Sindbis Virus Strains of Divergent Origin Isolated from Humans and Mosquitoes During a Recent Outbreak in Finland

Sindbis virus (SINV) is a mosquito-borne avian hosted virus that is widely distributed in Europe, Africa, Asia, and Oceania. Disease in humans is documented mainly from Northern Europe and South Africa and associated with genotype I. In 2018 under extremely warm climatic conditions, a small outbreak of 71 diagnosed SINV infections was recorded in Finland. We screened 52 mosquito pools (570 mosquitoes) and 223 human sera for SINV with real-time RT-PCR and the positive samples with virus isolation. One SINV strain was isolated from a pool (n = 13) of genusOchlerotatusmosquitoes and three strains from patient serum samples. Complete genome analysis suggested all the isolates to be divergent from one another and related to previous Finnish, Swedish, and German strains. The study provides evidence of SINV strain transfer within Europe across regions with different epidemiological characteristics. Whether these are influenced by different mosquito genera involved in the transmission remains to be studied.Peer reviewe

A novel negevirus isolated from Aedes vexans mosquitoes in Finland

Negeviruses are insect-specific enveloped RNA viruses that have been detected in mosquitoes and sandflies from various geographical locations. Here, we describe a new negevirus from Northern Europe, isolated from pool ofAedes vexansmosquitoes collected in Finland, designated as Mekrijarvi negevirus (MEJNV). MEJNV had a typical negevirus genome organization, is 9,740 nucleotides in length, and has a GC content of 47.53%. The MEJNV genome contains three ORFs, each containing the following identified conserved domains: ORF1 (7,068 nt) encodes a viral methyltransferase, an FtsJ-like methyltransferase, a viral RNA helicase, and an RNA-dependent RNA polymerase, ORF2 (1,242 nt) encodes a putative virion glycoprotein, and ORF3 (660 nt) encodes a putative virion membrane protein. A distinctive feature relative to other currently known negeviruses is a 7-nucleotide-long overlap between ORF1 and ORF2. MEJNV shares the highest sequence identity with Ying Kou virus from China, with 67.71% nucleotide and 75.19% and 59.00% amino acid sequence identity in ORF 1 and ORF 2, respectively. ORF3 had the highest amino acid sequence similarity to Daeseongdong virus 1 and negevirus Nona 1, both with 77.61% identity, and to Ying Kou virus, with 71.22% identity. MEJNV is currently the northernmost negevirus described. Our report supports the view that negeviruses are a globally distributed, diverse group of viruses that can be found from mosquitoes in a wide range of terrestrial biomes from tropical to boreal forests.Peer reviewe

Characterisation of the RNA Virome of Nine Ochlerotatus Species in Finland

RNA viromes of nine commonly encountered Ochlerotatus mosquito species collected around Finland in 2015 and 2017 were studied using next-generation sequencing. Mosquito homogenates were sequenced from 91 pools comprising 16–60 morphologically identified adult females of Oc. cantans, Oc. caspius, Oc. communis, Oc. diantaeus, Oc. excrucians, Oc. hexodontus, Oc. intrudens, Oc. pullatus and Oc. punctor/punctodes. In total 514 viral Reverse dependent RNA polymerase (RdRp) sequences of 159 virus species were recovered, belonging to 25 families or equivalent rank, as follows: Aliusviridae, Aspiviridae, Botybirnavirus, Chrysoviridae, Chuviridae, Endornaviridae, Flaviviridae, Iflaviridae, Negevirus, Partitiviridae, Permutotetraviridae, Phasmaviridae, Phenuiviridae, Picornaviridae, Qinviridae, Quenyavirus, Rhabdoviridae, Sedoreoviridae, Solemoviridae, Spinareoviridae, Togaviridae, Totiviridae, Virgaviridae, Xinmoviridae and Yueviridae. Of these, 147 are tentatively novel viruses. One sequence of Sindbis virus, which causes Pogosta disease in humans, was detected from Oc. communis from Pohjois-Karjala. This study greatly increases the number of mosquito-associated viruses known from Finland and presents the northern-most mosquito-associated viruses in Europe to date

Characterisation of the RNA Virome of Nine Ochlerotatus Species in Finland

RNA viromes of nine commonly encountered Ochlerotatus mosquito species collected around Finland in 2015 and 2017 were studied using next-generation sequencing. Mosquito homogenates were sequenced from 91 pools comprising 16–60 morphologically identified adult females of Oc. cantans, Oc. caspius, Oc. communis, Oc. diantaeus, Oc. excrucians, Oc. hexodontus, Oc. intrudens, Oc. pullatus and Oc. punctor/punctodes. In total 514 viral Reverse dependent RNA polymerase (RdRp) sequences of 159 virus species were recovered, belonging to 25 families or equivalent rank, as follows: Aliusviridae, Aspiviridae, Botybirnavirus, Chrysoviridae, Chuviridae, Endornaviridae, Flaviviridae, Iflaviridae, Negevirus, Partitiviridae, Permutotetraviridae, Phasmaviridae, Phenuiviridae, Picornaviridae, Qinviridae, Quenyavirus, Rhabdoviridae, Sedoreoviridae, Solemoviridae, Spinareoviridae, Togaviridae, Totiviridae, Virgaviridae, Xinmoviridae and Yueviridae. Of these, 147 are tentatively novel viruses. One sequence of Sindbis virus, which causes Pogosta disease in humans, was detected from Oc. communis from Pohjois-Karjala. This study greatly increases the number of mosquito-associated viruses known from Finland and presents the northern-most mosquito-associated viruses in Europe to date

Seroevidence of Zoonotic Viruses in Rodents and Humans in Kibera Informal Settlement, Nairobi, Kenya

Rodents are known reservoir hosts for a number of pathogens that can spillover into humans and cause disease. These threats are likely to be elevated in informal urban settlements (i.e., slums), where rodent and human densities are often high, rodents live in close proximity to humans, and human knowledge of disease risks and access to health care is often limited. While recent research attention has focused on zoonotic risks posed by urban rodents in major cities around the world, informal urban settlements have received far less attention. Here we report on a study in which samples were collected from 195 commensal rodents and 124 febrile human patients in the Kibera informal settlement in Nairobi, Kenya (one of the largest informal urban settlements in the world). Using immunofluorescence assays, samples were screened for antibodies against common rodent-borne zoonotic virus groups, namely orthopoxviruses, arenaviruses, and hantaviruses. We detected antibodies against orthopoxviruses in rodents (4.1% positive) and antibodies in humans against orthopoxviruses, arenaviruses, and hantaviruses (4.8%, 3.2%, and 8.1% positive, respectively). No rodents had antibodies against arenaviruses or hantaviruses. These results provide strong evidence for the circulation of zoonotic viruses in rodents and humans in Kibera urban settlement, but discordance between viruses detected in host groups indicates that other species or taxa may also serve as reservoirs for these zoonotic viruses or that humans testing positive could have been exposed outside of the Kibera settlement. More broadly, this study highlights the threat posed by zoonotic viruses in informal urban settlements and the need to mitigate human exposure risks.Peer reviewe

Dengue in Travelers: Kinetics of Viremia and NS1 Antigenemia and Their Associations with Clinical Parameters

Peer reviewe

Sindbis virus outbreak and evidence for geographical expansion in Finland, 2021

Sindbis virus (SINV) caused a large outbreak in Finland in 2021 with 566 laboratory-confirmed human cases and a notable geographical expansion. Compared with the last large outbreak in 2002, incidence was higher in several hospital districts but lower in traditionally endemic locations in eastern parts of the country. A high incidence is also expected in 2022. Awareness of SINV should be raised in Finland to increase recognition of the disease and prevent transmission through the promotion of control measures.Peer reviewe

Seroevidence of Zoonotic Viruses in Rodents and Humans in Kibera Informal Settlement, Nairobi, Kenya

Rodents are known reservoir hosts for a number of pathogens that can spillover into humans and cause disease. These threats are likely to be elevated in informal urban settlements (i.e., slums), where rodent and human densities are often high, rodents live in close proximity to humans, and human knowledge of disease risks and access to health care is often limited. While recent research attention has focused on zoonotic risks posed by urban rodents in major cities around the world, informal urban settlements have received far less attention. Here we report on a study in which samples were collected from 195 commensal rodents and 124 febrile human patients in the Kibera informal settlement in Nairobi, Kenya (one of the largest informal urban settlements in the world). Using immunofluorescence assays, samples were screened for antibodies against common rodent-borne zoonotic virus groups, namely orthopoxviruses, arenaviruses, and hantaviruses. We detected antibodies against orthopoxviruses in rodents (4.1% positive) and antibodies in humans against orthopoxviruses, arenaviruses, and hantaviruses (4.8%, 3.2%, and 8.1% positive, respectively). No rodents had antibodies against arenaviruses or hantaviruses. These results provide strong evidence for the circulation of zoonotic viruses in rodents and humans in Kibera urban settlement, but discordance between viruses detected in host groups indicates that other species or taxa may also serve as reservoirs for these zoonotic viruses or that humans testing positive could have been exposed outside of the Kibera settlement. More broadly, this study highlights the threat posed by zoonotic viruses in informal urban settlements and the need to mitigate human exposure risks.Peer reviewe

Detection of dengue virus type 2 of Indian origin in acute febrile patients in rural Kenya

Dengue virus (DENV) has caused recent outbreaks in coastal cities of Kenya, but the epidemiological situation in other areas of Kenya is largely unknown. We investigated the role of DENV infection as a cause of acute febrile disease in non-epidemic settings in rural and urban study areas in Kenya. Altogether, 560 patients were sampled in 2016-2017 in rural Taita-Taveta County (n = 327) and urban slums of Kibera, Nairobi (n = 233). The samples were studied for DENV IgM, IgG, NS1 antigen and flaviviral RNA. IgG seroprevalence was found to be higher in Taita-Taveta (14%) than in Nairobi (3%). Five Taita-Taveta patients were positive for flaviviral RNA, all identified as DENV-2, cosmopolitan genotype. Local transmission in Taita-Taveta was suspected in a patient without travel history. The sequence analysis suggested that DENV-2 strains circulating in coastal and southern Kenya likely arose from a single introduction from India. The molecular clock analyses dated the most recent ancestor to the Kenyan strains a year before the large 2013 outbreak in Mombasa. After this, the virus has been detected in Kilifi in 2014, from our patients in Taita-Taveta in 2016, and in an outbreak in Malindi in 2017. The results highlight that silent transmission occurs between epidemics and also affects rural areas. More information is needed to understand the local epidemiological characteristics and future risks of dengue in Kenya. Author summary Dengue virus (DENV) is an emerging mosquito-borne global health threat in the tropics and subtropics. The majority of the world's population live in areas at risk of dengue that can cause a wide variety of symptoms from febrile illness to haemorrhagic fever. Information of DENV in Africa is limited and fragmented. In Kenya, dengue is a recognized disease in coastal cities that have experienced recent outbreaks. We investigated the role of DENV infection as a cause of acute febrile disease in non-epidemic settings in rural and urban study areas in Kenya. We found DENV-2 in five febrile patients from rural Taita-Taveta, where no dengue has been reported before. Genetic analysis of the virus suggests it to be most likely of Indian origin. This Indian origin DENV-2 was detected in the Mombasa outbreak in 2013, in Kilifi in 2014, in Taita-Taveta in 2016 (our study samples) and again in the Malindi outbreak in 2017. The results suggest that dengue is unrecognized in rural Kenya and more studies are needed for local risk assessment. Our findings of virus transmission between epidemics contribute to better understanding of the epidemiological situation and origins of DENV in Kenya.Peer reviewe