Arboviruses in southern Africa: are we missing something?

Eilat virus isolated from Culex univittatus mosquitoes from the Namibian Zambezi Region influences in vitro superinfection with alpha- and flaviviruses in a virus-species-dependent manner

The genus Alphavirus harbors arboviruses of great concern, such as the Chikungunya virus and the equine encephalitis viruses. Transmission of pathogenic alphaviruses by mosquitoes could be influenced by insect-specific alphaviruses such as Eilat virus (EILV). However, insect-specific alphaviruses are rarely found in wild mosquitoes and only a few have been described in the literature. Here, we report the detection of EILV in a Culex univittatus mosquito from the north-eastern Namibian Zambezi region. Full genome analysis of MP458-NA-2018 showed 94.5% nucleotide identity to an EILV isolate from Israel. MP458-NA-2018 grouped with EILV in phylogenetic analysis and was placed within the clade of insect-specific alphaviruses. The virus was isolated in mosquito cells and shown to be restricted to insects as hosts by the inability to infect different vertebrate cell lines and a complete block of virus replication at 34°C. We further showed that infection of cells with EILV MP458-NA-2018 reduced production of infectious particles of Sindbis virus by 2000-fold over the entire course of infection, whereas reduction rates of Bagaza and Middleburg virus were approximately 3-10-fold and dependent on time after infection. While production of infectious particles of cells superinfected with the Chikungunya virus were approximately 30-fold reduced and more pronounced at a lower multiplicity of infection of 0.01, EILV seemed to enhance production of West Nile virus infectious particles by >5-fold when superinfected at a multiplicitiy of infection of 0.1. In summary, EILV from the Namibian Zambezi region influences in vitro replication of endemic flavi- and alphaviruses.

The monsoon-associated equine South African pointy mosquito 'Aedes caballus'; the first comprehensive record from southeastern Iran with a description of ecological, morphological, and molecular aspects

The equine South African pointy vector mosquito, Aedes caballus, poses a significant threat to human health due to its capacity for transmitting arboviruses. Despite favorable climate for its existence in southeast Iran, previous records of this species in the area have indicated very low abundance. This comprehensive field and laboratory study aimed to assess its current adult population status in this region, utilizing a combination of ecological, morphological and molecular techniques. Four distinct types of traps were strategically placed in three fixed and two variable mosquito sampling sites in the southern strip of Sistan and Baluchistan Province. Subsequently, DNA was extracted from trapped mosquitoes and subjected to PCR amplification using the molecular markers COI, ITS2, and ANT. In total, 1734 adult Ae. caballus specimens were collected from rural areas, with the majority being captured by CO2-baited bednet traps. A notable increase in the abundance of this species was observed following rainfall in February. The genetic analysis revealed multiple haplotypes based on COI and ITS2 sequences, with COI gene divergence at 0.89%, and ITS2 sequence divergence at 1.6%. This suggests that previous challenges in morphological identification may have led to misidentifications, with many adults previously classified as Ae. vexans potentially being Ae. caballus. The findings of this study hold significant implications for public health authorities, providing valuable insights for integrated and targeted vector control and disease management efforts.

Arbovirus surveillance in febrile patients attending selected health facilities in Rwanda

Arthropod-borne (arbo) viruses cause emerging diseases that affect the livelihoods of people around the world. They are linked to disease outbreaks resulting in high morbidity, mortality, and economic loss. In sub-Saharan Africa, numerous arbovirus outbreaks have been documented, but the circulation and magnitude of illness caused by these viruses during inter-epidemic periods remains unknown in many regions. In Rwanda, there is limited knowledge on the presence and distribution of arboviruses. This study aimed at determining the occurrence and distribution of selected arboviruses, i.e., chikungunya virus (CHIKV), o'nyong-nyong virus (ONNV), dengue virus (DENV), West Nile virus (WNV), Zika virus (ZIKV), Rift Valley fever virus (RVFV) and Crimean-Congo haemorrhagic fever virus (CCHFV), among febrile patients visiting health centres in Rwanda. A total of 2294 dry blood spots (DBS) were collected on filter papers during August 2019 - December 2020. Reverse-transcription polymerase chain reaction (RT-PCR) was performed on samples in pools of ten, using both quantitative (DENV, ZIKV, RVFV) and conventional PCR (CHIKV, ONNV, WNV, CCHFV) with virus specific primers, followed by sequencing. Demographic data and clinical manifestations of illness were analysed. ONNV infection was detected in 12 of 230 pools (5.2%) and ZIKV in three pools (1.3%). The other arboviruses were not detected. All ONNV cases were found in the Rwaniro health centre, while ZIKV infection was found among patients visiting the Kirinda and Zaza health centres. There was temporal variability in ONNV infections with most cases being recorded during the long dry season, while ZIKV infection occurred during both dry and wet seasons. Patients with ONNV were older and more were females. In conclusion, ONNV and ZIKV infection were detected in acute patients and can explain some of the feverish diseases in Rwanda.

Monolithic affinity columns in 3D printed microfluidics for chikungunya RNA detection

Mosquito-borne pathogens plague much of the world, yet rapid and simple diagnosis is not available for many affected patients. Using a custom stereolithography 3D printer, we created microfluidic devices with affinity monoliths that could retain, noncovalently attach a fluorescent tag, and detect oligonucleotide and viral RNA. We optimized the fluorescent binding and sample load times using an oligonucleotide sequence from chikungunya virus (CHIKV). We also tested the specificity of CHIKV capture relative to genetically similar Sindbis virus. Moreover, viral RNA from both viruses was flowed through capture columns to study the efficiency and specificity of the column for viral CHIKV. We detected ~107 loaded viral genome copies, which was similar to levels in clinical samples during acute infection. These results show considerable promise for development of this platform into a rapid mosquito-borne viral pathogen detection system.

Rapid reverse transcriptase recombinase polymerase amplification assay for flaviviruses using non-infectious in vitro transcribed RNA as positive controls

West Nile virus (WNV) and Wesselsbron virus (WSLV) are mosquito-borne viruses belonging to the Flavivirus genus, family Flaviviridae and cause outbreaks in southern Africa after heavy rain. Isothermal assays have been proposed for application in field situations as well as low resource settings and hence we developed a reverse-transcriptase recombinase polymerase amplification (RT-RPA) to detect WNV and WSLV known to occur in South Africa, causing sporadic outbreaks usually associated with good rainfall favouring mosquito breeding. Infectious virus can only be handled within a biosafety level (BSL) 3 facility, hence we opted to validate the assay with transcribed RNA. Specific RT-RPA primers and probes were designed for detection of WNV and WSLV and products detected using a rapid lateral flow device. The assay was performed in 30 min and detected 1.9 × 10¹ copies of WNV and 3.5 × 10° copies WSLV using noninfectious transcribed RNA controls. In addition, the assay was not inhibited by the presence of mosquito extracts in spiked samples. Mismatches between the WNV and WSLV probes and other flaviviruses will likely prevent cross reactivity. The sensitivity, low RPA incubation temperature and rapid processing time makes assay systems based on RPA technology ideally suited for fieldable diagnostics.

Zoonotic Alphaviruses in Fatal and Neurologic Infections in Wildlife and Nonequine Domestic Animals, South Africa

Alphaviruses from Africa, such as Middelburg virus (MIDV), and Sindbis virus (SINV), were detected in horses with neurologic disease in South Africa, but their host ranges remain unknown. We investigated the contribution of alphaviruses to neurologic infections and death in wildlife and domestic animals in this country. During 2010-2018, a total of 608 clinical samples from wildlife and nonequine domestic animals that had febrile, neurologic signs or unexplained deaths were tested for alphaviruses. We identified 32 (5.5%) of 608 alphavirus infections (9 SINV and 23 MIDV), mostly in neurotissue of wildlife, domestic animals, and birds. Phylogenetic analysis of the RNA-dependent RNA polymerase gene confirmed either SINV or MIDV. This study implicates MIDV and SINV as potential causes of neurologic disease in wildlife and nonequine domestic species in Africa and suggests a wide host range and pathogenic potential.

A lesson learnt from the emergence of Zika virus: What flaviviruses can trigger Guillain-Barré syndrome?

While Zika virus outbreaks raised the concern about rare viral infections in human, attention should also be paid to other Guillain-Barré syndrome (GBS) inducing viruses. This study aims to search for other flaviviruses likely to be associated with GBS. Amino acid (aa) sequence matching analysis was conducted to identify viruses molecularly similar to the Zika virus and human GBS-related proteins. A systematic review of clinical literature was performed to summarize the clinical findings of the GBS-associated flaviviruses identified in the aa sequence matching analysis. It was found that more than 10 pentapeptides were shared between 9 flaviviruses, Zika virus, and human GBS-related proteins. Twenty-six articles totaling 42 clinical cases were eligible for inclusion in the systematic review concerning the nine flaviviruses identified. While some patients showed signs of encephalitis, 5 out of 42 cases demonstrated typical GBS symptoms. Public health professionals should be aware of other GBS-associated flaviviruses and GBS cases with mild symptoms.

Mosquito community composition and abundance at contrasting sites in northern South Africa, 2014-2017

Most data on species associations and vector potential of mosquitoes in relation to arboviral infections in South Africa date back from the 1940s to late 1990s. Contextual information crucial for disease risk management and control, such as the sampling effort, diversity, abundance, and distribution of mosquitoes in large parts of South Africa still remains limited. Adult mosquitoes were collected routinely from two horse farms in Gauteng Province; two wildlife reserves in Limpopo Province, at Orpen Gate in Kruger National Park (KNP) and Mnisi Area in Mpumalanga Province between 2014-2017, using carbon dioxide-baited light and tent traps. Mosquito diversity and richness are greater in untransformed natural and mixed rural settings. In untransformed wilderness areas, the most dominant species were Culex poicilipes, Anopheles coustani, and Aedes mcintoshi, while in mixed rural settings such as the Mnisi area, the two most abundant species were Cx. poicilipes and Mansonia uniformis. However, in peri-urban areas, Cx. theileri, Cx. univittatus, and Cx. pipiens sensu lato were the most dominant. Aedes aegypti, Ae. mcintoshi, Ae. metallicus, Ae. vittatus, Cx. pipiens s.l., Cx. theileri, and Cx. univittatus had the widest geographical distribution in northern South Africa. Also collected were Anopheles arabiensis and An. vaneedeni, both known malaria vectors in South Africa. Arbovirus surveillance and vector control programs should be augmented in mixed rural and peri-urban areas where the risk for mosquito-borne disease transmission to humans and domestic stock is greater.

A simple and rapid approach to prepare Sindbis and West Nile viral RNA controls for differentiation between positive samples and laboratory contamination

Reverse transcription-polymerase chain reaction (RT-PCR) is frequently used for surveillance and diagnosis of arboviruses and emerging viruses. A disadvantage of RT-PCR assays, especially nested assays, is the potential for false-positive results caused by laboratory contamination from either positive controls or positive samples. Positive reactors usually require sequence determination for confirmation which delay timeous reporting of a result. Thus, the aim of the study was to use a simple technique to prepare a positive control allowing true positives to be differentiated from laboratory contamination based on size differentiation for conventional PCR, or melt temperatures for real time assays. A flavivirus positive control and an alphavirus positive control were prepared for two RT-PCR assays that we are currently using for arbovirus surveillance in South Africa. Primers targeting a region of the partial genes of interest cloned in pGEM®T-easy were modified at the 5' ends with non-viral nucleotides. The resulting amplicons were circularised, resulting in pGEM®T-easy constructs with 51 and 65 non-viral bases inserted into the partial flaviviral and alphaviral genes respectively and used as template for transcribing RNA. Sequence analysis was used to confirm the manipulation of the partial genes. Using virus specific primer pairs, viral RNA could be readily differentiated from the modified positive controls either by size differentiation, or melt temperature in a SYBR®Green real time RT-PCR. This study demonstrates how simple recombinant technology can be used to produce a positive control that has application in the laboratory for surveillance studies or as a diagnostic tool using synthetic genes to abrogate the requirement for handling infectious virus.

Arboviruses in the East African Community partner states: a review of medically important mosquito-borne Arboviruses

Mosquito-borne diseases, including arbovirus-related diseases, make up a large proportion of infectious disease cases worldwide, causing a serious global public health burden with over 700,000 deaths annually. Mosquito-borne arbovirus outbreaks can range from global to regional. In the East African Community (EAC) region, these viruses have caused a series of emerging and reemerging infectious disease outbreaks. Member states in the EAC share a lot in common including regional trade and transport, some of the factors highlighted to be the cause of mosquito-borne arbovirus disease outbreaks worldwide. In this review, characteristics of 24 mosquito-borne arboviruses indigenous to the EAC are reviewed, including lesser or poorly understood viruses, like Batai virus (BATV) and Ndumu virus (NDUV), which may escape their origins under perfect conditions to establish a foothold in new geographical locations. Factors that may influence the future spread of these viruses within the EAC are addressed. With the continued development observed in the EAC, strategies should be developed by the Community in improving mosquito and mosquito-borne arbovirus surveillance to prevent future outbreaks.

Mosquito-borne arboviruses of African origin: review of key viruses and vectors

Key aspects of 36 mosquito-borne arboviruses indigenous to Africa are summarized, including lesser or poorly-known viruses which, like Zika, may have the potential to escape current sylvatic cycling to achieve greater geographical distribution and medical importance. Major vectors are indicated as well as reservoir hosts, where known. A series of current and future risk factors is addressed. It is apparent that Africa has been the source of most of the major mosquito-borne viruses of medical importance that currently constitute serious global public health threats, but that there are several other viruses with potential for international challenge. The conclusion reached is that increased human population growth in decades ahead coupled with increased international travel and trade is likely to sustain and increase the threat of further geographical spread of current and new arboviral disease.