Byarugaba, D. K. | Search bioRxiv

bioRxiv2023

Wide distribution of Mediterranean and African Spotted fever agents and the first identification of Israeli Spotted Fever agent in ticks in Uganda

Rickettsia microorganisms are causative agents of several neglected emerging infectious diseases transmitted to humans by ticks among other arthropod vectors. In this study, ticks were collected from four geographical regions of Uganda, pooled in sizes of 1-179 ticks based on location, tick species, life stage, host, and time of collection, and were tested by real time PCR for Rickettsia species harboured. The tick pools were tested with primers targeting gltA, 17kDa and ompA genes, followed by Sanger sequencing of 17kDa and ompA genes. Of the 471 tick pools tested, 116 (24.6%) were positive for Rickettsia spp. by the gltA primers. The prevalence of Rickettsia varied by district with Gulu recording the highest (30.1%) followed by Luwero (28.1%) and Kasese had the lowest (14%). Tick pools with highest positivity rates were from livestock (cattle, goats, sheep, and pigs), 26.9%, followed by vegetation 23.1% and pets (dogs and cats) 19.7%. Of 116 gltA-positive tick pools, 86 pools were positive using 17kDa primers of which 48 purified PCR products were successfully sequenced. The predominant Rickettsia spp. identified was R. africae (n=15) in four tick species, followed by R. conorii (n=5) in three tick species (Haemaphysalis elliptica, Rhipicephalus appendiculatus, and Rh. decoloratus). Rickettsia conorii subsp. israelensis was detected in one tick pool. These findings indicate that multiple Rickettsia spp. capable of causing human illness are circulating in the four diverse geographical regions of Uganda including new strains previously known to occur in the Mediterranean region. Physicians should be informed about Rickettsia spp. infections as potential causes for acute febrile illnesses in these regions. Continued and expanded surveillance is essential to further identify and locate potential hotspots with Rickettsia spp. of concern. Author SummaryTick-borne rickettsioses are emerging infectious diseases of public health importance worldwide. Spotted fever rickettsioses transmitted by ticks can cause mild to severe human illness depending on the Rickettsia spp. and co-morbidities. Their diagnosis is challenging due to non-specific symptoms particularly in limited resource settings. Little is known about their prevalence in Uganda. Using entomological and molecular tools, we surveyed and studied tick-borne spotted fever rickettsioses in five districts from four diverse eco-regions of Uganda. Overall, 24.6% (116/471) tick pools were positive for Rickettsia species. By sequencing the 17kDa and ompA genes of Rickettsia, we identified R. africae as the most common agent, followed by R. conorii and R. conorii subsp. israelensis. The findings indicate multiple Rickettsia spp. that can cause febrile illness in humans are circulating in the four geographically diverse regions of Uganda. Physicians should be aware these agents are potential causes of febrile illness in these areas, particularly in individuals who encounter livestock or their grazing areas.

molecular biology↗

bioRxiv2020

The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus

SARS-CoV-1 and SARS-CoV-2 are not phylogenetically closely related; however, both use the ACE2 receptor in humans for cell entry. This is not a universal sarbecovirus trait; for example, many known sarbecoviruses related to SARS-CoV-1 have two deletions in the receptor binding domain of the spike protein that render them incapable of using human ACE2. Here, we report three sequences of a novel sarbecovirus from Rwanda and Uganda which are phylogenetically intermediate to SARS-CoV-1 and SARS-CoV-2 and demonstrate via in vitro studies that they are also unable to utilize human ACE2. Furthermore, we show that the observed pattern of ACE2 usage among sarbecoviruses is best explained by recombination not of SARS-CoV-2, but of SARS-CoV-1 and its relatives. We show that the lineage that includes SARS-CoV-2 is most likely the ancestral ACE2-using lineage, and that recombination with at least one virus from this group conferred ACE2 usage to the lineage including SARS-CoV-1 at some time in the past. We argue that alternative scenarios such as convergent evolution are much less parsimonious; we show that biogeography and patterns of host tropism support the plausibility of a recombination scenario; and we propose a competitive release hypothesis to explain how this recombination event could have occurred and why it is evolutionarily advantageous. The findings provide important insights into the natural history of ACE2 usage for both SARS-CoV-1 and SARS-CoV-2, and a greater understanding of the evolutionary mechanisms that shape zoonotic potential of coronaviruses. This study also underscores the need for increased surveillance for sarbecoviruses in southwestern China, where most ACE2-using viruses have been found to date, as well as other regions such as Africa, where these viruses have only recently been discovered.

evolutionary biology↗