Assessing global preparedness for the next pandemic: development and application of an Epidemic Preparedness Index

Abstract and Introduction: Robust metrics for national-level preparedness are critical for assessing global resilience to epidemic and pandemic outbreaks. However, existing preparedness assessments focus primarily on public health systems or specific legislative frameworks, and do not measure other essential capacities that enable and support public health preparedness and response. Methods: We developed an Epidemic Preparedness Index (EPI) to assess national-level preparedness. The EPI is global, covering 188 countries. It consists of five subindices measuring each country’s economic resources, public health communications, infrastructure, public health systems and institutional capacity. To evaluate the construct validity of the EPI, we tested its correlation with proxy measures for preparedness and response capacity, including the timeliness of outbreak detection and reporting, as well as vaccination rates during the 2009 H1N1 influenza pandemic. Results: The most prepared countries were concentrated in Europe and North America, while the least prepared countries clustered in Central and West Africa and Southeast Asia. Better prepared countries were found to report infectious disease outbreaks more quickly and to have vaccinated a larger proportion of their population during the 2009 pandemic. Conclusion: The EPI measures a country’s capacity to detect and respond to infectious disease events. Existing tools, such as the Joint External Evaluation (JEE), have been designed to measure preparedness within a country over time. The EPI complements the JEE by providing a holistic view of preparedness and is constructed to support comparative risk assessment between countries. The index can be updated rapidly to generate global estimates of pandemic preparedness that can inform strategy and resource allocation.

Emergence and Spread of Extended Spectrum β-Lactamase Producing Enterobacteriaceae (ESBL-PE) in Pigs and Exposed Workers: A Multicentre Comparative Study Between Cameroon and South Africa

Extended spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) represent a significant public health concern globally and are recognized by the World Health Organization as pathogens of critical priority. However, the prevalence of ESBL-PE in food animals and humans across the farm-to-plate continuum is yet to be elucidated in Sub-Saharan countries including Cameroon and South Africa. This work sought to determine the risk factors, carriage, antimicrobial resistance profiles and genetic relatedness of extended spectrum β-lactamase producing Enterobacteriaceae (ESBL-PE) amid pigs and abattoir workers in Cameroon and South Africa. ESBL-PE from pooled samples of 432 pigs and nasal and hand swabs of 82 humans were confirmed with VITEK 2 system. Genomic fingerprinting was performed by ERIC-PCR. Logistic regression (univariate and multivariate) analyses were carried out to identify risk factors for human ESBL-PE carriage using a questionnaire survey amongst abattoir workers. ESBL-PE prevalence in animal samples from Cameroon were higher than for South Africa and ESBL-PE carriage was observed in Cameroonian workers only. Nasal ESBL-PE colonization was statistically significantly associated with hand ESBL-PE (21.95% vs. 91.67%; p = 0.000; OR = 39.11; 95% CI 2.02⁻755.72; p = 0.015). Low level of education, lesser monthly income, previous hospitalization, recent antibiotic use, inadequate handwashing, lack of training and contact with poultry were the risk factors identified. The study highlights the threat posed by ESBL-PE in the food chain and recommends the implementation of effective strategies for antibiotic resistance containment in both countries.

Translating Predictions of Zoonotic Viruses for Policymakers

Recent outbreaks of Ebola virus disease and Zika virus disease highlight the need for disseminating accurate predictions of emerging zoonotic viruses to national governments for disease surveillance and response. Although there are published maps for many emerging zoonotic viruses, it is unknown if there is agreement among different models or if they are concordant with national expert opinion. Therefore, we reviewed existing predictions for five high priority emerging zoonotic viruses with national experts in Cameroon to investigate these issues and determine how to make predictions more useful for national policymakers. Predictive maps relied primarily on environmental parameters and species distribution models. Rift Valley fever virus and Crimean-Congo hemorrhagic fever virus predictions differed from national expert opinion, potentially because of local livestock movements. Our findings reveal that involving national experts could elicit additional data to improve predictions of emerging pathogens as well as help repackage predictions for policymakers.

High Herpesvirus Diversity in Wild Rodent and Shrew Species in Central Africa

Herpesviruses belong to a diverse order of large DNA viruses that can cause diseases in humans and animals. With the goal of gathering information about the distribution and diversity of herpesviruses in wild rodent and shrew species in central Africa, animals in Cameroon and the Democratic Republic of the Congo were sampled and tested by PCR for the presence of herpesvirus DNA. A broad range PCRs targeting either the Polymerase or the terminase gene were used for virus detection. Amplified products from PCR were sequenced and isolates analysed for phylogenetic placement. Overall, samples of 1,004 animals of various rodent and shrew species were tested and 24 were found to be positive for herpesvirus DNA. Six of these samples contained strains of known viruses, while the other positive samples revealed DNA sequences putatively belonging to 11 previously undescribed herpesviruses. The new isolates are beta- and gammaherpesviruses and the shrew isolates appear to form a separate cluster within the Betaherpesvirinae subfamily. The diversity of viruses detected is higher than in similar studies in Europe and Asia. The high diversity of rodent and shrew species occurring in central Africa may be the reason for a higher diversity in herpesviruses in this area.

The Discovery of Bombali Virus Adds Further Support for Bats as Hosts of Ebolaviruses

Here we describe the complete genome of a new ebolavirus, Bombali virus (BOMV) detected in free-tailed bats in Sierra Leone (little free-tailed (Chaerephon pumilus) and Angolan free-tailed (Mops condylurus)). The bats were found roosting inside houses, indicating the potential for human transmission. We show that the viral glycoprotein can mediate entry into human cells. However, further studies are required to investigate whether exposure has actually occurred or if BOMV is pathogenic in humans.

Mannitol-fermenting Methicillin-Resistant Staphylococci (MRS) in Pig Abattoirs in Cameroon and South Africa: A Serious Food Safety Threat

Food animals can be reservoirs of methicillin-resistant staphylococci (MRS) and are involved in their zoonotic transmission through the food chain. In Africa, there is a dearth of information about the food safety issues associated with their dissemination in the farm-to-plate continuum. This study sought to determine and compare the carriage, antimicrobial resistance profiles and clonal relatedness of circulating MRS strains among pigs and exposed workers in Cameroon and South Africa. A total of 288 nasal and rectal pooled samples collected from 432 pigs as well as nasal and hand swabs from 82 humans were cultured on mannitol salt agar supplemented with 6 mg/l cefoxitin. Presumptive MRS were screened for methicillin resistance using the cefoxitin disc test and confirmed with the VITEK 2 system. Selected isolates underwent genomic fingerprinting via REP-PCR. Univariate and multivariate logistic regression analyses were performed to identify risk factors for MRS carriage in humans from a questionnaire survey among slaughterhouse workers. Overall, 75% and 70% of nasal and rectal pooled samples were respectively positive for MRS. The MRS prevalence in all pooled pig samples from Cameroon was higher than that of South Africa. MRS prevalence of carriage (nasal and hand) was higher in Cameroonian exposed workers compared to those from South Africa, with high statistical significance. Nasal MRS colonization was highly statistically associated with hand MRS (31.58% vs 86.21%; p = 0.000; OR = 13.54; 95% CI 3.99-45.95; p = 0.015). Recent antibiotic use, previous hospitalization, occupation of relatives, years in the employment and contact with poultry were the main risk factors identified in the emergence and spread of MRS. MRS are emerging as serious foodborne pathogens and present a food safety threat. There is an urgent need to implement stringent and effective prevention and containment measures to curb antibiotic resistance in the farm-to-plate continuum in Cameroon and South Africa.

Rapid Confirmation of the Zaire Ebola Virus in the Outbreak of the Equateur Province in the Democratic Republic of Congo: Implications for Public Health Interventions

Ten days after the declaration of the Ebola outbreak in the Democratic Republic of Congo, rapid identification of the species Zaire Ebola virus using partial gene amplification and nanopore sequencing backed up the use of the recombinant vesicular stomatitis virus–Zaire Ebola virus vaccine in the recommended ring vaccination strategy.

DNA Indicative of Human Bocaviruses Detected in Non-Human Primates in the Democratic Republic of the Congo

Bocaparvoviruses are members of the family Parvovirinae and human bocaviruses have been found to be associated with respiratory and gastrointestinal disease. There are four known human bocaviruses, as well as several distinct ones in great apes. The goal of the presented study was to detect other non-human primate (NHP) bocaviruses in NHP species in the Democratic Republic of the Congo using conventional broad-range PCR. We found bocavirus DNA in blood and tissues samples in 6 out of 620 NHPs, and all isolates showed very high identity (>97 %) with human bocaviruses 2 or 3. These findings suggest cross-species transmission of bocaviruses between humans and NHPs.

Virus-encoded miRNAs in Ebola Virus Disease

Ebola virus (EBOV) is a negative-strand RNA virus that replicates in the cytoplasm and causes an often-fatal hemorrhagic fever. EBOV, like other viruses, can reportedly encode its own microRNAs (miRNAs) to subvert host immune defenses. miRNAs are short noncoding RNAs that can regulate gene expression by hybridizing to multiple mRNAs, and viral miRNAs can enhance viral replication and infectivity by regulating host or viral genes. To date, only one EBOV miRNA has been examined in human infection. Here, we assayed mouse, rhesus macaque, cynomolgus macaque, and human samples infected with three EBOV variants for twelve computationally predicted viral miRNAs using RT-qPCR. Ten miRNAs aligned to EBOV variants and were detectable in the four species during disease with several viral miRNAs showing presymptomatic amplification in animal models. miRNA abundances in both the mouse and nonhuman primate models mirrored the human cohort, with miR-1-5p, miR-1-3p, and miR-T3-3p consistently at the highest levels. These striking similarities in the most abundant miRNAs during infection with different EBOV variants and hosts indicate that these miRNAs are potential valuable diagnostic markers and key effectors of EBOV pathogenesis.

Taxonomy of the Family Arenaviridae and the Order Bunyavirales: Update 2018

In 2018, the family Arenaviridae was expanded by inclusion of 1 new genus and 5 novel species. At the same time, the recently established order Bunyavirales was expanded by 3 species. This article presents the updated taxonomy of the family Arenaviridae and the order Bunyavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and summarizes additional taxonomic proposals that may affect the order in the near future.