Jingmenviruses: Ubiquitous, understudied, segmented flavi-like viruses

Abstract

Jingmenviruses are a group of viruses identified recently, in 2014, and currently classified by the International Committee on Taxonomy of Viruses as unclassified Flaviviridae. These viruses closely related to flaviviruses are unique due to the segmented nature of their genome. The prototype jingmenvirus, Jingmen tick virus (JMTV), was discovered in Rhipicephalus microplus ticks collected from China in 2010. Jingmenviruses genomes are composed of four to five segments, encoding for up to seven structural proteins and two non-structural proteins, both of which display strong similarities with flaviviral non-structural proteins (NS2B/NS3 and NS5). Jingmenviruses are currently separated into two phylogenetic clades. One clade includes tick- and vertebrate-associated jingmenviruses, which have been detected in ticks and mosquitoes, as well as in humans, cattle, monkeys, bats, rodents, sheep, and tortoises. In addition to these molecular and serological detections, over a hundred human patients tested positive for jingmenviruses after developing febrile illness and flu-like symptoms in China and Serbia. The second phylogenetic clade includes insect-associated jingmenvirus sequences, which have been detected in a wide range of insect species, as well as in crustaceans, plants, and fungi. In addition to being found in various types of hosts, jingmenviruses are endemic, as they have been detected in a wide range of environments, all over the world. Taken together, all of these elements show that jingmenviruses correspond exactly to the definition of emerging viruses at risk of causing a pandemic, since they are already endemic, have a close association with arthropods, are found in animals in close contact with humans, and have caused sporadic cases of febrile illness in multiple patients. Despite these arguments, the vast majority of published data is from metagenomics studies and many aspects of jingmenvirus replication remain to be elucidated, such as their tropism, cycle of transmission, structure, and mechanisms of replication and restriction or epidemiology. It is therefore crucial to prioritize jingmenvirus research in the years to come, to be prepared for their emergence as human or veterinary pathogens.

Keywords: arbovirus; emerging virus; jingmenvirus; segmented flavivirus; tick-borne disease.

FIGURE 1

Genome organization of jingmenviruses. The layout of this figure is modified from Kobayashi et al. (2021). JMTV SY84, Jingmen tick virus strain SY84 (NC_024113-NC_024117); ALSV H3, Alongshan virus strain H3 (MH158415–MH158418); WHAV2 WHYC-2, Wuhan aphid virus 2 strain WHYC-2 (KR902725–KR902728); GCXV LO35, Guaico Culex virus strain LO35 (KM461666-KM461670). (A)_n, polyadenylation. NSP1, non-structural protein 1, RNA-dependent RNA polymerase and methyltransferase domains; VP, virus (structural) protein; nuORF, open reading frame identified by Kholodilov et al. (2020); NSP2, non-structural protein 2, serine protease and helicase domains. Red bar: signal peptide. The genome organization of JMTV and ALSV are representative of tick- and mammal-associated jingmenviruses; WHAV2 represents insect-associated jingmenviruses; GCXV represents mosquito-associated jingmenviruses.

FIGURE 2

Structures of NSP1 and NSP2 functional domains putatively involved in the replication. (A) Cartoon representation of the NSP1 MTase (turquoise) and RdRp (pink) domains of Guaico Culex virus (homology model). (B) Cartoon representation of the NSP2 protease domain of Jingmen tick virus (homology model) with the canonical Asp-His-Ser catalytic triad (top) and NSP2 helicase domain of Alongshan virus (PDB code 6M40, from X-ray crystallography data in Gao et al., 2020) organized in subdomains 1 (blue), 2 (green), and 3 (ochre) (bottom). All representations were prepared using PyMOL (Schrödinger).

FIGURE 3

(Top) World map of detections of jingmenvirus sequences. Countries in which tick-associated jingmenviruses have been detected in vertebrates contain red; countries in which tick-associated jingmenviruses have been detected in ticks and mosquitoes contain blue; countries in which insect-associated jingmenviruses have been detected contain yellow. (Bottom) Map of detections of jingmenvirus sequences in Chinese provinces. The province where jingmenviruses were first discovered is highlighted with a black star. Provinces in which Jingmen tick virus (JMTV) has been detected contain red; provinces in which Alongshan virus (ALSV) has been detected contain blue; provinces in which Yanggou tick virus (YGTV) has been detected contain purple; provinces in which Xinjiang tick virus (XJTV) has been detected contain black spots; provinces in which Guangdong jingmen-like virus (GDJLV) has been detected contain green; provinces in which Hainan jingmen-like virus (HJLV) has been detected contain orange; provinces in which insect-associated jingmenviruses have been detected contain yellow. All other provinces are in gray. These maps were drawn using the QGIS software and open-source geographic data.

FIGURE 4

Phylogenetic analysis of all published full-length NSP1 ORF amino acid sequences of JMTV strains, and the prototype strain of ALSV as an outgroup. This tree was built with PhyML with an LG substitution model and midpoint-rooted. The branches are labeled with the bootstrap proportion in percentages (out of 100 bootstraps), the tips are labeled with the sample collection location, and the bar represents 0.03 substitutions per nucleotide position. JMTV strains seem to cluster according to their detection location rather than host with two clear subclades, the European and Central American strains (shaded in blue) on one side and the Asian (shaded yellow) and African and South American (shaded green) strains on the other side. The hosts are represented with symbols on the side of the phylogenetic tree: ticks are green stars with eight branches, mosquitoes are blue stars with six branches, monkeys are purple squares, cattle are red circles, bats are orange triangles pointing up, rodents are yellow triangles pointing down and humans are black diamonds.

FIGURE 5

Phylogenetic analysis of all known jingmenvirus species with full-length NSP1 (Top) and NSP2 (Bottom) ORF amino acid sequences. These trees were built with PhyML with an LG substitution model and midpoint rooted. The branches are labeled with the bootstrap proportion in percentages (out of 1000 bootstraps) and the bars represent 0.3 substitutions per nucleotide position. Jingmenviruses cluster in two main clades, on the one hand the tick- and vertebrate-associated jingmenviruses (shaded in blue) and on the other hand, insect-associated jingmenviruses.