediated human rabies deaths by 2030, establishing effective surveillance tools is critical. Genomic data can provide important and unique insights into rabies spread and persistence that can direct control efforts. However, capacity for genomic research in low- and middle-income countries is held back by limited laboratory infrastructure, cost, supply chains and other logistical challenges. Here we present and validate an end-to-end workflow to facilitate affordable whole genome sequencing for rabies surveillance utilising nanopore technology. We used this workflow in Kenya, Tanzania and the Philippines to generate rabies virus genomes in two to three days, reducing costs to approximately £60 per genome. This is over half the cost of metagenomic sequencing previously conducted for Tanzanian samples, which involved exporting samples to the UK and a three- to six-month lag time. Ongoing optimization of workflows are likely to reduce these costs further. We also present tools to support routine whole genome sequencing and interpretation for genomic surveillance. Moreover, combined with training workshops to empower scientists in-country, we show that local sequencing capacity can be readily established and sustainable, negating the common misperception that cutting-edge genomic research can only be conducted in high resource laboratories. More generally, we argue that the capacity to harness genomic data is a game-changer for endemic disease surveillance and should precipitate a new wave of researchers from low- and middle-income countries.

Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes

Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries. Rabies is an almost invariably fatal viral disease that causes a large public health and economic burden in Asia and Africa, despite being entirely vaccine preventable. With policy efforts now directed towards achieving a global goal of zero dog-mediated human rabies deaths by 2030, establishing effective surveillance tools is critical. Genomic data can provide important and unique insights into rabies spread and persistence that can direct control efforts. However, capacity for genomic research in low- and middle-income countries is held back by limited laboratory infrastructure, cost, supply chains and other logistical challenges. Here we present and validate an end-to-end workflow to facilitate affordable whole genome sequencing for rabies surveillance utilising nanopore technology. We used this workflow in Kenya, Tanzania and the Philippines to generate rabies virus genomes in two to three days, reducing costs to approximately £60 per genome. This is over half the cost of metagenomic sequencing previously conducted for Tanzanian samples, which involved exporting samples to the UK and a three- to six-month lag time. Ongoing optimization of workflows are likely to reduce these costs further. We also present tools to support routine whole genome sequencing and interpretation for genomic surveillance. Moreover, combined with training workshops to empower scientists in-country, we show that local sequencing capacity can be readily established and sustainable, negating the common misperception that cutting-edge genomic research can only be conducted in high resource laboratories. More generally, we argue that the capacity to harness genomic data is a game-changer for endemic disease surveillance and should precipitate a new wave of researchers from low- and middle-income countries.

Comparative Antiviral Efficacy of Generic Sofosbuvir versus Brand Name Sofosbuvir with Ribavirin for the Treatment of Hepatitis C

BACKGROUND

Chronic hepatitis C infection is a major cause for liver failure and liver cancer and can be treated with highly effective all oral directly acting antiviral (DAA) drugs. Generic versions of these DAAs are available in India.

METHOD

This was an open-label, single-center, prospective, nonrandomized observational study for the comparative safety and efficacy of generic versus brand name sofosbuvir with ribavirin therapy for chronic hepatitis C infection (all genotypes). Between December 2014 and December 2015, 66 patients received either generic sofosbuvir (400mg) or brand name SOLVALDI (400mg) with weight based ribavirin for 24 weeks in a single multispecialty hospital in Mumbai. Monitoring viral loads and safety labs was performed as per national guidelines.

RESULTS

Sustained virologic response was 72.4% versus 75.7% (p=0.78) among patients treated with generics and SOVALDI, respectively. At 4 weeks on-treatment, approximately 90% of patients from both groups had undetectable or below the lower limit of quantification. Change in hemoglobin was comparable in both groups (p=0.26).

CONCLUSION

Generic versions of sofosbuvir reported in this study are safe and efficacious to treat hepatitis C. However, bioequivalency studies of all generic DAAs need to be performed before wider use of such drugs for the treatment of hepatitis C.

Low-dose irradiation as a measure to improve microbial quality of ice cream

The present study was undertaken to investigate the efficacy of low-dose irradiation to improve the microbial safety of ice cream. Initially three different flavors (vanilla, strawberry and chocolate) of ice cream were exposed, at -72 degrees C, to doses of 1, 2, 5, 10 and 30 kGy to gamma-radiation. Irradiation at 1 kGy resulted in reduction of microbial population by one log cycle, thus meeting the requirement limits prescribed by Bureau of Indian Standards. Pathogens such as Listeria monocytogenes 036, Yersinia enterocoliticta 5692 and Escherichia coli O157:H19, respectively, showed the D10 values 0.38, 0.15 and 0.2 kGy in ice cream at -72 degrees C suggesting the efficacy of low doses (1 kGy) in eliminating them. Sensory evaluation studies of ice cream irradiated at 1, 2, 3 and 5 kGy by a 15 member panel demonstrated that doses higher than 2 kGy irradiation induced off-odour and an aftertaste was evident in vanilla ice cream. A radiation dose of 1 kGy was sufficient to eliminate the natural number of pathogens present in the ice cream. No statistically significant differences were observed in the sensory attributes of all the three flavours of ice cream either unirradiated or exposed to 1 kGy (P < 0.05).

Laparoscopic accessory splenectomy for recurrent idiopathic thrombocytopenic purpura and hemolytic anemia

BACKGROUND

Laparoscopic splenectomy is an effective treatment for idiopathic thrombocytopenic purpura (ITP) and hemolytic anemia that has a remission rate of 80-90%. In some patients in whom the disease persists or recurs, a diagnosis of accessory spleen is made. The long-term efficacy of laparoscopic accessory splenectomy is unknown.

METHODS

Patients who underwent laparoscopic accessory splenectomy were followed in the outpatient clinic. The perioperative course, blood counts, and need for medical therapy to maintain a normal count were recorded.

RESULTS

Eight patients underwent laparoscopic accessory splenectomy. All procedures were completed laparoscopically, and all patients were discharged on the 1st postoperative day. Patients were available for a follow-up period of 15 months range, (3-27). None of the ITP patients achieved a complete remission. Two of them had a partial remission, and five ITP patients are now being treated with chronic corticosteroids to maintain a platelet count of >100,000/ml.

CONCLUSION

Laparoscopic accessory splenectomy is associated with a low rate of morbidity and a short hospital stay. Despite its success in removing all residual splenic tissue, most patients will probably not enjoy a complete remission.

A prospective randomized trial of feeding methods in very low birth weight infants

OBJECTIVE

To test the hypothesis that very low birth weight infants fed by continuous nasogastric gavage (CNG) would achieve full enteral feedings (100 kcal/kg/d) at an earlier postnatal age and have less feeding intolerance (FI) than infants fed by intermittent bolus gavage (IBG).

METHODS

Eighty infants were stratified by birth weight (700 to 1000 g and 1001 to 1250 g) and randomized into CNG or IBG feeding groups. CNG infants were comparable with IBG in birth weight, gestational age, sex, race, and day of onset of feeding (5.7 +/- 2.1 days vs 5.6 +/- 2.2 days, respectively). Feedings were given as undiluted Similac Special Care formula (Ross Laboratories, Columbus, OH) via a specific protocol designed for each 50 to 100 g birth weight category. Feedings were advanced isoenergetically by a maximum of 25 mL/kg/d until an endpoint of 100/kcal/kg/d for at least 48 hours was reached. An infant whose feedings were withheld for >12 hours based on predetermined criteria was considered to have an episode of FI.

RESULTS

Infants in the CNG group reached full enteral feeding at 17.1 +/- 8.9 days compared with 15.5 +/- 5.5 days in the IBG group; these were not statistically different. Secondary outcome variables such as days to regain birth weight (CNG, 12.6 +/- 5 days vs IBG, 12.5 +/- 3.7 days), days to reach discharge weight of 2040 g (CNG, 60 +/- 13.4 days vs IBG, 62 +/- 13.6 days), and number of episodes of FI were not significantly different between feeding methods. FI was primarily associated with birth weight </=1000 g (71%) vs 1001 to 1250 g (38%).

CONCLUSION

Feeding methods are associated with similar outcomes when feeding regimens are comparable.

Requiring on-line medical command for helicopter request prolongs computer-modeled transport time to the nearest trauma center

INTRODUCTION

Rapid transport from scene to closest trauma center requires optimal use of public safety first responder (FR), basic life support (BLS), advanced life support (ALS), and transport resources (ground or air). In some parts of this regional emergency medical services (EMS) system, on-scene ALS requires contact with on-line medical command (OLMC) to obtain authorization for air medical helicopter (AMH) dispatch, because some EMS medical directors believe that this may decrease overutilization of AMH services.

HYPOTHESIS

The hypothesis of this study was that requiring prior OLMC for AMH dispatch prolongs mean time to a trauma center versus either FR or BLS request for AMH.

METHODS

Computer mapping programs were used to model the most rapid driving time to the closest trauma center from 167 actual AMH responses to the scene of a motor vehicle accident. In an OLMC-ALS model, only OLMC-ALS can request an AMH. In a BLS model, BLS units arrive on the scene and the crew requests simultaneous dispatch of an ALS response and an AMH. In the FR model, on arrival at the scene, a FR requests simultaneous dispatch of a BLS unit, an ALS unit, and an AMH.

RESULTS

The OLMC-ALS model resulted in a longer mean value for time to trauma center by an AMH than did the computer model for all ground transport settings. The FR model yielded a shorter mean time for AMH compared with the mean values for time to trauma center for all settings. Differences in mean values for time in urban settings were small (ground: 42 minutes, air: 36 minutes), whereas those for the suburban (ground: 52 minutes, air: 41 minutes), and those for rural (ground: 69 minutes, air: 47 minutes) were significant clinically. For the BLS model, these differences persisted, but were significant clinically only in the rural setting (ground: 68 minutes, air: 53 minutes).

CONCLUSIONS

Optimal use of AMH requires balancing the need for early helicopter dispatch to fully exploit its speed advantage with the disadvantage of expensive overutilization. This computer model indicates that the best person to request AMH varies by venue: in urban settings, the OLMC physician should request AMH dispatch; in suburban venues, BLS should request AMH dispatch; and in rural venues, FRs should request AMH dispatch.

Measles antibody titers in early infancy

OBJECTIVE

To determine the prevalence of measles seronegativity among infants younger than 6 months and to ascertain their serologic response to measles vaccine.

DESIGN

Cross-sectional measles antibody survey during the 1989 measles epidemic in Chicago, Ill.

SETTING

Inner-city perinatal center.

PARTICIPANTS

Two hundred three infants younger than 6 months who had been admitted to the neonatal intensive care unit at birth; 130 (64%) of these infants were premature. Transplacental antibody transfer was evaluated in a subset of 89 mother-newborn pairs.

INTERVENTION

Administration of measles monovalent vaccine to seronegative infants.

MEASUREMENTS/RESULTS

Measles IgG antibody was measured using indirect fluorescent assay. At birth, 19 (38%) of 50 neonates born at less than 37 weeks' gestation had antibody titers that were twofold to fourfold lower than those of their mothers compared with three (8%) of 39 neonates born at more than 37 weeks' gestation (P < .01). Of the 203 study infants, fewer than 4% were seronegative at birth, while 74% of these infants aged 4 to 5 months were seronegative. Univariate logistic regression analysis indicated that the independent variables related to seronegativity were as follows: gestational age at birth (P = .007), chronological age (P < .001), history of having received three or more packed red blood cell transfusions (P < .001), and maternal age at delivery (P = .001). Multiple logistic regression analysis confirmed the association of seronegativity with chronological age (P < .001), gestational age (P < .02) and maternal age at delivery (P < .001). Seroconversion following administration of the measles vaccine was documented in 11 (79%) of 14 infants.

CONCLUSION

A significant proportion of 4- to 5-month-old infants who had been admitted to the neonatal intensive care unit at birth lack measurable measles antibody; this population should be taken into account when strategies to control measles are considered.

Comparison of effects of ozone, cadmium chloride and carbon tetrachloride on [14C]antipyrine metabolism in conscious rats

Previously, Graham et al. found evidence that pentobarbital-induced sleeping time was enhanced in various animals following exposure to 1 ppm of ozone in air. The present study was undertaken to investigate whether similar ozone exposure would cause inhibition of metabolism of another model drug, [14C]antipyrine, in conscious rats. Furthermore, this study also investigated whether, like that of ozone, other lipid-peroxidizing agents such as cadmium and carbon tetrachloride would affect metabolism of [14C]antipyrine in conscious rats. The results showed no significant effect of ozone exposure on subsequent metabolism of [14C]antipyrine in conscious rats as revealed by very similar 14CO2 exhalation rate (CER)-time profiles before and after ozone treatment under various exposure protocols. Even though the exposure to ozone caused no inhibition of antipyrine metabolism in conscious rats, cadmium and carbon tetrachloride, on the other hand, markedly inhibited metabolism of this model drug. In agreement with the reported sex-difference in toxic effects of cadmium, during the present study the cadmium-induced inhibitory effect on the CER-time profiles was observed in male but not in female rats. In contrast, no clear sex-dependency was noted in the inhibitory effect of carbon tetrachloride on [14C]antipyrine metabolism.