Deployment of whole genome next-generation sequencing of SARS-CoV-2 in a military maritime setting.

BACKGROUND: SARS-CoV-2 can spread rapidly on maritime platforms. Several outbreaks of SARS-CoV-2 have been reported on warships at sea, where transmission is facilitated by living and working in close quarters. Core components of infection control measures such as social distancing, patient isolation and quarantine of exposed persons are extremely difficult to implement. Whole genome sequencing (WGS) of SARS-CoV-2 has facilitated epidemiological investigations of outbreaks, impacting on outbreak management in real time by identifying transmission patterns, clusters of infection and guiding control measures. We suggest such a capability could mitigate against the impact of SARS-CoV-2 in maritime settings. METHODS: We set out to establish SARS-CoV-2 WGS using miniaturised nanopore sequencing technology aboard the Royal Fleet Auxiliary ARGUS while at sea. Objectives included designing a simplified protocol requiring minimal reagents and processing steps, the use of miniaturised equipment compatible for use in limited space, and a streamlined and standalone data analysis capability to allow rapid in situ data acquisition and interpretation. RESULTS: Eleven clinical samples with blinded SARS-CoV-2 status were tested at sea. Following viral RNA extraction and ARTIC sequencing library preparation, reverse transcription and ARTIC PCR-tiling were performed. Samples were subsequently barcoded and sequenced using the Oxford Nanopore MinION Mk1B. An offline version of the MinKNOW software was used followed by CLC Genomics Workbench for downstream analysis for variant identification and phylogenetic tree construction. All samples were correctly classified, and relatedness identified. CONCLUSIONS: It is feasible to establish a small footprint sequencing capability to conduct SARS-CoV-2 WGS in a military maritime environment at sea with limited access to reach-back support. This proof-of-concept study has highlighted the potential of deploying such technology in the future to military environments, both maritime and land-based, to provide meaningful clinical data to aid outbreak investigations.

Mapping of host-parasite-microbiome interactions reveals metabolic determinants of tropism and tolerance in Chagas disease.

Chagas disease (CD) is a parasitic disease caused by Trypanosoma cruzi protozoa, presenting with cardiomyopathy, megaesophagus, and/or megacolon. To determine the mechanisms of gastrointestinal (GI) CD tissue tropism, we systematically characterized the spatial localization of infection-induced metabolic and microbiome alterations, in a mouse model of CD. Notably, the impact of the transition between acute and persistent infection differed between tissue sites, with sustained large-scale effects of infection in the esophagus and large intestine, providing a potential mechanism for the tropism of CD within the GI tract. Infection affected acylcarnitine metabolism; carnitine supplementation prevented acute-stage CD mortality without affecting parasite burden by mitigating infection-induced metabolic disturbances and reducing cardiac strain. Overall, results identified a previously-unknown mechanism of disease tolerance in CD, with potential for new therapeutic regimen development. More broadly, results highlight the potential of spatially resolved metabolomics to provide insight into disease pathogenesis and infectious disease drug development.

Lethal and nonlethal murine malarial infections differentially affect apoptosis, proliferation, and CD8 expression on thymic T cells.

Although thymic atrophy and apoptosis of the double-positive (DP) T cells have been reported in murine malaria, comparative studies investigating the effect of lethal and nonlethal Plasmodium infections on the thymus are lacking. We assessed the effects of P. yoelii lethal (17XL) and nonlethal (17XNL) infections on thymic T cells. Both strains affected the thymus. 17XL infection induced DP T-cell apoptosis and a selective decrease in surface CD8 expression on developing thymocytes. By contrast, more severe but reversible effects were observed during 17XNL infection. DP T cells underwent apoptosis, and proliferation of both DN and DP cells was affected around peak parasitemia. A transient increase in surface CD8 expression on thymic T cells was also observed. Adult thymic organ culture revealed that soluble serum factors, but not IFN-γ or TNF-α, contributed to the observed effects. Thus, lethal and nonlethal malarial infections led to multiple disparate effects on thymus. These parasite-induced thymic changes are expected to impact the naïve T-cell repertoire and the subsequent control of the immune response against the parasite. Further investigations are required to elucidate the mechanism responsible for these disparate effects, especially the reversible involution of the thymus in case of nonlethal infection.

Patterns of proopiomelanotropin and proopiocortin gene expression and of immunohistochemistry for gonadotropin-releasing hormones (lGnRH-I and III) during the life cycle of a nonparasitic lamprey: relationship to this adult life history type.

There are two adult life history types among lamprey species, nonparasitic and parasitic, with the former commencing the final interval of sexual maturation immediately after metamorphosis. There are no extensive studies that directly compare hormone profiles during the life cycles of nonparasitic and parasitic lamprey species, yet such data may explain differences in development, reproductive maturation, and feeding status. The present study uses immunohistochemistry to show the life cycle profiles for gonadotropin-releasing hormones (GnRH-I and -III) in the brain of the nonparasitic species, the American brook lamprey, Lampetra appendix, for comparison with the extensive, published, immunohistochemical data on these hormones in the parasitic species, the sea lamprey, Petromyzon marinus. The complete cDNAs for the two lamprey prohormones, proopiocortin (POC), and proopiomelanotropin (POM), were cloned for L. appendix and both nucleotide and deduced amino acid sequences were compared with those previously published for P. marinus. The POC and POM cDNAs for both species were used in expression studies, with Northern blotting, throughout their life cycles. Although GnRH-I and -III immunohistochemistry revealed a similar distribution of immunoreactive cells and fibers in the two species during the life cycles, a qualitative evaluation of staining intensity in L. appendix, implied early activity in the brains of metamorphosis of this species, particularly in GnRH-I. GnRH-III seems to be important in larval life and early metamorphosis in both species. A novel feature of this immunohistochemical study is the monthly observations of the distribution and relative intensity of the two GnRHs during the critical period of final sexual maturation that lead to spawning and then the spent animal. L. appendix POC and POM nucleotide sequences had 92.9 and 94.6% identity, respectively, with P. marinus POC and POM and there was an earlier increase in their expression during metamorphosis and postmetamorphic life. Since there was some correlation between the timing of metamorphic development, gonad maturation, and brain irGnRH intensity with POC and POM expression in L. appendix, it was concluded that these prohormones yield posttranslational products that likely play a substantial role in development and maturation events that lead to the nonparasitic adult life history of this species.

Mid-arm circumference: an alternative measure for screening low birth weight babies.

Birth weight is a reliable and sensitive indicator for predicting the immediate or later outcome of a newborn child. In a developing country like Bangladesh, where more than 75% of deliveries occur in rural community and are mostly attended by Traditional Birth Attendants (TBA) or relatives, birth weight cannot be recorded mainly due to paucity of suitable weighing scale. To overcome the problem associated with weighing the newborn, it was considered justified to find out other simpler measurements that could be used as substitute of weighing, in order to identify low birth weight babies. A cross sectional, analytical, hospital based study was conducted at Dhaka city on 560 newborn babies born during a period of 18 months in 2000-2001 to examine relative validity of mid-arm circumference as a screening measure of low birth weight babies. Mid-arm circumference, length, head circumference, chest circumference, abdominal girth, and calf circumference were considered. The study showed a strong correlation (p < 0.001) between mid-arm circumference (r = 0.956) and birth weight, followed by calf circumference (r = 0.946) and birth weight. Other parameters were also strongly correlated (p < 0.001). The study showed that in identifying newborns of <2500 gm a mid-arm circumference of <9 cm had the best sensitivity (96.2%) and specificity (97.3%). A value of <8 cm and <6.8 cm for mid-arm circumference showed highest validity for picking up newborns weighing <2000 gm and <1500 gm respectively. Measurement of arm circumference is easier, convenient and statistically superior to other anthropometrical parameters in this work. The researchers recommend designing of simple 'Tri-colored tape' for early detection of 'At Risk' newborns in rural community for their timely management.

Correlation of anthropometric measurements of mothers and their newborns.

This cross-sectional study was designed to assess the influence of the nutritional status of the mother upon the anthropometric measures of their babies. It was conducted at three different hospitals of Dhaka city during a short period of 5 weeks in 1992. One hundred and fifty mothers with their newborns were studied to correlate their anthropometric measurements. Weight, height/length and mid-arm-circumference were measured. The study showed that the correlation between weight of mother and weight of her newborn was stronger than that between heights (length) and mid-arm-circumferences of the mothers and the newborn. Correlation between mid-arm-circumference of mother and newborn was statistically insignificant whereas correlations of other variables were statistically significant. Height of mother and length of newborn daughter were less well correlated than height of mother and length of newborn son which showed relatively significant correlation (p < 0.05). The study indicates that the anthropometric measures of the newborn babies might be an outcome of the nutritional status of the mother.

PIP: The influence of maternal nutritional status on infant anthropometric measures was investigated in a cross-sectional study conducted at three hospitals in Dhaka, Bangladesh, in a 5-week period in 1992. Weight, height/length, and mid-arm circumference were measured in 150 mother-infant pairs. Of strongest significance was the association of maternal weight with birth weight, especially in male infants. Also significant were positive correlations between maternal height and the length of male newborns, maternal weight and the length of both male and female infants, maternal height and birth weight, and maternal mid-arm circumference and birth weight. The only nonsignificant association was that between maternal and infant mid-arm circumferences.

Self-assessment of confidence of internee doctors in performing common surgical operations.

A total of 140 internee doctors who had just completed or were about to complete their internship training from four leading Medical College Hospitals of Bangladesh were asked to fill up a pre-tested structured questionnaire. Of them 115 were male and 25 were female. All the participants had 6 months compulsory training in Medicine, 123 had 6 months training in Surgery and 17 had 6 months training in Obstetrics-Gynecology. Over 50% doctors expressed lack of confidence in performing ligation, vasectomy, splinting simple fractures, venesection, episiotomy, hydrocele operation, circumcision, proctoscopy and inguinal herniorrhaphy and expressed the need for further training in those procedures. Only 10% and 1.43% internees stated that they were confident about performing ligation and vasectomy independently. Internees from Chittagong Medical College Hospitals expressed their inability to perform ligation and/or vasectomy independently. So it was recommended that surgical training should be made mandatory for all internee Doctors with extension of the Internship period by at least 6 months. Emphasis should be laid on training in vasectomy and ligation. A pre-registration evaluation test may be introduced at the end of their training period.

PIP: A total of 140 internee doctors who had just completed or were about to complete their internship training from four leading Medical College Hospitals of Bangladesh were asked to complete a pretested structured questionnaire. Of them, 115 were male and 25 were female. All the participants had 6 months compulsory training in medicine, 123 had 6 months training in surgery, and 17 had 6 months training in obstetrics-gynecology. Over 50% of the doctors expressed lack of confidence in performing ligation, vasectomy, splinting simple fractures, venesection, episiotomy, hydrocele operation, circumcision, proctoscopy, and inguinal herniorrhaphy, and expressed the need for further training in those procedures. Only 10% and 1.43% of internees stated that they were confident about performing ligation and vasectomy independently. Internees from Chittagong Medical College Hospitals expressed their inability to perform ligation and/or vasectomy independently. So it was recommended that surgical training should be made mandatory for all internee doctors with extension of the internship period by at least 6 months. Emphasis should be put on training in vasectomy and ligation. A preregistration evaluation test may be introduced at the end of their training period.

Decreased gastric acid secretion and bacterial colonization of the stomach in severely malnourished Bangladeshi children.

To assess the effect of malnutrition on gastric acidity and gastric bacterial colonization, we studied 35 severely malnourished Bangladeshi children before (0 wk) and after (3 wk) they received nutritional rehabilitation for 3 wk. These results were compared with those obtained from a similarly examined group of 20 better-nourished Bangladeshi children. Gastric acid output, both basal and after betazole stimulation, was significantly lower in the malnourished group at 0 wk compared with the better-nourished children (p less than 0.01): basal 0.22 vs. 0.52 mEq HCl/h and stimulated 0.90 vs. 2.5 mEq HCl/h. Both the concentration of acid and the rate at which gastric juice was secreted were decreased in the malnourished group but serum gastrin levels were not significantly different. After 3 wk, the malnourished children had improved from 61% (+/- 9.0%; SD) to 81% (+/- 8.1%) of expected weight-for-height and were not significantly different than the better-nourished group (86% +/- 11%). Nevertheless, gastric acid concentration remained depressed in the 3-wk group, although the rate of gastric juice secretion equaled levels observed in the better-nourished group. None of the better-nourished children had detectable gram-negative bacterial colonization of their gastric juice. In contrast, 26 of 32 (81%) malnourished children at 0 wk were colonized--even after betazole stimulation, 11 of 33 (33%) gastric juice samples yielded viable organisms--suggesting that the decrease in gastric acid output greatly reduced the gastric acid barrier. Interestingly, only 9 of 20 (45%) better-nourished children had gastric juice with basal pH values below 4.0, suggesting that the gastric acid barrier may be an intermittent defense factor in Bangladeshi children.

Scabies in urban Bangladesh.

As a part of a larger project on hygiene education and diarrhoeal diseases we followed 766 children less than 6 years of age from October 1984 to September 1985 in Dhaka, Bangladesh. The aims were to estimate the annual risk of infestation with scabies in children, to describe its involvement of other family members, and to determine some of the familial and individual risk factors for apparent infestation by scabies. During this period 589 (77%) children appeared to have been infected with scabies, and 125 (16%) children were infested for more than 6 months. Of the factors examined, direct and indirect indicators of decreased wealth and incorrect hygiene practices correlated with higher rates of apparent infestation, although scabies rates remained high at all socioeconomic levels.

Male factors in infertility--a preliminary report.

Findings in 325 consecutive primary seminal analysis done at the Infertility Treatment Centre of IPGMR, are discussed. The clinical profile of the infertile couples was recorded. Semen was examined for quantity, sperm density, motility and morphology. An attempt was also made to correlate past illnesses with the quality of semen. 65 patients (20%) showed azoospermia, while 29 (8.9%) showed sperm count of less than 10 million/ml. History of past illnesses which contribute to azoospermia/oligospermia was obtained in 46% of azoospermia cases compared to only 10% in subjects showing sperm count of over 10 million/ml. Commonest association between azoospermia and past illness was found in the case of small-pox, where out of 31 subjects with past history of small-pox, 15 showed complete azoospermia, one showed sperm density of less then 10 million/ml.