Isolation and phylogenetic grouping of equine encephalosis virus in Israel

During 2008-2009 in Israel, equine encephalosis virus (EEV) caused febrile outbreaks in horses. Phylogenetic analysis of segment 10 of the virus strains showed that they form a new cluster; analysis of segment 2 showed ≈92% sequence identity to EEV-3, the reference isolate. Thus, the source of this emerging EEV remains uncertain.     

A first molecular epidemiological study of SAT-2 type foot-and-mouth disease viruses in West Africa

Thirty-one viruses causing SAT-2 outbreaks in seven West African countries between 1974 and 1991, and four viruses representative of East and Central Africa were genetically characterized in this study. Four major viral lineages (I-IV) were identified by phylogenetic analysis of an homologous 480 nucleotide region corresponding to the C-terminus end of VP1. Lineage I comprised two West African genotypes with viruses clustering according to year of isolation rather than geographical origin. Lineage II was represented by viruses isolated between 1979 and 1983 in two neighbouring West African countries, Senegal and The Gambia. Viruses from Nigeria and Eritrea, representative of West and East Africa respectively, constituted lineage III, whilst lineage IV, comprising viruses from Central and East Africa, was regionally and genetically distinct. This study revealed that unrestricted animal movement in West Africa is a major factor in disease dissemination and has also provided the first indication of trans-regional virus transmission.     

The evolution of dengue-2 viruses in Malindi,Kenya and greater East Africa: Epidemiological and immunological implications

Kenya experiences a substantial burden of dengue, yet there are very few DENV-2 sequence data available from this country and indeed the entire continent of Africa. We therefore undertook whole genome sequencing and evolutionary analysis of fourteen dengue virus (DENV)-2 strains sampled from Malindi sub-County Hospital during the 2017 DENV-2 outbreak in the Kenyan coast. We further performed an extended East African phylogenetic analysis, which leveraged 26 complete African env genes. Maximum likelihood analysis showed that the 2017 outbreak was due to the Cosmopolitan genotype, indicating that this has been the only confirmed human DENV-2 genotype circulating in Africa to date. Phylogeographic analyses indicated transmission of DENV-2 viruses between East Africa and South/South-West Asia. Time-scaled genealogies show that DENV-2 viruses shows spatial structure at the country level in Kenya, with a time-to-most-common-recent ancestor analysis indicating that these DENV-2 strains were circulating for up to 5.38 years in Kenya before detection in the 2017 Malindi outbreak. Selection pressure analyses indicated sampled Kenyan DENV strains uniquely being under positive selection at 6 sites, predominantly across the non-structural genes, and epitope prediction analyses showed that one of these sites corresponds to a putative predicted MHC-I CD8+ DENV-2 Cosmopolitan virus epitope only evident in a sampled Kenyan virus. Taken together, our findings indicate that the 2017 Malindi DENV-2 outbreak arose from a strain which had circulated for several years in Kenya before recent detection, has experienced diversifying selection pressure, and may contain new putative immunogens relevant to vaccine design. These findings prompt further genomic epidemiology studies in this and other Kenyan locations to further elucidate the transmission dynamics of DENV in this region.     

Observations on rinderpest in Kenya, 1986-1989.

Rinderpest was confirmed in Kenya in 1986, 1987, 1988 and 1989. Three epidemiologically distinct events appear to have occurred: repeated outbreaks in West Pokot district related to cross-border movement of stock, an outbreak in Marsabit district in 1987 (thought to have been caused by illegal movement of cattle, possibly in vehicles, from countries further north) and a series of related outbreaks in and near Nairobi between 1988 and 1989 due to the unauthorized movement from abattoirs and holding grounds of slaughter stock possibly introduced from West Pokot or Marsabit. In West Pokot the disease affected unvaccinated calves and yearlings. In Marsabit cattle of all ages were affected. In August 1988, a major outbreak was confirmed in Kiambu and Kajiado districts in central Kenya, near Nairobi. At the same time a provisional diagnosis of rinderpest was made in a herd of cattle at a slaughterhouse in Nairobi. Rinderpest virus was isolated from sick cattle in all the outbreaks. Experimental infection of susceptible cattle with the Kiambu isolate demonstrated this to be of low virulence. Emergency vaccination and quarantine measures instituted immediately after confirmation eliminated clinical disease within three to four weeks in West Pokot, Kiambu and Nairobi. In Kajiado, however, the disease persisted for at least nine months, during which time a series of virus isolates was recovered. There was no evidence of infection in susceptible wildlife. This increase in the incidence of rinderpest in Kenya in recent years serves to highlight the problems of control and the need for concerted efforts to eradicate the threat of the disease from East Africa.     

Transmission patterns of African horse sickness and equine encephalosis viruses in South African donkeys

African horse sickness (AHS) and equine encephalosis (EE) viruses are endemic to southern Africa. AHS virus causes severe epidemics when introduced to naive equine populations, resulting in severe restrictions on the movement of equines between AHS-positive and negative countries. Recent zoning of South Africa has created an AHS-free zone to facilitate equine movement, but the transmission dynamics of these viruses are not fully understood. Here, we present further analyses of serosurveys of donkeys in South Africa conducted in 1983-5 and in 1993-5. Age-prevalence data are used to derive estimates of the force of infection, A. For both viruses, A was highest in the northeastern part of the country and declined towards the southwest. In most of the country, EE virus had a higher transmission rate than AHS. The force of infection increased for EE virus between 1985 and 1993, but decreased for AHS virus. Both viruses showed high levels of variation in transmission between districts within the same province, particularly in areas of intermediate transmission. These data emphasize the focal nature of these viruses, and indicate areas where further data will assist in understanding the geographical variation in transmission.     

New vectors of Rift Valley fever in West Africa.

After an outbreak of Rift Valley fever in Southern Mauritania in 1987, entomologic studies were conducted in a bordering region in Sénégal from 1991 to 1996 to identify the sylvatic vectors of Rift Valley fever virus. The virus was isolated from the floodwater mosquitoes Aedes vexans and Ae. ochraceus. In 1974 and 1983, the virus had been isolated from Ae. dalzieli. Although these vectors differ from the main vectors in East and South Africa, they use the same type of breeding sites and also feed on cattle and sheep. Although enzootic vectors have now been identified in West Africa, the factors causing outbreaks remain unclear.     

African horse sickness in The Gambia: circulation of a live-attenuated vaccine-derived strain

African horse sickness virus serotype 9 (AHSV-9) has been known for some time to be circulating amongst equids in West Africa without causing any clinical disease in indigenous horse populations. Whether this is due to local breeds of horses being resistant to disease or whether the AHSV-9 strains circulating are avirulent is currently unknown. This study shows that the majority (96%) of horses and donkeys sampled across The Gambia were seropositive for AHS, despite most being unvaccinated and having no previous history of showing clinical signs of AHS. Most young horses (<3 years) were seropositive with neutralizing antibodies specific to AHSV-9. Eight young equids (<3 years) were positive for AHSV-9 by serotype-specific RT-PCR and live AHSV-9 was isolated from two of these horses. Sequence analysis revealed the presence of an AHSV-9 strain showing 100% identity to Seg-2 of the AHSV-9 reference strain, indicating that the virus circulating in The Gambia was highly likely to have been derived from a live-attenuated AHSV-9 vaccine strain.     

Rift Valley fever outbreak with East-Central African virus lineage in Mauritania, 2003

In October 2003, 9 human cases of hemorrhagic fever were reported in 3 provinces of Mauritania, West Africa. Test results showed acute Rift Valley fever virus (RVFV) infection, and a field investigation found recent circulation of RVFV with a prevalence rate of 25.5% (25/98) and 4 deaths among the 25 laboratory-confirmed case-patients. Immunoglobulin M against RVFV was found in 46% (25/54) of domestic animals. RVFV was also isolated from the mosquito species Culex poicilipes. Genetic comparison of virion segments indicated little variation among the strains isolated. However, phylogenetic studies clearly demonstrated that these strains belonged to the East-Central African lineage for all segments. To our knowledge, this is the first time viruses of this lineage have been observed in an outbreak in West Africa. Whether these strains were introduced or are endemic in West Africa remains to be determined.     

Selection of vaccine strains for serotype O foot-and-mouth disease viruses (2007–2012) circulating in Southeast Asia,East Asia and Far East

Foot-and-mouth disease (FMD) is endemic in Southeast Asia (SEA) and East Asia with circulation of multiple serotypes and multiple genotypes within each serotype of the virus. Although countries like Japan and South Korea in the Far East were free of FMD, in 2010 FMD serotype O (O/Mya-98) outbreaks were recorded and since then South Korea has experienced several FMD outbreaks despite regular vaccination. In this study a total of 85 serotype O FMD viruses (FMDV) isolated from 2007 to 2012 from SEA, East Asia and Far East were characterized by virus neutralisation tests using antisera to four existing (O/HKN/6/83, O/IND/R2/75, O/SKR/2010 and O/PanAsia-2) and one putative (O/MYA/2009) vaccine strains, and by full capsid sequencing. Serological studies revealed broad cross-reactivity with the vaccine strains; O/PanAsia-2 exhibited a good match with 95.3%, O/HKN/6/83 with 91.8%, O/IND/R2/75 with 80%, and the putative strain O/MYA/2009 with 89.4% isolates employed in this study. Similarly O/PanAsia-2 and O/IND/R2/75 vaccines showed a good match with all eight viruses belonging to O-Ind-2001d sublineage whereas the vaccines of O/Mya-98 lineage, O/MYA/2009 and O/SKR/2010 exhibited the lowest match indicating their unsuitability to protect infections from O-Ind-2001d viruses. A Bayesian analysis of the capsid sequence data indicated these circulating viruses (n = 85) to be of either SEA or Middle East-South Asian (ME-SA) topotype. The ME-SA topotype viruses were mainly detected in Lao PDR, Vietnam, Myanmar and Thailand reflecting the trade links with the Indian subcontinent, and also within the SEA countries. Implications of these results in the context of FMD control in SEA and East Asian countries are discussed.     

Molecular epidemiology of African and Asian Crimean-Congo haemorrhagic fever isolates

Phylogenetic relationships were examined for 70 Crimean-Congo haemorrhagic fever (CCHF) isolates from southern, central and West Africa, the Middle East and Greece using sequence data determined for a region of the S segment of the genome. Analysis revealed up to 18% genetic differences. Tree topology supports previous evidence for the existence of three groups of genetically related isolates, A, B and C. Within group A there are two clades: an African clade and a predominantly Asian clade comprising isolates from Pakistan, China, Iran, Russia and Madagascar. Group B includes isolates from southern and West Africa and Iran, and group C includes a single isolate from Greece. Despite the potential which exists for dispersal of the virus between Africa and Eurasia, it appears that circulation of the virus is largely compartmentalized within the two land masses, and the inference is that the geographic distribution of phylogenetic groups is related to the distribution and dispersal of tick vectors of the virus.     

Phylogenetic relationships of southern African West Nile virus isolates

Phylogenetic relationships were examined for 29 southern African West Nile virus (formal name West Nile virus [WNV]) isolates from various sources in four countries from 1958 to 2001. In addition, sequence data were retrieved from GenBank for another 23 WNV isolates and Kunjin and Japanese encephalitis viruses. All isolates belonged to two lineages. Lineage 1 isolates were from central and North Africa, Europe, Israel, and North America; lineage 2 isolates were from central and southern Africa and Madagascar. No strict correlation existed between grouping and source of virus isolate, pathogenicity, geographic distribution, or year of isolation. Some southern African isolates have been associated with encephalitis in a human, a horse, and a dog and with fatal hepatitis in a human and death of an ostrich chick.     

Isolation and characterization of West Nile virus from the blood of viremic patients during the 2000 outbreak in Israel

We report the isolation of West Nile (WN) virus from four patient serum samples submitted for diagnosis during an outbreak of WN fever in Israel in 2000. Sequencing and phylogenetic analysis revealed two lineages, one closely related to a 1999 New York isolate and the other to a 1999 Russian isolate.     

West Nile virus in Morocco, 2003

West Nile virus (WNV) reemerged in Morocco in September 2003, causing an equine outbreak. A WNV strain isolated from a brain biopsy was completely sequenced. On the basis of phylogenetic analyses, Moroccan WNV strains isolated during the 1996 and 2003 outbreaks were closely related to other strains responsible for equine outbreaks in the western Mediterranean basin.     

Vaccine development for emerging virulent infectious diseases

The recent outbreak of Zaire Ebola virus in West Africa altered the classical paradigm of vaccine development and that for emerging infectious diseases (EIDs) in general. In this paper, the precepts of vaccine discovery and advancement through pre-clinical and clinical assessment are discussed in the context of the recent Ebola virus, Middle East Respiratory Syndrome coronavirus (MERS-CoV), and Zika virus outbreaks. Clinical trial design for diseases with high mortality rates and/or high morbidity in the face of a global perception of immediate need and the factors that drive design in the face of a changing epidemiology are presented. Vaccines for EIDs thus present a unique paradigm to standard development precepts.     

Sociocultural aspects of risk to pregnant women during the 2013–2015 multinational Ebola virus outbreak in West Africa

Researchers reflect on sociocultural aspects of the Ebola outbreak in West Africa and critically analyze the epidemic's effects on pregnant mothers and their babies. We address structural inequalities contributing to poor maternal health in lower-income countries, while reflecting on how the Ebola outbreak highlights the still-marginalized role of pregnant women. Drawing on prior research in West and East Africa, we discuss health care providers’ responses to risk of infection during maternity work under normal circumstances and in times of crisis. We end with recommendations for preventing such detrimental effects on the health of pregnant women in the case of another epidemic.     

Lineage 1 and 2 strains of encephalitic West Nile virus, central Europe

Two different West Nile virus (WNV) strains caused lethal encephalitis in a flock of geese and a goshawk in southeastern Hungary in 2003 and 2004, respectively. During the outbreak in geese, 14 confirmed human cases of WNV encephalitis and meningitis were reported in the same area. Sequencing of complete genomes of both WNV strains and phylogenetic analyses showed that the goose-derived strain exhibits closest genetic relationship to strains isolated in 1998 in Israel and to the strain that emerged in 1999 in the United States. WNV derived from the goshawk showed the highest identity to WNV strains of lineage 2 isolated in central Africa. The same strain reemerged in 2005 in the same location, which suggests that the virus may have overwintered in Europe. The emergence of an exotic WNV strain in Hungary emphasizes the role of migrating birds in introducing new viruses to Europe.     

Investigations on outbreaks of African horse sickness in the surveillance zone in South Africa

Confirmed outbreaks of African horse sickness (AHS) occurred in the surveillance zone of the Western Cape in 1999 and 2004, both of which led to a two-year suspension on the export of horses. Light trap surveys in the outbreak areas showed that known vector competent Culicoides species, notably C. imicola, were abundant and present in numbers equal to those in the traditional AHS endemic areas. Isolations of AHS virus serotypes 1 and 7, equine encephalosis virus, and bluetongue virus from field-collected C. imicola in the surveillance zone demonstrated that this species was highly competent and could transmit viruses belonging to different serogroups of the Orbivirus genus. Molecular identification of recovered virus isolates indicated that at least two incursions of AHS into the surveillance zone had taken place in 2004. The designation of an AHS-free zone in the Western Cape remains controversial since it can be easily compromised, as evidenced by the two recent outbreaks. In light of the results reported in the present study, the policy of maintaining a large population of unvaccinated horses in the surveillance zone should be reconsidered, as it leaves them vulnerable to infection with AHS virus, which is the most pathogenic of all equine viruses.     

Influenza in East Africa, 1969-70

Very little information is available concerning the frequency of influenza in East Africa. Following recent outbreaks of influenza in Uganda, that were due to the A2/Hong Kong/68 virus, it was considered useful to obtain information relating to the prevalence of infection due to this virus and to the current strain of influenza B virus, not only in Uganda but also in the neighbouring territories of Kenya and Tanzania. The results of serological testing of sera showed that widespread outbreaks of influenza A2/Hong Kong/68 infection had occurred recently in all three territories, while there was evidence of sporadic infection in all territories by the current influenza B strain. Despite the favourable climate of East Africa, it is evident that widespread outbreaks of influenza can occur, and these may arise during the period of the year when influenza is rare in countries with temperate climates. Influenza can easily spread to other countries via air travellers to and from East Africa.     

Foot-and-mouth disease virus serotype A in Egypt

We describe the characterization of a foot-and-mouth disease (FMD) serotype A virus responsible for recent outbreaks of disease in Egypt. Phylogenetic analysis of VP1 nucleotide sequences demonstrated a close relationship to recent FMD virus isolates from East Africa, rather than to viruses currently circulating in the Middle East.