Ancient ancestry of KFDV and AHFV revealed by complete genome analyses of viruses isolated from ticks and mammalian hosts

Background

Alkhurma hemorrhagic fever virus (AHFV) and Kyasanur forest disease virus (KFDV) cause significant human disease and mortality in Saudi Arabia and India, respectively. Despite their distinct geographic ranges, AHFV and KFDV share a remarkably high sequence identity. Given its emergence decades after KFDV, AHFV has since been considered a variant of KFDV and thought to have arisen from an introduction of KFDV to Saudi Arabia from India. To gain a better understanding of the evolutionary history of AHFV and KFDV, we analyzed the full length genomes of 16 AHFV and 3 KFDV isolates.

Methodology/Principal Findings

Viral genomes were sequenced and compared to two AHFV sequences available in GenBank. Sequence analyses revealed higher genetic diversity within AHFVs isolated from ticks than human AHFV isolates. A Bayesian coalescent phylogenetic analysis demonstrated an ancient divergence of AHFV and KFDV of approximately 700 years ago.

Conclusions/Significance

The high sequence diversity within tick populations and the presence of competent tick vectors in the surrounding regions, coupled with the recent identification of AHFV in Egypt, indicate possible viral range expansion or a larger geographic range than previously thought. The divergence of AHFV from KFDV nearly 700 years ago suggests other AHFV/KFDV-like viruses might exist in the regions between Saudi Arabia and India. Given the human morbidity and mortality associated with these viruses, these results emphasize the importance of more focused study of these significant public health threats.     

Human Alkhumra hemorrhagic Fever: Emergence,history and epidemiological and clinical profiles

Alkhumra hemorrhagic fever (AHF) is a severe, often fatal hemorrhagic disease in humans. It is caused by Alkhumra hemorrhagic fever virus (AHFV), a newly described flavivirus first isolated in 1995 in Alkhumra district, south of Jeddah City, Saudi Arabia. It is transmitted from infected livestock animals to humans by direct contact with infected animals or by tick bites. In the recent past, the incidence of AHF has increased, with a total of 604 confirmed cases have been reported in Saudi Arabia between 1995 and 2020. Yet, no specific treatment or control strategies have been developed and implemented against this infection. Hence, the likelihood of increased prevalence or the occurrence of outbreaks is high, particularly in the absence of appropriate prevention and control strategies. This narrative review presents an overview of the current knowledge and future concerns about AHF globally.     

Molecular diagnosis of begomovirus associated with Chilli leaf curl disease in Jeddah,Saudi Arabia

Chilli (Capsicum annum L.) is well known as ‘wonder spice’. This is a very valuable cash crop grown as a vegetable globally. Chilli leaf curl disease is a major threat and global concern for the cultivation of Chilli by farmers and growers. In this work, the molecular diagnosis, genetic diversity, phylogenetic relationship, and begomovirus association with Chilli leaf curl disease have been discussed. The infected leaves were randomly harvested from the Chilli field, at Jeddah, Saudi Arabia. A group of begomovirus vector, whiteflies were also observed on the Chilli crop and infected weeds growing in the neighboring field. The begomovirus was confirmed by coat protein gene specific primer, dot blot hybridization, sequencing and sequence analysis. The full coat protein gene was found to have 774 nucleotides. The nucleotide sequences analysis shared the highest identity with Tomato yellow leaf curl virus reported earlier infecting tomato from Saudi Arabia, and the lowest identity was observed with Tomato yellow leaf curl virus Oman isolate. The overall sequence identity ranged from more than ninety percent among the analyzed sequences. The phylogenetic relationship analysis formed the major three clusters and showed the closed clustering with Tomato yellow leaf curl virus isolates. The natural spread of the Tomato yellow leaf curl virus on the Chilli crop from other crops poses an important and serious threat to Chili cultivation in the Kingdom of Saudi Arabia. Based on the literature review and current evidence, this is the first report of leaf curl disease of Chilli from Saudi Arabia.     

双单克隆抗体ELISA间接夹心法检测流行性出血热病毒抗原

建立了检测流行性出血热(EHF)病毒抗原的双单克隆抗体(McAb)ELISA同接夹心法,用本法和间接荧光抗体技术(IFAT)相比较,IFAT检出感染细胞内病毒抗原的高峰在感染后第8天,而ELISA检测感染上清中病毒抗原的高峰在第14天,两方法检测179份人工感染EHF病毒的乳鼠脑和肺组织标本,阳性检出率分别为72.1％和68.2％,实验结果表明,本法特异,敏感,简便,不仅可用于EHF病原学研究,也适用于流行病学调查检测大量鼠肺标本。     

The 2000 epidemic of Rift Valley fever in Saudi Arabia: mosquito vector studies

In mid-September 2000, Rift Valley fever (RVF) virus was diagnosed as the cause of infection in humans and livestock in Jizan Region, Saudi Arabia. This is the first time that this arbovirus has been found outside Africa and Madagascar. Collections of mosquitoes (Diptera: Culicidae) were therefore undertaken (from 25 September to 10 October) at eight sites during the epidemic to obtain mosquitoes for attempted RVF virus isolation. Among 23 699 mosquito females tested, six isolations of RVF virus were made from 15 428 Culex (Culex) tritaeniorhynchus Giles and seven from 8091 Aedes (Aedimorphus) vexans arabiensis Patton [corrected]. Minimum mosquito infection rates per 1000 at sites with infected mosquitoes were 0.3-13.8 Cx. tritaeniorhynchus and 1.94-9.03 Ae. v. arabiensis. Viral activity moved northwards as collecting was in progress and collectors 'caught up' with the virus at the two most northerly sites on the last two trapping evenings. Other species occurred in small numbers and were identified but not tested. Both Cx. tritaeniorhynchus and Ae. v. arabiensis were susceptible to RVF virus and transmitted between hamsters, and an additional quantitative test with Cx. tritaeniorhynchus showed that 71-73% of mosquitoes became infected after ingesting 6.9-7.9 log10 FFU/mL of virus; transmission rates were 10% (post-infection day 14) and 26% (post-infection day 20). It was concluded that both species were vectors on grounds of abundance, distribution, preference for humans and sheep, the virus isolations and vector competence tests.     

流行性出血热病毒在人B淋巴母细胞中复制增殖

本文应用细胞培养、免疫荧光及电镜技术研究了B淋巴母细胞对EHF病毒的易感性。结果表明EHF病毒可在该细胞中增殖。感染细胞无明显细胞病变,在形态上与对照组无差别。虽然大部分感染细胞呈现明亮病毒抗原荧光,但在电镜下却难以找到完整的病毒颗粒,仅在扩张的囊泡中发现一些性质待定的微丝样物质。人B淋巴母细胞持续感染的建立,提示患者外周血中大量出现的异型淋巴细胞可能允许EHF病毒在其中复制。     

埃博拉出血热及埃博拉病毒的研究进展

埃博拉病毒可以引起一种人畜共患烈性传染病,即埃博拉出血热,此病于1976年始发于埃博拉河流域,并且于该区域严重流行,故而得名。人类一旦感染埃博拉病毒,死亡率可高达88%,从而引起医学界的广泛关注,世界卫生组织已将埃博拉病毒列为对人类危害最为严重的病毒之一。深入地了解埃博拉出血热及埃博拉病毒,及其致病机理,对于埃博拉出血热的预防和控制具有非常重要的意义。     

流行性出血热病毒在Vero一E6细胞内引起细胞病变作用的新发现

自McCormick等发现Vero-E6细胞对流行性出血热病毒的敏感性后,国内外已有不少学者应用该细胞进行病毒分离和试验研究,但均未发现病毒在该细胞内规律性病变。病毒的存在和滴度只能按免疫荧光法(IFA)证实和测出。本文应用我国分离的出血热病毒在Vero-E6细胞上培养和观察,发现病毒在该细胞上出现有规律的病变并能测出病毒滴度,病变能被特异性中和抗体中和。现将结果报道如下。     

Comparative Pathogenesis of Alkhumra Hemorrhagic Fever and Kyasanur Forest Disease Viruses in a Mouse Model

Kyasanur Forest disease virus (KFDV) and Alkhumra hemorrhagic fever virus (AHFV) are genetically closely-related, tick-borne flaviviruses that cause severe, often fatal disease in humans. Flaviviruses in the tick-borne encephalitis (TBE) complex typically cause neurological disease in humans whereas patients infected with KFDV and AHFV predominately present with hemorrhagic fever. A small animal model for KFDV and AHFV to study the pathogenesis and evaluate countermeasures has been lacking mostly due to the need of a high biocontainment laboratory to work with the viruses. To evaluate the utility of an existing mouse model for tick-borne flavivirus pathogenesis, we performed serial sacrifice studies in BALB/c mice infected with either KFDV strain P9605 or AHFV strain Zaki-1. Strikingly, infection with KFDV was completely lethal in mice, while AHFV caused no clinical signs of disease and no animals succumbed to infection. KFDV and high levels of pro-inflammatory cytokines were detected in the brain at later time points, but no virus was found in visceral organs; conversely, AHFV Zaki-1 and elevated levels of cytokines were found in the visceral organs at earlier time points, but were not detected in the brain. While infection with either virus caused a generalized leukopenia, only AHFV Zaki-1 induced hematologic abnormalities in infected animals. Our data suggest that KFDV P9605 may have lost its ability to cause hemorrhagic disease as the result of multiple passages in suckling mouse brains. However, likely by virtue of fewer mouse passages, AHFV Zaki-1 has retained the ability to replicate in visceral organs, cause hematologic abnormalities, and induce pro-inflammatory cytokines without causing overt disease. Given these striking differences, the use of inbred mice and the virus passage history need to be carefully considered in the interpretation of animal studies using these viruses.     

HCV infection among Saudi population: high prevalence of genotype 4 and increased viral clearance rate

HCV is a major etiological agent of liver disease with a high rate of chronic evolution. The virus possesses 6 genotypes with many subtypes. The rate of spontaneous clearance among HCV infected individuals denotes a genetic determinant factor. The current study was designed in order to estimate the rate of HCV infection and ratio of virus clearance among a group of infected patients in Saudi Arabia from 2008 to 2011. It was additionally designed to determine the genotypes of the HCV in persistently infected patients. HCV seroprevalence was conducted on a total of 15,323 individuals. Seropositive individuals were tested by Cobas AmpliPrep/Cobas TaqMan HCV assay to determine the ratio of persistently infected patients to those who showed spontaneous viral clearance. HCV genotyping on random samples from persistently infected patients were conducted based on the differences in the 5'untranslated region (5'UTR). Anti-HCV antibodies were detected in 7.3% of the totally examined sera. A high percentage of the HCV infected individuals experienced virus clearance (48.4%). HCV genotyping revealed the presence of genotypes 1 and 4, the latter represented 97.6% of the tested strains. Evidences of the widespread of the HCV genotype 4 and a high rate of HCV virus clearance were found in Saudi Arabia.     

检测流行性出血热病毒滴度和中和抗体效价的半微量空斑法

建立了检测流行性出血热病毒滴度和中和抗体效价的半微量空斑法。小牛血清与胎牛血清的培养效果无差异。7株不同来源的出血热病毒均能在E6细胞上形成空斑。接种的病毒浓度与形成的空斑数呈直线关系。用空斑法测得的病毒滴度稍低于荧光TCIE50滴定法。空斑减少中和试验的敏感性较荧光中和试验高30倍左右。同时还初步表明了本方法可用于流行性出血热病毒的抗原性分析。     

Ebola and Marburg virus diseases in Africa: Increased risk of outbreaks in previously unaffected areas?

Filoviral hemorrhagic fever (FHF) is caused by ebolaviruses and marburgviruses, which both belong to the family Filoviridae. Egyptian fruit bats (Rousettus aegyptiacus) are the most likely natural reservoir for marburgviruses and entry into caves and mines that they stay in has often been associated with outbreaks of MVD. On the other hand, the natural reservoir for ebola viruses remains elusive; however, handling of wild animal carcasses has been associated with some outbreaks of EVD. In the last two decades, there has been an increase in the incidence of FHF outbreaks in Africa, some being caused by a newly found virus and some occurring in previously unaffected areas such as Guinea, Liberia and Sierra Leone, in which the most recent EVD outbreak occurred in 2014. Indeed, the predicted geographic distribution of filoviruses and their potential reservoirs in Africa includes many countries in which FHF has not been reported. To minimize the risk of virus dissemination in previously unaffected areas, there is a need for increased investment in health infrastructure in African countries, policies to facilitate collaboration between health authorities from different countries, implementation of outbreak control measures by relevant multi‐disciplinary teams and education of the populations at risk.     

流行性出血热病毒感染NIH裸鼠免疫组织化学研究

流行性出血热病毒（ＥｐｉｄｅｍｉｃＨｅｍｏｒｒｈａｇｉｃＦｅｖｅｒｖｉｒｕｓ,ＥＨＦＶ）感染ＮＩＨ裸鼠后,濒死状态取材,应用免疫组织化学方法（ＡＢＣ）检测各组织中的特异性病毒抗原。结果表明,ＮＩＨ裸鼠对ＥＨＦＶ感染敏感,感染后其脑、肺、肝、肾和心脏组织实质细胞浆内均可检出特异性抗原。     

流行性出血热病毒沙鼠肾细胞培养灭活疫苗免疫家兔的抗体反应及保护试验

利用自流行性出血热(EHF)病人血液中分离的EHF病毒浙10株,感染长爪沙鼠肾单层细胞,经培养后,按流行性乙型脑炎的生物制品法规要求研制成灭活疫苗。取1ml经肌肉免疫家兔,6天后即可在血液中检出荧光抗体,至第14～21天为最高峰,荧光抗体效价可达320～2560。经活EHF病毒攻击,有明显的保护作用,保护率达90％以上。疫苗经1:10或1:30稀释后免疫家兔,荧光抗体阳转率仍达100％,但抗体滴度明显降低。肌肉接种优于皮下接种。本研究证明,甲醛灭活EHF病毒可破坏血凝素活性,从而影响疫苗血凝抑制抗体的产生,可能也会影响中和病毒的能力。     

Sequence analysis of sub-genotype D hepatitis B surface antigens isolated from Jeddah,Saudi Arabia

Little is known about the prevalence of HBV genotypes/sub-genotypes in Jeddah province, although the hepatitis B virus (HBV) was identified as the most predominant type of hepatitis in Saudi Arabia. To characterize HBV genotypes/sub-genotypes, serum samples from 15 patients with chronic HBV were collected and subjected to HBsAg gene amplification and sequence analysis. Phylogenetic analysis of the HBsAg gene sequences revealed that 11 (48%) isolates belonged to HBV/D while 4 (18%) were associated with HBV/C. Notably, a HBV/D sub-genotype phylogenetic tree identified that eight current isolates (72%) belonged to HBV/D1, whereas three isolates (28%) appeared to be more closely related to HBV/D5, although they formed a novel cluster supported by a branch with 99% bootstrap value. Isolates belonging to D1 were grouped in one branch and seemed to be more closely related to various strains isolated from different countries. For further determination of whether the three current isolates belonged to HBV/D5 or represented a novel sub-genotype, HBV/DA, whole HBV genome sequences would be required. In the present study, we verified that HBV/D1 is the most prevalent HBV sub-genotype in Jeddah, and identified novel variant mutations suggesting that an additional sub-genotype designated HBV/DA should be proposed. Overall, the results of the present HBsAg sequence analyses provide us with insights regarding the nucleotide differences between the present HBsAg/D isolates identified in the populace of Jeddah, Saudi Arabia and those previously isolated worldwide. Additional studies with large numbers of subjects in other areas might lead to the discovery of the specific HBV strain genotypes or even additional new sub-genotypes that are circulating in Saudi Arabia.     

Phytophagous and predaceous mites associated with vegetable crops from Riyadh,Saudi Arabia

This study was conducted to investigate phytophagous and predatory mites associated with vegetable plants in Riyadh, Saudi Arabia. Eight phytophagous and 10 predacious mites were collected from 14 species of vegetable crops covering five major production localities. Out of these 18 mite species, 13 species are new to the mite fauna of Saudi Arabia. In addition, the two species, Tenuipalpus punicae and Agistemus exsertus, are reported for the first time on vegetable crops in Saudi Arabia. For each mite species found, notes on host plant association and occurrence period are given. An illustrated key for the identification of the 18 mite species reported in this study is provided and this can be used to improve the IPM programs by applying the local natural predatory mites in controlling mite pests in Saudi Arabia.