Severe morbidity and hospital-based mortality from Rift Valley fever disease between November 2017 and March 2020 among humans in Uganda

In this study, we investigated the mortality and morbidity among RVF confirmed cases reported to the UVRI and NRRT. Slightly more than half (53%) of all the confirmed acute cases between November 2017 and March 2020 died, a stark contrast to the absence of mortality among cases diagnosed in the country in 2016 and the 1960s. This mortality is higher than that reported by Nanyingi and colleagues [4], and more than two-fold higher than estimated in a recent meta-analysis [2]. Similarly, the proportion of RVF patients that required hospitalisation, the basis on which we defined severe disease [11] was 70%, out of whom 64% succumbed to the illness. The mortality was higher in district (80%) and regional referral hospitals (69%) compared to private hospitals (33%) and health care centre level III (50%). This severity of disease should concern us all as it is atypical of most RVF outbreaks. A review by Baba et al. in 2015 reported an increasing severity of RVF disease in endemic areas [14].

Patients die due to a delay in seeking health care, slow referral mechanisms, and initiating hospital based supportive care [15]. As illustrated in Fig. 6a - d, patients lived in remote locations some inaccessible by road during the rainy seasons when RVF outbreaks occur. In this study there was a delay of 7 days between onset of symptoms and laboratory confirmation of RVF despite a laboratory turn-around time of 24 hours. Such delays would have been avoided if rapid point-of-care diagnostics were readily available [16]. Nearly all (96%) hospitalised patients presented with pyrexia and haemorrhage at admission, out of whom 63% died. Haemorrhagic manifestations accounted for nearly 50% of death among RVF patients in some parts of Saudi Arabia [17], and dominated in Sudan [18] and Madagascar [19] outbreaks.

In this study, all patients who were above 44 years died. These findings contrast with those reported in Kenya where death occurred in patients much younger (21–30-year) and possibly related to greater exposure through male mandated pastoral duties with the animals [20]. The relationship between advanced age and mortality has been well characterised with viral infections and thought to be related to reduced adaptive immune responses as a result of natural age related involution of the thymus [21] as well as other comorbidities that affect the integrity of the immune system. In other RVF studies, mortality was associated with hospitalisation [20], HIV positive status [22], and RVF viral loads greater than 2.1 × 10⁴ viral particles/ml [23] during the first week since onset of symptoms. The high mortality in males mirrors the dominancy of the same gender in domestic animal care duties, trade, and veterinary service delivery. In this outbreak over 90% of RVF cases were males and the only sex enrolled in the follow-up study. Other potentially risky occupations included herding, farming, assisting animal birth, touching sick and dead animals, slaughtering animals, nursing febrile patients, and death of family members from febrile illness. Most survivors self-reported consumption of milk, meat, and ghee, although two patients independently reported consumption of wild game (squirrel) and an animal fetus delivered by caesarean section. We did not ascertain the RVF infection status for the fetus, cow or other consumed products through the laboratory. Another study undertaken in animals from RVF outbreak areas will provide insight on the possible correlation between human and animal cases [8]. Fetuses potentially have high viral loads and patients who acquire infections as a result of assisting animal births and disposal of fetuses are likely to present with severe disease [24].

In Uganda, cases of RVF in the 1960s were mild and none required hospital admission [6]. The cases were detected in a village whose inhabitants did not keep livestock and near the location of the UVRI in Entebbe, then Mpigi district. This area is geographically distant from the current RVF outbreak locations. It is possible that earlier RVF virus studies with laboratory animals in the 1940s could have posed a risk to the surrounding communities through mosquito transmission, as there is evidence of accidental infections among laboratory workers at the time [25]. There was no reported human disease for nearly 50 years till 2016 when three cases occurred in the southwestern district of Kabale [26]. These presented features of severe disease such as hepatitis, haemorrhage, and hospitalisation but there was no death. Between November 2017 and March 2020, over 50% of the cases died, 70% hospitalised, and presented with hepatic, renal, visual, haemorrhage, the severe forms of disease. It is possible that this increase in cases and disease severity is apparent due to increased awareness, surveillance and detection, and access to health care. Conversely, the increase in cases could be related to changes in climatic conditions such as heavy rains and flooding with subsequently increased breeding of different mosquito vectors, and/or from increased human activity that link the sylvatic and domestic RVF transmission cycles such as grazing cattle in gazetted wild game reserves. The communities of three districts from which confirmed cases were identified share an unfenced border with the Lake Mburo game park. In addition, the high human death from RVF could be related to unknown underlying co-morbidities in patients, and/or depict a trend of possibly worsening disease presentation over the years. Some phylogenetic studies have shown evolutionary changes in the RVF genome that mirror the virulence and severity of disease in humans [14]. Using next generation sequencing, two viral lineages: the Kenya 2 and the K/E lineages caused this outbreak [8]. The S-segment sequences for the K/E lineage had homology with the Beijing strain isolated in a patient from Angola in 2016. The Beijing-Angola patient presented with a life-threatening RVFV mediated cytokine release syndrome and the virus had reassortment of the L and M segments from Lineage E and the S segment from lineage A [27]. Lineage A viruses were associated with over 200,000 human cases and 598 deaths in Egypt in 1977–1979 [4, 28], and are known to be highly pathogenic and fatal in Wistar-furth rats, thus are a major virulence factor [28]. The Kenya-2 lineage contained sequences similar to viruses that caused outbreaks in Kenya 2006/2007 [8]. Although nucleotide sequences belonging to this lineage are highly conserved with minimal sequence variation in the order of 0.69%, 0.7%, and 0.86% for L, M, and S segments respectively, they are known to have undergone distinct RNA segment mutations that resulted to between 0.15 and 2.2% amino acid substitutions in the nucleoprotein, NSm, NSs, Gn, Gc, and RNA polymerase proteins [29]. The highest rate and uniqueness of mutations occurred in the Gn protein which is responsible for cell attachment, fusion and entry, and is the main target for neutralising antibodies. These substitutions, though rare could be responsible for the viral virulence of RVF as occurrence of minor changes in amino acid sequences of other arboviruses such as West Nile virus [30] and Chikungunya [31] have resulted in viruses with increased virulence and transmission effectiveness respectively. The occurrence of amino acid alterations in the viral strains within this outbreak require further evaluation. This could aid our understanding of the increased frequency and severity of disease as well as designing appropriate interventions. One major challenge that might be encountered is the occurrence of outbreaks big enough and persisting for quite a long time to conduct effectiveness studies. Our epidemiological cluster tree showed cases sparsely distributed over wide geographical areas with many villages or districts having a single case. This is not typical of case distribution during outbreaks and may be due to reporting bias but also, majority of RVF cases present with subclinical disease. Therefore epidemiological, and interventional studies may need to adapt to designs centred around confirmed cases.

Gastro-intestinal (GI) manifestations were the most common presentation among survivors. The dominancy of GI syndrome presentation was reported in one part of Saudi Arabia [32] and is characterised as a mild form of disease [11]. We observed a persistence of symptoms such as fever or feverishness, headache, muscle pain, joint pains and GI symptoms over 2–4 months and we believe this is unlikely to be a continuation of the acute illness. RVF symptoms lasting 4 to 120 days have also been reported in Tanzania [22]. This phenomenon has been observed in relation with other viral infections including severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) [33, 34] and described as post viral exhaustion syndrome (PVES) [35], a form of chronic fatigue syndrome (CFS) or myalgic encephalomyelitis (ME) [36]. The occurrence of this syndrome has not been previously described in relation with RVF. Studies of CFS/ME following viral infections have provided some compelling pathophysiological insight, that the cytokine storm [34, 37] and mitochondrial/oxidative stress [38] during acute infection mediate the persistence of symptoms. The high cytokine milieu causes mitochondrial damage, an organelle responsible for 90–95% of body energy production [38]. The defects in cellular energy production manifest in patients as fatigue, cognitive impairment, myalgia, feverishness, or other systemic manifestations, against a backdrop of normal full blood count (FBC).

Acute RVF causes a pancytopenia characterised by leukopenia, anaemia, thrombocytopenia, and neutropenia in humans [17, 26, 32]. Long-term haematological follow-up studies have not been conducted among survivors. We followed up survivors to investigate whether haematological parameters were deranged in the long-term by the acute infection. Our results show that all FBC parameters recovered to normal levels by three months and were maintained during the one-year follow-up. The absence of a long-term bone marrow suppression is reassuring for survivors and in vaccine development. Other viral infections are known to impair the reconstitution of long-term hematopoietic stem cells (LT-HSC) [39]. The bone marrow niche hosts long lived plasma cells which persistently produce high affinity antibodies following infection or vaccination [40].

Elevation of liver enzymes such as AST, ALT, and ALP is a characteristic feature of RVF in humans [17, 32]. The liver is the main target organ for RVF, and causes varying degrees of hepatic necrosis. Hepatic regeneration starts within 5 days post infection in mice [41], however, long-term liver recovery has not been reported in humans. In our study, liver enzymes returned to normal within three months and were maintained throughout follow up. This study used cross-sectional, retrospective and prospective approaches to data collection. Medical history obtained months after the acute illness is prone to recall bias. The longitudinal follow-up of survivors has provided insight into possibilities of RVF associated CFS/ME and assurance that patients regain normal FBC and liver enzyme levels in the long-term. We had limited clinical and laboratory data during the acute phase of the illness as hospital records were not accessed, and symptoms of PVES/CFS/ME were not systematically solicited thus our inference on PVES is suspected or incidental. The lack of negative controls or infection status of the potential sources of risk limits our inferences on RVF risk factors as these could as well be normal levels of exposure to these disease determinants in the general population. Finally, the study had a small sample size and most likely captured patients with severe disease that presented to the health care system.

In conclusions, RVF causes high mortality, acute and long-lasting morbidity in patients that present to the health care system with the disease. Patients report late for care when the role of antivirals to maintain life would be limited, therefore, point-of-care diagnostics, serum markers of prognosis and potential biologics should be identified to improve patient care. One-health combined interventions should be developed to improve environmental and livestock surveillance, prevent infections and promptly detect outbreaks. These and more measures would be composite in curbing the sparingly known disability adjusted life years (DALYs) associated with RVF.