Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak

The 2018 Nigerian Lassa fever season saw the largest ever recorded upsurge of cases, raising concerns over the emergence of a strain with increased transmission rate. To understand the molecular epidemiology of this upsurge, we performed, for the first time at the epicenter of an unfolding outbreak, metagenomic nanopore sequencing directly from patient samples, an approach dictated by the highly variable genome of the target pathogen. Genomic data and phylogenetic reconstructions were communicated immediately to Nigerian authorities and the World Health Organization to inform the public health response. Real-time analysis of 36 genomes and subsequent confirmation using all 120 samples sequenced in the country of origin revealed extensive diversity and phylogenetic intermingling with strains from previous years, suggesting independent zoonotic transmission events and thus allaying concerns of an emergent strain or extensive human-to-human transmission.

Applying the One Health principles: a trans-sectoral coordination framework for preventing and responding to Rift Valley fever outbreaks

Rift Valley fever (RVF) is a good example of a disease for which a One Health approach can significantly improve the management of outbreaks: RVF is a vector- borne zoonotic disease, its dynamics differ between eco-epidemiological patterns and are modulated by eco-climatic factors. Therefore, collaboration between sectors, disciplines and role players, as well as an understanding of the local epidemiology of the disease, are key prerequisites for proper risk assessment and outbreak control. These principles drove the Food and Agriculture Organization of the United Nations (FAO) and the World Health Organization (WHO) to develop an inter-sectoral strategic approach, with specific actions recommended for each of the four periods in the development of the outbreak (forecasting and preparedness, alert, epidemic control, post-epidemic). Through several outbreak response missions between 2006 and 2012 in various countries, an implementation framework was developed by WHO, FAO and the national authorities of affected countries and used to build national response action plans. The framework proposes a structured attribution of duty and responsibilities to committees made up of representatives of the various institutional and operational role players, and with clear mandates and terms of reference (TOR). Such an approach, ensuring real-time sharing of information, coherence in the various aspects of the response, and ownership of the strategy, has proven its efficiency. It could also be used, with appropriate adjustments in the TOR, for other zoonotic diseases.

Strategic approach to control of viral haemorrhagic fever outbreaks in the Eastern Mediterranean Region: report from a regional consultation

The viral haemorrhagic fevers (VHF) are a growing public health threat in the Eastern Mediterranean Region. Nearly all of them are of zoonotic origin. VHF often cause outbreaks with high fatalities and, except for yellow fever, currently there are no specific treatment or vaccination options available. In response to this growing threat, the Regional Office for the Eastern Mediterranean of the World Health Organization convened a technical consultation in Tehran on 27-30 November 2011 to review the current gaps in prevention and control of VHF outbreaks in the Region. The meeting recommended a number of strategic public health approaches for prevention and control of VHF outbreaks through synergizing effective collaboration between the human and animal health sectors on areas that involve better preparedness, early detection and rapid response. Implementation of these approaches would require working together with vision, commitment and a sense of purpose involving partnerships and cooperation from all relevant sectors.

Establishment of public health security in Saudi Arabia for the 2009 Hajj in response to pandemic influenza A H1N1

Mass gatherings of people challenge public health capacities at host locations and the visitors' places of origin. Hajj--the yearly pilgrimage by Muslims to Saudi Arabia--is one of the largest, most culturally and geographically diverse mass gatherings in the world. With the 2009 pandemic influenza A H1N1 and upcoming Hajj, the Saudi Arabian Ministry of Health (MoH) convened a preparedness consultation in June, 2009. Consultants from global public health agencies met in their official capacities with their Saudi Arabian counterparts. The MoH aimed to pool and share public health knowledge about mass gatherings, and review the country's preparedness plans, focusing on the prevention and control of pandemic influenza. This process resulted in several practical recommendations, many to be put into practice before the start of Hajj and the rest during Hajj. These preparedness plans should ensure the optimum provision of health services for pilgrims to Saudi Arabia, and minimum disease transmission on their return home. Review of the implementation of these recommendations and their effect will not only inform future mass gatherings in Saudi Arabia, but will also strengthen preparedness efforts in other settings.

Risk factors for Nipah virus encephalitis in Bangladesh

Patients in Goalando were likely infected by direct contact with fruit bats or their secretions, rather than through contact with an intermediate host.

Nipah virus (NiV) is a paramyxovirus that causes severe encephalitis in humans. During January 2004, twelve patients with NiV encephalitis (NiVE) were identified in west-central Bangladesh. A case–control study was conducted to identify factors associated with NiV infection. NiVE patients from the outbreak were enrolled in a matched case-control study. Exact odds ratios (ORs) and 95% confidence intervals (CIs) were calculated by using a matched analysis. Climbing trees (83% of cases vs. 51% of controls, OR 8.2, 95% CI 1.25–∞) and contact with another NiVE patient (67% of cases vs. 9% of controls, OR 21.4, 95% CI 2.78–966.1) were associated with infection. We did not identify an increased risk for NiV infection among persons who had contact with a potential intermediate host. Although we cannot rule out person-to-person transmission, case-patients were likely infected from contact with fruit bats or their secretions.

Clinical presentation of nipah virus infection in Bangladesh

BACKGROUND

In Bangladesh, 4 outbreaks of Nipah virus infection were identified during the period 2001-2004.

METHODS

We characterized the clinical features of Nipah virus-infected individuals affected by these outbreaks. We classified patients as having confirmed cases of Nipah virus infection if they had antibodies reactive with Nipah virus antigen. Patients were considered to have probable cases of Nipah virus infection if they had symptoms consistent with Nipah virus infection during the same time and in the same community as patients with confirmed cases.

RESULTS

We identified 92 patients with Nipah virus infection, 67 (73%) of whom died. Although all age groups were affected, 2 outbreaks principally affected young persons (median age, 12 years); 62% of the affected persons were male. Fever, altered mental status, headache, cough, respiratory difficulty, vomiting, and convulsions were the most common signs and symptoms; clinical and radiographic features of acute respiratory distress syndrome of Nipah illness were identified during the fourth outbreak. Among those who died, death occurred a median of 6 days (range, 2-36 days) after the onset of illness. Patients who died were more likely than survivors to have a temperature >37.8 degrees C, altered mental status, difficulty breathing, and abnormal plantar reflexes. Among patients with Nipah virus infection who had well-defined exposure to another patient infected with Nipah virus, the median incubation period was 9 days (range, 6-11 days).

CONCLUSIONS

Nipah virus infection produced rapidly progressive severe illness affecting the central nervous and respiratory systems. Clinical characteristics of Nipah virus infection in Bangladesh, including a severe respiratory component, appear distinct from clinical characteristics reported during earlier outbreaks in other countries.

[Emergent pathogens, international surveillance and international health regulations (2005)]

In order to address the vitality of the microbial world, to detect emerging infectious diseases, to determine their potential threat to public health, and to establish effective interventions, the World Health Organization (WHO) has developed and coordinates the Global Outbreak Alert and Response Network (GOARN) which connects several surveillance networks. Some of these networks are specific to epidemic-prone diseases, such as influenza, dengue, yellow fever or meningitis. Others were especially designed to track unusual events--such as the emergence of SARS--that are naturally-occurring, accidental, or deliberately created (biological weapons, bio-terrorism). Lastly, a special effort is being made at the international level to modernize the International Health Regulations, now obsolete, and to support all the countries in the reinforcement of their outbreak alert and response capacity.

[Clinical management of patients and deceased during the Ebola outbreak from October to December 2003 in Republic of Congo]

Outbreaks of Ebola virus hemorrhagic fever (EVHF) have been reported since 2001 in the Cuvette Ouest department, a forested area located in the Western North of Congo. At the end of October 2003 a new alarm came from this department which was quickly confirmed as being an epidemic of EVHF. The outbreak response was organized by the ministry of health with the assistance of an international team under the aegis of WHO. The case management of suspect cases was done in an isolation ward set up at the hospital; when patients refused to go to the ward for care they were isolated in their house according to a protocol "transmission risks reduction at home". Safe burials were performed by specialized teams which respected the major aspects of the funeral to allow the process of mourning of the families. An active surveillance system was set up in order to organize the detection of new cases and the follow-up of their contacts. A case definition was adopted. From October 11 to December 2, 2003, 35 cases including 29 deaths were reported, 16 cases were laboratory confirmed. The first four cases had been exposed to monkey meat (Cercopithecus nictitans). The epidemic spread was due to family transmission. The population interpretation of the disease, in particular questions around wizards and evil-minded persons, is a factor which must be taken into account by the medical teams during communication meetings for behavioral change of the populations. The case management of patient in isolation wards to prevent the transmission of the virus in the community remains the most effective means to dam up Ebola virus hemorrhagic fever outbreaks. The good perception by the community of the safe funerary procedures is an important aspect in the establishment of confidence relations with the local population.

[Multiple Ebola virus haemorrhagic fever outbreaks in Gabon, from October 2001 to April 2002]

Outbreaks of Ebola virus haemorrhagic fever have been reported from 1994 to 1996 in the province of Ogooué Ivindo, a forest zone situated in the Northeast of Gabon. Each time, the great primates had been identified as the initial source of human infection. End of November 2001 a new alert came from this province, rapidly confirmed as a EVHV outbreak. The response was given by the Ministry of Health with the help of an international team under the aegis of WHO. An active monitoring system was implemented in the three districts hit by the epidemic (Zadié, Ivindo and Mpassa) to organize the detection of cases and their follow-up. A case definition has been set up, the suspected cases were isolated at hospital, at home or in lazarets and serological tests were performed. These tests consisted of the detection of antigen or specific IgG and the RT-PCR. A classification of cases was made according to the results of biological tests, clinical and epidemiological data. The contact subjects were kept watch over for 21 days. 65 cases were recorded among which 53 deaths. The first human case, a hunter died on the 28th of October 2001. The epidemic spreads over through family transmission and nosocomial contamination. Four distinct primary foci have been identified together with an isolated case situated in the South East of Gabon, 580 km away from the epicenter. Deaths happened within a delay of 6 days. The last death has been recorded on the 22nd of March 2002 and the end of the outbreak was declared on the 6th of May 2002. The epidemic spreads over the Gabon just next. Unexplained deaths of animals had been mentionned in the nearby forests as soon as August 2001: great primates and cephalophus. Samples taken from their carcasses confirmed a concomitant animal epidemic.

Medical anthropology and Ebola in Congo: cultural models and humanistic care

Seldom have medical anthropologists been involved in efforts to control high mortality diseases such as Ebola hemorrhagic fever (EHF) This paper describes the results of two distinct but complementary interventions during the first phases of an outbreak in the Republic of Congo in 2003. The first approach emphasized understanding local peoples cultural models and political-economic explanations for the disease while the second approach focused on providing more humanitarian care of patients by identifying and incorporating local beliefs and practices into patient care and response efforts.

[Isolated case of haemorrhagic fever observed in Gabon during the 2002 outbreak of Ebola but distant from epidemic zones]

During the last outbreak of Ebola virus haemorrhagic fever that occurred concurrently in Gabon and Congo, several primary foci were identified in the Ogooue Ivindo province (Northeast Gabon), where previous outbreaks had occurred. A 48-year-old woman living in Franceville located 580 Km from the epicentre presented fever with haemorrhagic signs. She was evacuated to Libreville where Ebola infection was suspected. Diagnosis was confirmed at the Centre International de Recherches Médicales of Franceville on the basis of detection of specific antibodies. Symptoms had already subsided by the time diagnosis was documented. An epidemiological investigation was undertaken to identify the source of contamination and detect secondary cases. No human or nonhuman primate source of contamination could be formally identified. Direct contact with the virus reservoir could not be ruled out. No secondary cases were detected. The favourable outcome, absence of secondary, and failure to identify a source of contamination suggest that epidemiologically undefined cases may go unnoticed during and outside of outbreaks.

[Practical guidelines for the management of Ebola infected patients in the field]

Ebola hemorrhagic fever appears after an incubation of 3 days to 3 weeks. The first symptoms are fever accompanied by general and hemorrhagic signs leading to death in 50 to 90% of cases. During epidemics definition of cases permits prompt diagnosis. Due to the high risk of person-to-person and nosocomial transmission associated with Ebola hemorrhagic fever, management is based on isolation of patients and institution of protected care. Hands and soiled material are often decontaminated using sodium hypochlorite. Patient waste is decontaminated and incinerated. Treatment is essentially supportive. There is currently no vaccine available. Persons having been in close contact with patient should be kept under medical surveillance for 21 days. Recovering patients should use condoms for three months. Bodies of deceased patients should be handled by trained teams and buried quickly.

[Outbreak of Ebola hemorrhagic fever in the Republic of the Congo, 2003: a new strategy?]

This article describes the last Ebola haemorrhagic fever (EHF) outbreak that occurred in the Cuvette Ouest Region of the Republic of Congo from January to April 2003. Epidemiological study demonstrated that the first patient, in whom diagnosis was made retrospectively, became ill on December 25, 2002. Subsequently until May 7, 2003, a total of 143 cases were recorded in the Mbomo and Kéllé health districts including 129 fatalities. Thirteen cases were laboratory confirmed and 130 were epidemiologically linked. Fifty-three percent of patients were male. Age ranged form 5 days to 80 years. Transmission involved direct contact with an infected person especially within families. Epidemiological data traced introduction of Ebola virus into the population to three primary cases mainly involving hunters. In all three cases development of the disease followed contact with non-human primates (gorillas) and other mammals (antelope) that had either been killed or found dead. Three health care workers were infected during the epidemic but nosocomial transmission played a minor role in the epidemic. On June 5, the Minister of Health and Population of the Congo Republic officially declared that the outbreak of EHF was over in the Cuvette Ouest Region. The last case was recorded on April 22 in the small village of Ndjoukou.

Histopathological and immunohistochemical studies of lesions associated with Ebola virus in a naturally infected chimpanzee

Lesions caused by the Côte d'Ivoire subtype of Ebola virus in a naturally infected young chimpanzee were characterized by histopathological and immunohistochemical methods. The predominant lesions consisted of multifocal necrosis in the liver and diffuse fibrinoid necrosis in the red pulp of the spleen. In these sites, macrophages contained large eosinophilic intracytoplasmic inclusion bodies. Immunohistochemical staining indicated that macrophages were a major site of viral replication. The absence of bronchiolar and pulmonary lesions and the paucity of antigen-containing macrophages in the lung suggested that aerosol transmission by this animal was unlikely. There were necrotic foci and antigen-containing macrophages in intestinal lymph nodes, in association with lesions caused by intestinal parasites, suggesting the possibility of virus entry through the digestive tract.

Ebola virus outbreak among wild chimpanzees living in a rain forest of Côte d'Ivoire

An outbreak of Ebola in nature is described for the first time. During a few weeks in November 1994, approximately 25% of 43 members of a wild chimpanzee community disappeared or were found dead in the Taï National Park, Côte d'Ivoire. A retrospective cohort study was done on the chimpanzee community. Laboratory procedures included histology, immunohistochemistry, bacteriology, and serology. Ebola-specific immunohistochemical staining was positive for autopsy tissue sections from 1 chimpanzee. Demographic, epidemiologic, and ecologic investigations were compatible with a point-source epidemic. Contact activities associated with a case (e.g., touching dead bodies or grooming) did not constitute significant risk factors, whereas consumption of meat did. The relative risk of meat consumption was 5.2 (95% confidence interval, 1.3-21.1). A similar outbreak occurred in November 1992 among the same community. A high mortality rate among apes tends to indicate that they are not the reservoir for the disease causing the illness. These points will have to be investigated by additional studies.

Human infection due to Ebola virus, subtype Côte d'Ivoire: clinical and biologic presentation

In November 1994 after 15 years of epidemiologic silence, Ebola virus reemerged in Africa and, for the first time, in West Africa. In Côte d'Ivoire, a 34-year-old female ethologist was infected while conducting a necropsy on a wild chimpanzee. Eight days later, the patient developed a syndrome that did not respond to antimalarial drugs and was characterized by high fever, headache, chills, myalgia, and cough. The patient had abdominal pain, diarrhea, vomiting, and a macular rash, and was repatriated to Switzerland. The patient suffered from prostration and weight loss but recovered without sequelae. Laboratory findings included aspartate aminotransferase and alanine aminotransferase activity highly elevated, thrombocytopenia, lymphopenia, and, subsequently, neutrophilia. A new subtype of Ebola was isolated from the patient's blood on days 4 and 8. No serologic conversion was detected among contact persons in Côte d'Ivoire (n = 22) or Switzerland (n = 52), suggesting that infection-control precautions were satisfactory.

Identification of trypanosomes isolated by KIVI from wild mammals in Côte d'Ivoire: diagnostic, taxonomic and epidemiological considerations

In Côte d'Ivoire, a comparative study was carried out on 122 wild mammals by parasitological and serological examination and by in vitro isolation of trypanosomes from fresh blood (KIVI). Thirteen isolated stocks were studied by isoenzymes and compared with Trypanosoma congolense and T. brucei bouaflé group reference stocks. Of the 122 animals, only 22 were positive on blood smears while 88 were KIVI positive and 92 were CATT/T. b. gambiense positive. For six stocks identified by isoenzymes as T. congolense, the agreement between ELISA and CATT was good (75%). As compared with CATT, antigen detection ELISA was not satisfactory for T. brucei (20%). Out of 18, 16 stocks represented a separate zymodeme (seven T. congolense and nine T. brucei) and a high genetic heterogeneity was observed. For T. congolense, savanna, kilifi and forest groups were represented by one zymodeme each. The four remaining zymodemes while put into this T. congolense group, were strongly independent of each other. Morphology indicated that those new zymodemes correspond to T. congolense. In the other hand, five new zymodemes fit into T. brucei classification.

Isolation and partial characterisation of a new strain of Ebola virus

We have isolated a new strain of Ebola virus from a non-fatal human case infected during the autopsy of a wild chimpanzee in the Côte-d'Ivoire. The wild troop to which this animal belonged has been decimated by outbreaks of haemorrhagic syndromes. This is the first time that a human infection has been connected to naturally-infected monkeys in Africa. Data from the long-term survey of this troop of chimpanzees could answer questions about the natural reservoir of the Ebola virus.

[Epidemiologic study of bluetongue in sheep, cattle and different species of wild animals in the Ivory Coast]

Between 1992 and 1993, a serological survey was conducted in Côte d'Ivoire on 623 sera from sheep, 215 sera from cattle and 211 sera from wild herbivores. These sera were tested for bluetongue virus (BTV) antibodies using an agar gel immunodiffusion test. The purpose of this survey was twofold: to establish the incidence of bluetongue in the country, and to analyse the putative role of BTV in the reproductive pathology of sheep. Seroprevalence was 52 +/- 4% in sheep, 95 +/- 3% in cattle, and 56 +/- 7% in wild herbivores. The authors found antibodies against BTV in kob (Kobus kob Erxleben, 1777), common waterbuck (Kobus ellipsiprymnus Ogilby, 1833), roan antelope (Hippotragus equinus Desmarest, 1804), buffalo (Syncerus caffer Sparrman, 1779), hartebeest (Alcelaphus buselaphus Pallas, 1766) and elephant (Loxodonta africana Blumenbach, 1797). A significant difference was found in seroprevalence in sheep between the three areas covered by the survey. Antibody prevalence increased significantly with age in sheep and wild herbivores, and seroprevalence was higher in dams with a history of abortion. It can therefore be concluded that bluetongue is enzootic in Côte d'Ivoire.

[Nervous syndrome in sheep on the Ivory Coast. I. Epidemiological and clinical study, methods of diagnosis and treatment]

The ovine nervous syndrome in Côte-d'Ivoire is similar to the cerebrocortical necrosis (CCN) due to vitamin B1 deficiency. All classical symptoms of CCN were observed (locomotor ataxia with subsequent paralysis) and histological evidence for polioencephalomalacia was given. However, the circumstances for occurrence of the disease are very different in the two cases, i.e. CCN is a disease encountered in young fattening ruminants in developed countries while the ovine nervous syndrome is mainly observed in Côte-d'Ivoire during the dry season when pastures become sparse and dry and when the feed supply is insufficient. Thus, the main cause, which is rather univocal, is a sudden decrease in the nutritive value of the diet, but the accurate etiopathogenesis of the disease has not yet been determined. In a flock where 10-30% of the animals are ill, the mortality may reach 80-90%. No classical biochemical assays were specific enough to establish a precise diagnosis of the nervous syndrome. However, it should be pointed out that the CK (creatinine kinase) values very regularly rose and that the ASAT (aspartate aminotransferase) values were high in 75% of the cases. In the present African field conditions, the precise diagnosis is based on the efficiency of the vitamin B1 treatment and, for the dead animals, on the histological analysis of the brain.