Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria

Effective infectious disease surveillance in high-risk regions is critical for clinical care and pandemic preemption; however, few clinical diagnostics are available for the wide range of potential human pathogens. Here, we conduct unbiased metagenomic sequencing of 593 samples from febrile Nigerian patients collected in three settings: i) population-level surveillance of individuals presenting with symptoms consistent with Lassa Fever (LF); ii) real-time investigations of outbreaks with suspected infectious etiologies; and iii) undiagnosed clinically challenging cases. We identify 13 distinct viruses, including the second and third documented cases of human blood-associated dicistrovirus, and a highly divergent, unclassified dicistrovirus that we name human blood-associated dicistrovirus 2. We show that pegivirus C is a common co-infection in individuals with LF and is associated with lower Lassa viral loads and favorable outcomes. We help uncover the causes of three outbreaks as yellow fever virus, monkeypox virus, and a noninfectious cause, the latter ultimately determined to be pesticide poisoning. We demonstrate that a local, Nigerian-driven metagenomics response to complex public health scenarios generates accurate, real-time differential diagnoses, yielding insights that inform policy.

Clinical Correlates of Non-alcoholic Steatohepatitis in Nigerian Patients with Metabolic Syndrome

BACKGROUND

Non-alcoholic steatohepatitis (NASH) is a progressive form of non-alcoholic fatty liver disease (NAFLD). NASH is frequently associated with metabolic syndrome (MetS) and its prevalence is increasing due to rising global epidemics of MetS. This study aimed at determining the prevalence, risk factors and correlates of NASH in patients with MetS in a tertiary hospital in Nigeria.

METHODS

We caried out a hospital based cross-sectional study of 81 subjects with MetS. The diagnosis of NASH was made by ultrasound evidence of hepatic steatosis, and exclusion of significant consumption of alcohol as well as histologic evidence of NASH on liver biopsy. Subjects gave informed consent and ethical approval was obtained from the ethics committee of the hospital. Data obtained were entered into SPSS version 20 and analyzed using simple and inferential statistics. A p-value of < 0.05 was considered statistically significant.

RESULTS

Total of 81 subjects with MetS were studied, males 36(44.4%), females 45(55.6%), mean age(SD) of 49.77 (12.08) years. Ten (12.3%) subjects were diagnosed with NASH. Subjects with NASH had significant association with obesity, dyslipidaemia, and poor glycemic control. Regression analysis showed that morbid obesity, low HDL and presence of type 2 diabetes mellitus were independent risk factors for the development of NASH.

CONCLUSION

NASH is common in Nigerian patients with MetS and its presence is significantly associated with obesity, dyslipidemia, and type 2 diabetes mellitus.

Development of an RT-LAMP assay for the detection of Lassa viruses in southeast and south-central Nigeria

Lassa virus (LASV) causes Lassa fever (LF), a viral hemorrhagic fever endemic in West Africa. LASV strains are clustered into six lineages according to their geographic location. To confirm a diagnosis of LF, a laboratory test is required. Here, a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay using a portable device for the detection of LASV in southeast and south-central Nigeria using three primer sets specific for strains clustered in lineage II was developed. The assay detected in vitro transcribed LASV RNAs within 23 min and was further evaluated for detection in 73 plasma collected from suspected LF patients admitted into two health settings in southern Nigeria. The clinical evaluation using the conventional RT-PCR as the reference test revealed a sensitivity of 50% in general with 100% for samples with a viral titer of 9500 genome equivalent copies (geq)/mL and higher. The detection limit was estimated to be 4214 geq/mL. The assay showed 98% specificity with no cross-reactivity to other viruses which cause similar symptoms. These results suggest that this RT-LAMP assay is a useful molecular diagnostic test for LF during the acute phase, contributing to early patient management, while using a convenient device for field deployment and in resource-poor settings.

Cutaneous metastasis from hepatocellular carcinoma: a rare presentation and review of the literature

A 53-year-old male Nigerian with a rare cutaneous metastasis and a late manifestation of hepatocellular carcinoma is presented. The skin nodules were umbilicated, painless. firm and spread on the chest, abdomen and back. Ultrasonography showed a huge mass in the right lobe of the liver. Fine needle aspiration cytology of the liver revealed hepatocellular carcinoma and the skin nodule, metastatic carcinoma of hepatic origin. The immunological marker HBsAg was positive while Anti-HCV Ab and alpha-feto-protein were negative. Patient died and consent for post-mortem examination was refused.

Fine needle aspiration cytology diagnosis of liver diseases in the University of Maiduguri Teaching Hospital, Maiduguri

The study is aimed at classifying liver diseases diagnosed by fine needle aspiration cytology (FNAC) in our environment and to emphasize the importance of the procedure for management of our patients. Forty-two patients were referred by the physicians for fine needle aspiration cytology diagnosis in Histopathology Department, University of Maiduguri Teaching Hospital between January 2001 and December 2003. There were 30 males and 12 females (2.5:1) with mean age of 44.7 years. The peak age is in the 5th decade of life. The commonest hepatic disease is primary hepatic malignancy, which accounted for 78.6% (33 patients); 3 suspicious of malignancy, one case each of metastatic carcinoma, amoebic liver abscess; liver storage disease and large cell dysplasia. The technique has gained popularity in our center because it is cheap, convenient, minimally invasive, quick and has high precision in obtaining samples. We therefore recommend this procedure in centers where liver diseases are common as a means of initial investigation.

Diversion procto-colitis: response to treatment with short-chain fatty acids

BACKGROUND/PURPOSE

Diversion procto-colitis (DPC) results from a deficiency of luminal short-chain fatty acids (SCFAs). Endoscopic and histopathologic features of the disorder are almost universally present in defunctioned bowel, but symptomatic DPC is less common.

METHODS

Five children with symptomatic DPC underwent endoscopy and rectosigmoid biopsies. An endoscopic index (EI) was used to quantify disease severity. An SCFA mixture was administered into the defunctioned bowel.

RESULTS

A good clinical response and improvement in the endoscopic index occurred in all children. Undiversion or rectal excision was carried out in 4 and was curative in each case. One child is awaiting a redo pull through.

CONCLUSIONS

DPC should be considered in children with a defunctioned colon presenting with evidence of colitis. Histopathology provides supportive evidence and SCFAs may provide effective relief of symptoms. Stoma reversal or rectal excision is curative.

Intestinal ulceration, obstruction, and haemorrhage in congenital syphilis

Intestinal obstruction and bleeding are uncommon complications of congenital syphilis (CS). A VDRL-positive infant developed incomplete intestinal obstruction and rectal bleeding. Despite conservative management, his symptoms continued. At laparotomy, terminal ileal inflammation and stenosis were demonstrated. He underwent ileal resection and primary end-to-end anastomosis with resolution of his symptoms. Histopathological examination demonstrated heavy plasmacytic infiltration of the lamina propria and submucosa with ulceration of the mucosa, consistent with syphilitic ileitis. This report documents for the first time bleeding from ileal ulcers associated with intestinal obstruction in CS and highlights an unusual presentation of the disease.