Arthropod-borne infections are a medical and economic threat to humans and livestock. Over the last three decades, several unprecedented viral outbreaks have been recorded in the Western part of the Arabian Peninsula. However, little is known about the circulation and diversity of arthropod-borne viruses in this region. To prepare for new outbreaks of vector-borne diseases, it is important to detect which viruses circulate in each vector population. In this study, we used a metagenomics approach to characterize the RNA virome of ticks infesting dromedary camels (Camelus dromedaries) in Makkah province, Saudi Arabia. Two hundred ticks of species Hyalomma dromedarii (n = 196) and Hyalomma impeltatum (n = 4) were collected from the Alkhurma district in Jeddah and Al-Taif city. Virome analysis showed the presence of several tick-specific viruses and tick-borne viruses associated with severe illness in humans. Some were identified for the first time in the Arabian Peninsula. The human disease-associated viruses detected included Crimean Congo Hemorrhagic fever virus and Tamdy virus (family Nairoviridae), Guertu virus (family Phenuiviridae), and a novel coltivirus that shares similarities with Tarumizu virus, Tai forest reovirus and Kundal virus (family Reoviridae). Furthermore, Alkhurma hemorrhagic virus (Flaviviridae) was detected in two tick pools by specific qPCR. In addition, tick-specific viruses in families Phenuiviridae (phleboviruses), Iflaviridae, Chuviridae, Totiviridae and Flaviviridae (Pestivirus) were detected. The presence of human pathogenetic viruses warrants further efforts in tick surveillance, xenosurveillence, vector control, and sero-epidemiological investigations in human and animal populations to predict, contain and mitigate future outbreaks in the region.
Background SARS-CoV-2 related research has increased in importance worldwide since December 2019. Several new variants of SARS-CoV-2 have emerged globally, of which the most notable and concerning currently are the UK variant B.1.1.7, the South African variant B1.351 and the Brazilian variant P.1. Detecting and monitoring novel variants is essential in SARS-CoV-2 surveillance. While there are several tools for assembling virus genomes and performing lineage analyses to investigate SARS-CoV-2, each is limited to performing singular or a few functions separately. Results Due to the lack of publicly available pipelines, which could perform fast reference-based assemblies on raw SARS-CoV-2 sequences in addition to identifying lineages to detect variants of concern, we have developed an open source bioinformatic pipeline called HAVoC (Helsinki university Analyzer for Variants of Concern). HAVoC can reference assemble raw sequence reads and assign the corresponding lineages to SARS-CoV-2 sequences. Conclusions HAVoC is a pipeline utilizing several bioinformatic tools to perform multiple necessary analyses for investigating genetic variance among SARS-CoV-2 samples. The pipeline is particularly useful for those who need a more accessible and fast tool to detect and monitor the spread of SARS-CoV-2 variants of concern during local outbreaks. HAVoC is currently being used in Finland for monitoring the spread of SARS-CoV-2 variants. HAVoC user manual and source code are available at https://www.helsinki.fi/en/projects/havoc and https://bitbucket.org/auto_cov_pipeline/havoc, respectively.
T he most recent SARS-CoV-2 variant of concern, Omicron (Pango lineage B.1.1.529), was first detected in South Africa (1), although it might have emerged elsewhere, and has since spread globally at an unforeseen speed. Notable examples include a superspreading event in Norway (2) and the rapid increase in incidence in Denmark (3) despite high vaccination coverage (83% of infected persons had received 2-3 vaccine doses). This rapid spread indicates the novel variant's exceptional transmissibility, as well as its potential for reinfection and vaccination breakthrough. We describe the genotypes of cases of Omicron entering Finland from their early spread up to established community transmission through the first week of January 2022. No ethics approval was needed because this study was based on routine CO-VID-19 surveillance data. The study regarding Helsinki University Hospital (HUH) samples was approved by the local ethical and research committee (Helsinki and Uusimaa Hospital District [HUS]; Clinical microbiology of COVID-19: diagnostics, laboratory findings and biorisks; HUS/244/2021). The StudyA total of 99,988 samples found positive for SARS-CoV-2 by reverse transcription PCR, 12.1% of 825,006 total samples tested, were detected in Finland during the study period, November 29, 2021-January 6, 2022 (Figure 1). Weekly positivity rates among persons tested rose from 6.1% of 156,077 in week 48 to 25.6% of 172,451 (3.1% of the Finnish population) in week 52 (https://sampo.thl.fi). In HUS, test positivity increased from 5.0% to 36.7% over the corresponding weeks 48-52. After a change in testing strategy favoring home antigen testing, the number of registered SARS-CoV-2 cases dropped (Appendix, https://wwwnc.cdc.gov/ EID/article/28/6/22-0515-App1.pdf).We estimated the proportions of Omicron variant lineages BA.1 and BA.1.1 within HUS by comparing PCR-based data on S-gene target failure (SGTF) to that of other circulating lineages (Figure 1; Appendix). The results showed a decrease in SGTF rates from week 24, when the proportion of the Alpha variant (B.1.1.7) was declining, to near 0 when the Delta variant (B.1.617.2) was dominant. This decrease aligns well with sequence-confirmed lineage turnover
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