Crimean-Congo Hemorrhagic Fever (CCHF) in Pakistan: The Daunting Threat of an Outbreak as Eid-ul-Azha Approaches.

The Crimean-Congo hemorrhagic fever (CCHF) virus is a tick-borne virus that can spread from infected people and other animals, including cattle and ticks of the Hyalomma genus. People who are infected describe symptoms that range from flu-like manifestations to severe multi-organ failure. With a death rate between 10% and 30%, the virus is undoubtedly a disease of high concern. With 10,000-15,000 cases/y, it is endemic in parts of Asia, Africa, and South-Eastern Europe. There has been a recent CCHF outbreak in Iraq, with 212 cases documented, 80% of which were reported between April and May and led to 27 fatalities.

Potentially Zoonotic Viruses in Wild Rodents, United Arab Emirates, 2019-A Pilot Study.

The majority of emerging viral infectious diseases in humans originate from wildlife reservoirs, such as rodents and bats. We investigated a possible reservoir, namely wild gerbils and mice trapped in a desert reserve within the emirate of Dubai, United Arab Emirates (UAE). In total, 52 gerbils and 1 jird (Gerbillinae), 10 house mice (Mus musculus), and 1 Arabian spiny mouse (Acomys dimidiatus) were sampled. Oro-pharyngeal swabs, fecal samples, attached ticks, and organ samples (where available) were screened by (RT-q)PCR for the following viruses: Middle East respiratory syndrome-related coronavirus, Crimean-Congo hemorrhagic fever orthonairovirus, Alkhumra hemorrhagic fever virus, hantaviruses, Lymphocytic choriomeningitis mammarenavirus, Rustrela virus, poxviruses, flaviviruses, and herpesviruses. All of the samples were negative for all investigated viruses, except for herpesviruses: 19 gerbils (35.8%) and seven house mice (70.0%) were positive. The resulting sequences were only partly identical to sequences in GenBank. Phylogenetic analysis revealed three novel betaherpesviruses and four novel gammaherpesviruses. Interestingly, species identification of the positive gerbils resulted in eight individuals clustering in a separate clade, most closely related to Dipodillus campestris, the North African gerbil, indicating either the expansion of the geographic range of this species, or the existence of a closely related, yet undiscovered species in the UAE. In conclusion, we could not find evidence of persistence or shedding of potentially zoonotic viruses in the investigated rodent cohorts of limited sample size.

[The Importance of Differential Diagnosis During Pandemic: A Case Report with Coexistence of COVID-19, Brucellosis and Crimean-Congo Hemorrhagic Fever]. / Pandemi Döneminde Ayirici Taninin Önemi: COVID-19, Bruselloz ve Kirim-Kongo Kanamali Atesi Birlikteligi Olan Bir Olgu Sunumu.

The coronavirus disease-2019 (COVID-19) pandemic, which affects millions of people around the world, has been affecting our country since March 2020. The fact that the symptoms such as fever, myalgia, headache, joint pain which are common in COVID-19 patients are quite similar to the symptoms of diseases such as Crimean-Congo hemorrhagic fever (CCHF) and Brucellosis. This may cause a diagnostic confusion in regions where these diseases are seen as endemic. In this report, a patient hospitalized with a pre-diagnosis of COVID-19 and diagnosed with acute Brucellosis, CCHF and COVID-19 during followup was presented. A 31-year-old female patient living in a rural area admitted to the emergency service with complaints of fever, weakness, headache, and body/joint pain. Physical examination revealed a temperature of 38.3°C, a pulse rate of 102/minute, and a peripheral capillary oxygen saturation of 97% in room air. The system examination was normal. In the laboratory findings, an increase in liver enzymes and acute phase reactants was observed and the platelet count was at the lower limit of the normal range. In terms of COVID-19, no involvement compatible with COVID-19 was detected in the thorax computed tomography (CT) of the patient whose nasopharyngeal and oropharyngeal mixed swab samples were taken.The patient was transferred to our infectious diseases service with a pre-diagnosis of COVID-19 and CCHF. Serum samples were sent to the Public Health Agency Microbiology Reference Laboratory Department (PHA-MRLD) for CCHF diagnostic tests and supportive treatment was started. Brucella Rose Bengal and Coombs' immuncapture (1/1280 titer) tests were found as positive in the patient, who was examined for brucellosis because of living in a rural area and having a history of consuming fresh dairy products. In the tests performed at PHA-MRLD, CCHF-specific IgM positivity and the presence of viral RNA were detected. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) reverse-transcriptase polymerase chain reaction (RT-PCR) test was negative. For Brucellosis, doxycycline and rifampicin were added to the treatment of the patient whom was given supportive therapy for CCHF. In the followup, the patient's fever was persisting and loss of taste and smell complaint developed. In this context, COVID-19 test was repeated and resulted as positive. Upon this, hydroxychloroquine sulfate treatment was started due to the recommendation of the current Ministry of Health Scientific Committee Guide. No new infiltration was detected in the chest radiography of the patient. The patient's fever subsided during follow-up and laboratory findings improved. The treatment of brucellosis was completed to eight weeks at the outpatient clinic. No problems were detected in the follow-up. This report was prepared because of a case with simultaneous brucellosis, CCHF and COVID-19 infections which could not be encountered in the literature review. As a result; in regions such as our country where both brucellosis and CCHF are seen as endemic, it is very important to keep these diseases in mind in the differential diagnosis of COVID-19 infection.

Prevalence of IgG and IgM to SARS-CoV-2 and other human coronaviruses in The Democratic Republic of Congo, Sierra Leone and Uganda: A Longitudinal Study (preprint)

Objectives We assessed the prevalence of immunoglobulin G (IgG) and immunoglobulin M (IgM) against four endemic human coronaviruses (HCoVs) and two SARS-CoV-2 antigens, among vaccinated and unvaccinated staff at health care centres in Uganda, Sierra Leone, and the Democratic Republic of Congo (DRC). Methods Government health facility staff who had patient contact in Goma (DRC), Kambia District (Sierra Leone), and Masaka District (Uganda) were enrolled. Questionnaires and blood samples were collected at three timepoints over four months. Blood samples were analysed with the Luminex MAGPIX. Results Among unvaccinated participants, the prevalence of IgG/IgM antibodies against SARS-CoV-2 RBD or N-protein at enrolment was 70% in Goma (138/196), 89% in Kambia (112/126) and 89% in Masaka (190/213). IgG responses against endemic HCoVs at baseline were not associated with SAR-CoV-2 sero-acquisition during follow-up. Among vaccinated participants, those who had evidence of SARS-CoV-2 IgG/IgM at baseline tended to have higher IgG responses to vaccination compared to those SARS-CoV-2 seronegative at baseline, controlling for the time of sample collection since vaccination. Conclusions The high levels of natural immunity and hybrid immunity should be incorporated into both vaccination policy and prediction models of the impact of subsequent waves of infection in these settings.

Changing Disease Course of Crimean-Congo Hemorrhagic Fever in Children, Turkey.

Crimean-Congo hemorrhagic fever (CCHF), endemic in certain regions of the world, is listed as a priority disease with pandemic potential. Since CCHF was first identified in Turkey, children have been known to experience milder disease than adults. However, during the COVID-19 pandemic, we observed an unusually severe disease course, including hemophagocytic lymphohistiocytosis (HLH). We examined cytokine/chemokine profiles of 9/12 case-patients compared with healthy controls at 3 time intervals. Interferon pathway-related cytokines/chemokines, including interleukin (IL) 18, macrophage inflammatory protein 3α, and IL-33, were elevated, but tumor necrosis factor-α, IL-6, CXCL8 (formerly IL-8), and cytokines acting through C-C chemokine receptor 2 and CCR5 were lower among case-patients than controls. Interferon pathway activation and cytokines/chemokines acting through CCR2 and CCR5 improved health results among children with severe CCHF. Children can experience severe CCHF, including HLH, and HLH secondary to CCHF can be successfully treated with intravenous immunoglobulin and steroid therapy.

The Prevalence of Viral Pathogens among Bats in Kazakhstan.

Bats carry thousands of viruses from 28 different families. To determine the presence of various pathogens in bat populations in Kazakhstan, 1149 samples (393 oropharyngeal swabs, 349 brain samples, 407 guano) were collected. The samples were collected from four species of bats (Vespertilio murinus, Nyctalus noctula, Myotis blythii, Eptesicus serotinus) in nine regions. The Coronavirus RNA was found in 38 (4.75%) samples, and the rabies virus in 27 (7.74%) samples from bats. Coronaviruses and the rabies virus were found in bats in six out of nine studied areas. The RNAs of SARS-CoV-2, MERS, TBE, CCHF, WNF, influenza A viruses were not detected in the bat samples. The phylogeny of the RdRp gene of 12 samples made it possible to classify them as alphacoronaviruses and divide them into two groups. The main group (n = 11) was closely related to bat coronaviruses from Ghana, Zimbabwe and Kenya. The second group (n = 1) was closely related to viruses previously isolated in the south of Kazakhstan. The phylogeny of the N gene sequence from a bat from west Kazakhstan revealed its close relationship with isolates from the Cosmopolitan group of rabies viruses (Central Asia). These results highlight the need for a continuous monitoring of volatile populations to improve the surveillance and detection of infectious diseases.

Crimean-Congo Hemorrhagic Fever Outbreak in Refugee Settlement during COVID-19 Pandemic, Uganda, April 2021.

Crimean-Congo hemorrhagic fever (CCHF) was detected in 2 refugees living in a refugee settlement in Kikuube district, Uganda. Investigations revealed a CCHF IgG seroprevalence of 71.3% (37/52) in goats within the refugee settlement. This finding highlights the need for a multisectoral approach to controlling CCHF in humans and animals in Uganda.

Crimean Congo Hemorrhagic Fever Epidemic During COVID-19 in Iraq: A “double whammy”? (preprint)

The Nairovirus causing the Crimean Congo Hemorrhagic Fever (CCHF) is transferred mainly via ticks and farm animals. Its incidence is spread over several countries broadly categorized into continents, including Europe, Asia, and Africa. This editorial is shedding light on this concerning pathogen and suggesting several strategies to tackle it.

Degenerate sequence-based CRISPR diagnostic for Crimean-Congo hemorrhagic fever virus.

CRISPR (clustered regularly interspaced short palindromic repeats), an ancient defense mechanism used by prokaryotes to cleave nucleic acids from invading viruses and plasmids, is currently being harnessed by researchers worldwide to develop new point-of-need diagnostics. In CRISPR diagnostics, a CRISPR RNA (crRNA) containing a "spacer" sequence that specifically complements with the target nucleic acid sequence guides the activation of a CRISPR effector protein (Cas13a, Cas12a or Cas12b), leading to collateral cleavage of RNA or DNA reporters and enormous signal amplification. CRISPR function can be disrupted by some types of sequence mismatches between the spacer and target, according to previous studies. This poses a potential challenge in the detection of variable targets such as RNA viruses with a high degree of sequence diversity, since mismatches can result from target variations. To cover viral diversity, we propose in this study that during crRNA synthesis mixed nucleotide types (degenerate sequences) can be introduced into the spacer sequence positions corresponding to viral sequence variations. We test this crRNA design strategy in the context of the Cas13a-based SHERLOCK (specific high-sensitivity enzymatic reporter unlocking) technology for detection of Crimean-Congo hemorrhagic fever virus (CCHFV), a biosafety level 4 pathogen with wide geographic distribution and broad sequence variability. The degenerate-sequence CRISPR diagnostic proves functional, sensitive, specific and rapid. It detects within 30-40 minutes 1 copy/µl of viral RNA from CCHFV strains representing all clades, and from more recently identified strains with new mutations in the CRISPR target region. Also importantly, it shows no cross-reactivity with a variety of CCHFV-related viruses. This proof-of-concept study demonstrates that the degenerate sequence-based CRISPR diagnostic is a promising tool of choice for effective detection of highly variable viral pathogens.

Multi-omics insights into host-viral response and pathogenesis in Crimean-Congo hemorrhagic fever viruses for novel therapeutic target.

The pathogenesis and host-viral interactions of the Crimean-Congo hemorrhagic fever orthonairovirus (CCHFV) are convoluted and not well evaluated. Application of the multi-omics system biology approaches, including biological network analysis in elucidating the complex host-viral response, interrogates the viral pathogenesis. The present study aimed to fingerprint the system-level alterations during acute CCHFV-infection and the cellular immune responses during productive CCHFV-replication in vitro. We used system-wide network-based system biology analysis of peripheral blood mononuclear cells (PBMCs) from a longitudinal cohort of CCHF patients during the acute phase of infection and after one year of recovery (convalescent phase) followed by untargeted quantitative proteomics analysis of the most permissive CCHFV-infected Huh7 and SW13 cells. In the RNAseq analysis of the PBMCs, comparing the acute and convalescent-phase, we observed system-level host's metabolic reprogramming towards central carbon and energy metabolism (CCEM) with distinct upregulation of oxidative phosphorylation (OXPHOS) during CCHFV-infection. Upon application of network-based system biology methods, negative coordination of the biological signaling systems like FOXO/Notch axis and Akt/mTOR/HIF-1 signaling with metabolic pathways during CCHFV-infection were observed. The temporal quantitative proteomics in Huh7 showed a dynamic change in the CCEM over time and concordant with the cross-sectional proteomics in SW13 cells. By blocking the two key CCEM pathways, glycolysis and glutaminolysis, viral replication was inhibited in vitro. Activation of key interferon stimulating genes during infection suggested the role of type I and II interferon-mediated antiviral mechanisms both at the system level and during progressive replication.

Crimean-Congo hemorrhagic fever (CCHF) is an emerging disease that is increasingly spreading to new populations. The condition is now endemic in almost 30 countries in sub-Saharan Africa, South-Eastern Europe, the Middle East and Central Asia. CCHF is caused by a tick-borne virus and can cause uncontrolled bleeding. It has a mortality rate of up to 40%, and there are currently no vaccines or effective treatments available. All viruses depend entirely on their hosts for reproduction, and they achieve this through hijacking the molecular machinery of the cells they infect. However, little is known about how the CCHF virus does this and how the cells respond. To understand more about the relationship between the cell's metabolism and viral replication, Neogi, Elaldi et al. studied immune cells taken from patients during an infection and one year later. The gene activity of the cells showed that the virus prefers to hijack processes known as central carbon and energy metabolism. These are the main regulator of the cellular energy supply and the production of essential chemicals. By using cancer drugs to block these key pathways, Neogi, Elaldi et al. could reduce the viral reproduction in laboratory cells. These findings provide a clearer understanding of how the CCHF virus replicates inside human cells. By interfering with these processes, researchers could develop new antiviral strategies to treat the disease. One of the cancer drugs tested in cells, 2-DG, has been approved for emergency use against COVID-19 in some countries. Neogi, Elaldi et al. are now studying this further in animals with the hope of reaching clinical trials in the future.

Emerging and re-emerging viral infections in India.

The number of outbreaks have progressively increased since many years in India. In this era of globalization and rapid international travel, any infectious disease in one country can become a potential threat to the entire globe. Outbreaks of Nipah, Zika, Crimean-Congo Haemorrhagic Fever and Kyasanur Forest Disease have been reported since a decade and now we are facing COVID-19 pandemic. One of the challenges in the prevention of these outbreaks is that as the cases decrease, the felt need declines, the public demand decreases and the mitigation responses get overshadowed by the need of emergency responses elsewhere. The One Health approach is a movement to promote alliance between medicine field, veterinary medicine and environmental sciences to upgrade the health of humans, animals, and ecosystem. The data in this article is compiled from different websites and publications of World Health Organization (WHO), Centre for Disease Control and Prevention (CDC), Integrated Disease Surveillance Programme (IDSP), grey literature and media. There is an urgent need for better surveillance and disease burden assessments in the country and to gain detailed insights into vector biology, factors of environment influencing the diseases, mapping of endemic areas, strengthen intersectoral coordination, infection control practices, and ensure use of Personal Protective Equipment's (PPE) and availability of drugs and vaccines to handle the outbreaks in a better way.

Crimean Congo hemorrhagic fever in the COVID-19 pandemic: a case study (preprint)

In the COVID-19 pandemic, the overlap of clinical features between the other viral infections, make a reliable diagnosis difficult in the initial stage of illness. We describe the first confirmed case of CCHF in Tehran province during this year, who first misdiagnosed as COVID-19 infection.

Efficient incorporation and template-dependent polymerase inhibition are major determinants for the broad-spectrum antiviral activity of remdesivir (preprint)

Remdesivir (RDV) is a direct antiviral agent that is approved in several countries for the treatment of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). RDV exhibits broad-spectrum antiviral activity against positive-sense RNA viruses, e.g., SARS-CoV-2 and hepatitis C virus (HCV) and non-segmented negative-sense RNA viruses, e.g., Nipah virus (NiV), while several segmented negative-sense RNA viruses such as influenza (Flu) virus or Crimean-Congo hemorrhagic fever virus (CCHFV) are not sensitive to the drug. The reasons for this apparent pattern are unknown. Here, we expressed and purified representative RNA-dependent RNA polymerases (RdRp) and studied three biochemical parameters that have been associated with the inhibitory effects of RDV-triphosphate (TP): (i) selective incorporation of the nucleotide substrate RDV-TP, (ii) the effect of the incorporated RDV-monophosphate (MP) on primer extension, and (iii) the effect of RDV-MP in the template during incorporation of the complementary UTP. The results of this study revealed a strong correlation between antiviral effects and efficient incorporation of RDV-TP. Delayed chain-termination is heterogeneous and usually inefficient at higher NTP concentrations. In contrast, template-dependent inhibition of UTP incorporation opposite the embedded RDV-MP is seen with all polymerases. Molecular modeling suggests a steric conflict between the 1'-cyano group of RDV-MP and conserved residues of RdRp motif F. We conclude that future efforts in the development of nucleotide analogues with a broader spectrum of antiviral activities should focus on improving rates of incorporation while capitalizing on the inhibitory effects of a bulky 1'-modification.

Crimean-Congo Hemorrhagic Fever Virus: Current Advances and Future Prospects of Antiviral Strategies.

Crimean-Congo hemorrhagic fever virus (CCHFV) is a widespread, tick-borne pathogen that causes Crimean-Congo hemorrhagic fever (CCHF) with high morbidity and mortality. CCHFV is transmitted to humans through tick bites or direct contact with patients or infected animals with viremia. Currently, climate change and globalization have increased the transmission risk of this biosafety level (BSL)-4 virus. The treatment options of CCHFV infection remain limited and there is no FDA-approved vaccine or specific antivirals, which urges the identification of potential therapeutic targets and the design of CCHF therapies with greater effort. In this article, we discuss the current progress and some future directions in the development of antiviral strategies against CCHFV.

Cross-Reactivity of SARS-CoV-2 Laboratory Diagnostics to Endemic Diseases in Africa: A Diagnostic Accuracy Study (preprint)

Background: Serology is a great tool to assess the level of immunity against SARS-CoV-2 in settings with limited access to molecular diagnostics. However, African populations displays a particular immunological profile with massive circulation of infectious agents from different aetiologies that can affect assays performance.Methods: We evaluated the OMEGA Diagnostics COVID-19 ELISA-IgG and the ID Screen® SARS-CoV-2-N IgG Indirect in Senegal using a panel of 636 blood samples covering several African-endemic diseases and healthy donors to determine test sensitivity and specificity. The sensitivity panel of sera includes 461 serum samples collected from 91 patients hospitalized for COVID-19 disease. COVID-19 cases were confirmed by qRT-PCR and samples were collected on an interval of three days until viral clearance. In addition, 272 sera obtained from COVID-19 negative individuals were selected from a well-documented biobank of sera collected before the COVID-19 outbreak.Finding: High-cross reactivity have been found in individuals with a history of exposure to Chikungunya, HIV, malaria (Plasmodium falciparum), rheumatoid factor as well as healthy donors with respective specificities of 55%, 41.8%, 70%, 70% and 75%. ELISA experiments with commercial assays targeting either SARS-CoV-2 Nucleocapsid protein and Spike 2 protein or nucleocapsid protein only suggest that cross-reactivity might be directed against Spike 2 protein and not Nucleocapsid protein. Further samples characterisation reveals that anti-malaria IgG is the leading cause of such poor specificities, but exposure to other diseases contributed as well.Interpretation: We anticipate that COVID-19 seroprevalence can be biased if assays are not contextualized. Since malaria is endemic in African settings, we propose that a particular attention must be given in serological surveillance of COVID-19 or anti-SARS-CoV-2 antibodies quantification as vaccines are being rolled out.FundingUK Foreign, Commonwealth and Development Office/Wellcome Trust Joint Initiative for Research in Epidemic Preparedness and Response (JIREP grant number 220764/Z/20/Z).Funding Information: UK Foreign, Commonwealth and Development Office/Wellcome Trust Joint Initiative for Research in Epidemic Preparedness and Response (JIREP grant number 220764/Z/20/Z).Declaration of Interests: JRAF was an employee of Mologic Ltd, which was the development partner of one of the ELISAs adopted in this study. The remaining authors declare no competing interest.Ethics Approval Statement: Pre-COVID-19 samples for malaria (PCR), dengue, yellow fever, Zika, Chikungunya, Influenza A/B, HIV, rheumatoid arthritis and samples tested negative for the same diseases and also Crimean Congo haemorrhagic fever, West Nile fever encephalitis and Rift Valley fever were part of national public health surveillance program of the Senegalese Ministry of Social Action and Health performed in collaboration with Institut Pasteur de Dakar. Therefore, consultation with ethics committee was not required. Pre-COVID-19 samples for malaria endemic areas were from a longitudinal cohort survey performed in Dielmo village and approved by the Senegalese National Ethics Committee for Research in Health (reference number 00000007/MSAS/CNERS/Sec 26 January 2021). Samples from COVID-19 RT-PCR positive patients were obtained from a multicentre cohort survey approved by the Senegalese National Ethics Committee for Research in Health (reference number 00000068/MSAS/CNERS/Sec, 10 April 2020).

The Integration of Human and Veterinary Studies for Better Understanding and Management of Crimean-Congo Haemorrhagic Fever.

Outbreaks that occur as a result of zoonotic spillover from an animal reservoir continue to highlight the importance of studying the disease interface between species. One Health approaches recognise the interdependence of human and animal health and the environmental interplay. Improving the understanding and prevention of zoonotic diseases may be achieved through greater consideration of these relationships, potentially leading to better health outcomes across species. In this review, special emphasis is given on the emerging and outbreak pathogen Crimean-Congo Haemorrhagic Fever virus (CCHFV) that can cause severe disease in humans. We discuss the efforts undertaken to better understand CCHF and the importance of integrating veterinary and human research for this pathogen. Furthermore, we consider the use of closely related nairoviruses to model human disease caused by CCHFV. We discuss intervention approaches with potential application for managing CCHFV spread, and how this concept may benefit both animal and human health.

[COVID-19 Co-infection in a patient with Crimean Congo Hemorrhagic Fever: A Case Report]. / Kirim Kongo Kanamali Atesi Hastasinda COVID-19 Ko-enfeksiyonu: Bir Olgu Sunumu.

Crimean-Congo Hemorrhagic Fever (CCHF) is an acute viral zoonotic disease. Coronavirus disease-2019 (COVID-19) is a newly emerging viral disease and it is caused by "severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)". In this article, a case diagnosed with CCHF and COVID-19 coinfection confirmed by the polymerase chain reaction (PCR) method and its management was presented. A thirtyfive years old female patient admitted to the hospital with the complaint of fever for one day and common body pain. It was learned that three days before the onset of her complaints, she removed a tick adhering to the anterior abdominal wall with no precaution. Her body temperature was 38°C degrees and her respiratory rate was 22 per minute. The leucocyte count was 3660/mm³ and the platelet count was 138.000/mm³. It was determined that prothrombin time was 15.4 seconds, international normalized ratio (INR) was 1.35 seconds, and D-dimer level was 1310 ng/ml. The patient was hospitalized with prediagnosis of CCHF. Supportive treatment was started. On the second day at the clinical follow-up of the patient, complaints of sore throat and cough without sputum started. A combined nasopharyngeal and throat swab sample was taken from the patient because of the suspicion of COVID-19. COVID-19 PCR test result was reported as positive. Favipiravir treatment was started. The CCHF-PCR test, which was studied from the serum sample sent to the Microbiology Reference Laboratories was reported as positive. From the third day of favipiravir treatment; the patient did not have a fever and her complaints regressed. On the ninth day of her hospitalization, she was discharged. In this case; it is important to show that both diseases, especially in regions where CCHF disease is endemic, can be confused due to the similarity of the clinical picture with COVID-19 and to know that they can coexist.