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Two SARS-CoV-2 Variants of Concern, Alpha (~ 80%) and Beta (~ 23%) rapidly became dominant in Finland in the spring of 2021 but diminished near summer. To assess their temporal epidemiological dynamics among Finnish cases, we began large-scale sequencing efforts to identify spreading events and sources via phylogenetic clustering analyses. The results show the majority belonged to clusters spreading in the community while few sequenced samples were singletons. The results highlight the importance of surveillance and preventative policies in controlling the epidemic.
Ravi Kant; Phuoc Truong Nguyen; Soile Blomqvist; Mert Erdin; Hussein Alburkat; Maija Suvanto; Fathiah Zakham; Veera Salminen; Viktor Olander; Minna Paloniemi; Leena Huhti; Sara Lehtinen; Bruno Luukinen; Hanna Jarva; Hannimari Kallio-Kokko; Satu Kurkela; Maija Lappalainen; Hanna Liimatainen; Sari Hannula; Jani Halkilahti; Jonna Ikonen; Niina Ikonen; Otto Helve; Marianne Gunell; Tytti Vuorinen; Ilya Plyusnin; Erika Lindh; Pekka Ellonen; Tarja Sironen; Carita Savolainen-Kopra; Teemu Smura; Olli Vapalahti. The rise and fall of Alpha and Beta variants of SARS-CoV2 in Finland in spring of 2021. 2021, 1 .
AMA StyleRavi Kant, Phuoc Truong Nguyen, Soile Blomqvist, Mert Erdin, Hussein Alburkat, Maija Suvanto, Fathiah Zakham, Veera Salminen, Viktor Olander, Minna Paloniemi, Leena Huhti, Sara Lehtinen, Bruno Luukinen, Hanna Jarva, Hannimari Kallio-Kokko, Satu Kurkela, Maija Lappalainen, Hanna Liimatainen, Sari Hannula, Jani Halkilahti, Jonna Ikonen, Niina Ikonen, Otto Helve, Marianne Gunell, Tytti Vuorinen, Ilya Plyusnin, Erika Lindh, Pekka Ellonen, Tarja Sironen, Carita Savolainen-Kopra, Teemu Smura, Olli Vapalahti. The rise and fall of Alpha and Beta variants of SARS-CoV2 in Finland in spring of 2021. . 2021; ():1.
Chicago/Turabian StyleRavi Kant; Phuoc Truong Nguyen; Soile Blomqvist; Mert Erdin; Hussein Alburkat; Maija Suvanto; Fathiah Zakham; Veera Salminen; Viktor Olander; Minna Paloniemi; Leena Huhti; Sara Lehtinen; Bruno Luukinen; Hanna Jarva; Hannimari Kallio-Kokko; Satu Kurkela; Maija Lappalainen; Hanna Liimatainen; Sari Hannula; Jani Halkilahti; Jonna Ikonen; Niina Ikonen; Otto Helve; Marianne Gunell; Tytti Vuorinen; Ilya Plyusnin; Erika Lindh; Pekka Ellonen; Tarja Sironen; Carita Savolainen-Kopra; Teemu Smura; Olli Vapalahti. 2021. "The rise and fall of Alpha and Beta variants of SARS-CoV2 in Finland in spring of 2021." , no. : 1.
Finland has had a low incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) infections as compared to most European countries. Here we report the origins and turnover of SARS-CoV-2 lineages circulating in Finland in 2020. SARS-CoV-2 introduced to Finland in January 2020 and spread rapidly across southern Finland during spring. We observed rapid turnover among Finnish lineages during this period. Clade 20C became the most prevalent among sequenced cases and was replaced by other strains in fall 2020. Bayesian phylogeographic reconstructions suggested 42 independent introductions into Finland during spring 2020, mainly from Italy, Austria, and Spain, which might have been the source for a third of cases. The investigations of the original introductions of SARS-CoV-2 to Finland during the early stages of the pandemic and of the subsequent lineage dynamics could be utilized to assess the role of transboundary movements and effects of early intervention and public health measures.
Phuoc Truong Nguyen; Ravi Kant; Frederik Van Den Broeck; Maija T. Suvanto; Hussein Alburkat; Jenni Virtanen; Ella Ahvenainen; Robert Castren; Samuel L. Hong; Guy Baele; Maarit J. Ahava; Hanna Jarva; Suvi Tuulia Jokiranta; Hannimari Kallio-Kokko; Eliisa Kekäläinen; Vesa Kirjavainen; Elisa Kortela; Satu Kurkela; Maija Lappalainen; Hanna Liimatainen; Marc A. Suchard; Sari Hannula; Pekka Ellonen; Tarja Sironen; Philippe Lemey; Olli Vapalahti; Teemu Smura. The phylodynamics of SARS-CoV-2 during 2020 in Finland — Disappearance and re-emergence of introduced strains. 2021, 1 .
AMA StylePhuoc Truong Nguyen, Ravi Kant, Frederik Van Den Broeck, Maija T. Suvanto, Hussein Alburkat, Jenni Virtanen, Ella Ahvenainen, Robert Castren, Samuel L. Hong, Guy Baele, Maarit J. Ahava, Hanna Jarva, Suvi Tuulia Jokiranta, Hannimari Kallio-Kokko, Eliisa Kekäläinen, Vesa Kirjavainen, Elisa Kortela, Satu Kurkela, Maija Lappalainen, Hanna Liimatainen, Marc A. Suchard, Sari Hannula, Pekka Ellonen, Tarja Sironen, Philippe Lemey, Olli Vapalahti, Teemu Smura. The phylodynamics of SARS-CoV-2 during 2020 in Finland — Disappearance and re-emergence of introduced strains. . 2021; ():1.
Chicago/Turabian StylePhuoc Truong Nguyen; Ravi Kant; Frederik Van Den Broeck; Maija T. Suvanto; Hussein Alburkat; Jenni Virtanen; Ella Ahvenainen; Robert Castren; Samuel L. Hong; Guy Baele; Maarit J. Ahava; Hanna Jarva; Suvi Tuulia Jokiranta; Hannimari Kallio-Kokko; Eliisa Kekäläinen; Vesa Kirjavainen; Elisa Kortela; Satu Kurkela; Maija Lappalainen; Hanna Liimatainen; Marc A. Suchard; Sari Hannula; Pekka Ellonen; Tarja Sironen; Philippe Lemey; Olli Vapalahti; Teemu Smura. 2021. "The phylodynamics of SARS-CoV-2 during 2020 in Finland — Disappearance and re-emergence of introduced strains." , no. : 1.
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.
Fathiah Zakham; Aishah Albalawi; Abdullah Alanazi; Phuoc Truong Nguyen; Abdulaziz Alouffi; Altaf Alaoui; Tarja Sironen; Teemu Smura; Olli Vapalahti. Viral RNA Metagenomics of Hyalomma Ticks Collected from Dromedary Camels in Makkah Province, Saudi Arabia. Viruses 2021, 13, 1396 .
AMA StyleFathiah Zakham, Aishah Albalawi, Abdullah Alanazi, Phuoc Truong Nguyen, Abdulaziz Alouffi, Altaf Alaoui, Tarja Sironen, Teemu Smura, Olli Vapalahti. Viral RNA Metagenomics of Hyalomma Ticks Collected from Dromedary Camels in Makkah Province, Saudi Arabia. Viruses. 2021; 13 (7):1396.
Chicago/Turabian StyleFathiah Zakham; Aishah Albalawi; Abdullah Alanazi; Phuoc Truong Nguyen; Abdulaziz Alouffi; Altaf Alaoui; Tarja Sironen; Teemu Smura; Olli Vapalahti. 2021. "Viral RNA Metagenomics of Hyalomma Ticks Collected from Dromedary Camels in Makkah Province, Saudi Arabia." Viruses 13, no. 7: 1396.
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.
Phuoc Thien Truong Nguyen; Ilya Plyusnin; Tarja Sironen; Olli Vapalahti; Ravi Kant; Teemu Smura. HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences. BMC Bioinformatics 2021, 22, 1 -8.
AMA StylePhuoc Thien Truong Nguyen, Ilya Plyusnin, Tarja Sironen, Olli Vapalahti, Ravi Kant, Teemu Smura. HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences. BMC Bioinformatics. 2021; 22 (1):1-8.
Chicago/Turabian StylePhuoc Thien Truong Nguyen; Ilya Plyusnin; Tarja Sironen; Olli Vapalahti; Ravi Kant; Teemu Smura. 2021. "HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences." BMC Bioinformatics 22, no. 1: 1-8.
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains a severe health threat. The COVID-19 infections occurring in humans and animals render human-animal interfaces hot spots for spreading the pandemic. Lessons from the past point towards the antiviral properties of copper formulations; however, data showing the “contact-time limit” surface inhibitory efficacy of copper formulations to contain SARS-CoV-2 are limited. Here, we show the rapid inhibition of SARS-CoV-2 after only 1 and 5 min on two different surfaces containing copper-silver (Cu-Ag) nanohybrids. We characterized the nanohybrids’ powder and surfaces using a series of sophisticated microscopy tools, including transmission and scanning electron microscopes (TEM and SEM) and energy-dispersive X-ray spectroscopy (EDX). We used culturing methods to demonstrate that Cu-Ag nanohybrids with high amounts of Cu (~65 and 78 wt%) and lower amounts of Ag (~7 and 9 wt%) inhibited SARS-CoV-2 efficiently. Collectively, the present work reveals the rapid SARS-CoV-2 surface inhibition and the promising application of such surfaces to break the SARS-CoV-2 transmission chain. For example, such applications could be invaluable within a hospital or live-stock settings, or any public place with surfaces that people frequently touch (i.e., public transportation, shopping malls, elevators, and door handles) after the precise control of different parameters and toxicity evaluations.
Dina Mosselhy; Lauri Kareinen; Ilkka Kivistö; Kirsi Aaltonen; Jenni Virtanen; Yanling Ge; Tarja Sironen. Copper-Silver Nanohybrids: SARS-CoV-2 Inhibitory Surfaces. Nanomaterials 2021, 11, 1820 .
AMA StyleDina Mosselhy, Lauri Kareinen, Ilkka Kivistö, Kirsi Aaltonen, Jenni Virtanen, Yanling Ge, Tarja Sironen. Copper-Silver Nanohybrids: SARS-CoV-2 Inhibitory Surfaces. Nanomaterials. 2021; 11 (7):1820.
Chicago/Turabian StyleDina Mosselhy; Lauri Kareinen; Ilkka Kivistö; Kirsi Aaltonen; Jenni Virtanen; Yanling Ge; Tarja Sironen. 2021. "Copper-Silver Nanohybrids: SARS-CoV-2 Inhibitory Surfaces." Nanomaterials 11, no. 7: 1820.
For the last 13 years, the fur industry in Europe has suffered from epidemic spouts of a severe necrotizing pyoderma. It affects all species currently farmed for fur and causes animal welfare problems and significant losses to the farmers. The causative agent of this disease was identified as Arcanobacterium phocae. Previously, this bacterium has been isolated from seals and other marine mammals, apparently causing wound and lung infections. Attempts at antibiotic treatment have been unsuccessful and the current advice on preventing the disease is to cull all animals with clinical signs. This poses an urgent question regarding possible vaccine development, as well as the need for further understanding of the pathogenicity of this organism. This study compared the whole genomes of 42 A. phocae strains isolated from seals, blue foxes, finnraccoons, mink and otter. The sequences were created using the Illumina technology and annotations were done using the RAST pipeline. A phylogenetic analysis identified a clear separation between the seal strains and the fur-animal-derived isolates, but also indicated that the bacterium readily adapts to new environments and host species with reasonable diversity. A pan- and core-genome was created and analyzed for proteins. A further analysis identified several virulence factors as well as multiple putative and secreted proteins of special interest for vaccine development.
Kirsi J. Aaltonen; Ravi Kant; Nanett Kvist Nikolaisen; Mikkel Lindegaard; Mirja Raunio-Saarnisto; Lars Paulin; Olli Vapalahti; Tarja Sironen. Comparative Genomics of 42 Arcanobacterium phocae Strains. Antibiotics 2021, 10, 740 .
AMA StyleKirsi J. Aaltonen, Ravi Kant, Nanett Kvist Nikolaisen, Mikkel Lindegaard, Mirja Raunio-Saarnisto, Lars Paulin, Olli Vapalahti, Tarja Sironen. Comparative Genomics of 42 Arcanobacterium phocae Strains. Antibiotics. 2021; 10 (6):740.
Chicago/Turabian StyleKirsi J. Aaltonen; Ravi Kant; Nanett Kvist Nikolaisen; Mikkel Lindegaard; Mirja Raunio-Saarnisto; Lars Paulin; Olli Vapalahti; Tarja Sironen. 2021. "Comparative Genomics of 42 Arcanobacterium phocae Strains." Antibiotics 10, no. 6: 740.
Background: Rodents are reservoirs for several zoonotic pathogens that can cause human infectious diseases, including orthohantaviruses, mammarenaviruses and orthopoxviruses. Evidence exists for these viruses circulating among rodents and causing human infections in the Americas, but much less evidence exists for their presence in wild rodents in the Caribbean. Methods: Here, we conducted serological and molecular investigations of wild rodents in Barbados to determine the prevalence of orthohantavirus, mammarenavirus and orthopoxvirus infections, and the possible role of these rodent species as reservoirs of zoonotic pathogens. Using immunofluorescent assays (IFA), rodent sera were screened for the presence of antibodies to orthohantavirus, mammarenavirus (Lymphocytic choriomeningitis virus—LCMV) and orthopoxvirus (Cowpox virus—CPXV) infections. RT-PCR was then conducted on orthohantavirus and mammarenavirus-seropositive rodent sera and tissues, to detect the presence of viral RNA. Results: We identified antibodies against orthohantavirus, mammarenavirus, and orthopoxvirus among wild mice and rats (3.8%, 2.5% and 7.5% seropositivity rates respectively) in Barbados. No orthohantavirus or mammarenavirus viral RNA was detected from seropositive rodent sera or tissues using RT–PCR. Conclusions: Key findings of this study are the first serological evidence of orthohantavirus infections in Mus musculus and the first serological evidence of mammarenavirus and orthopoxvirus infections in Rattus norvegicus and M. musculus in the English-speaking Caribbean. Rodents may present a potential zoonotic and biosecurity risk for transmission of three human pathogens, namely orthohantaviruses, mammarenaviruses and orthopoxviruses in Barbados.
Kirk Douglas; Claire Cayol; Kristian Forbes; Thelma Samuels; Olli Vapalahti; Tarja Sironen; Marquita Gittens-St. Hilaire. Serological Evidence of Multiple Zoonotic Viral Infections among Wild Rodents in Barbados. Pathogens 2021, 10, 663 .
AMA StyleKirk Douglas, Claire Cayol, Kristian Forbes, Thelma Samuels, Olli Vapalahti, Tarja Sironen, Marquita Gittens-St. Hilaire. Serological Evidence of Multiple Zoonotic Viral Infections among Wild Rodents in Barbados. Pathogens. 2021; 10 (6):663.
Chicago/Turabian StyleKirk Douglas; Claire Cayol; Kristian Forbes; Thelma Samuels; Olli Vapalahti; Tarja Sironen; Marquita Gittens-St. Hilaire. 2021. "Serological Evidence of Multiple Zoonotic Viral Infections among Wild Rodents in Barbados." Pathogens 10, no. 6: 663.
Increasing evidence suggests that some newly emerged SARS-CoV-2 variants of concern (VoCs) resist neutralization by antibodies elicited by the early-pandemic wild-type virus. We applied neutralization tests to paired recoveree sera (n = 38) using clinical isolates representing the first wave (D614G), VoC1, and VoC2 lineages (B.1.1.7 and B 1.351). Neutralizing antibodies inhibited contemporary and VoC1 lineages, whereas inhibition of VoC2 was reduced 8-fold, with 50% of sera failing to show neutralization. These results provide evidence for the increased potential of VoC2 to reinfect previously SARS-CoV-infected individuals. The kinetics of NAbs in different patients showed similar decline against all variants, with generally low initial anti-B.1.351 responses becoming undetectable, but with anti-B.1.1.7 NAbs remaining detectable (>20) for months after acute infection.
Jenni Virtanen; Ruut Uusitalo; Essi Korhonen; Kirsi Aaltonen; Teemu Smura; Suvi Kuivanen; Sari Pakkanen; Sointu Mero; Anu Patjas; Marianna Riekkinen; Anu Kantele; Visa Nurmi; Klaus Hedman; Jussi Hepojoki; Tarja Sironen; Eili Huhtamo; Olli Vapalahti. Kinetics of Neutralizing Antibodies of COVID-19 Patients Tested Using Clinical D614G, B.1.1.7, and B 1.351 Isolates in Microneutralization Assays. Viruses 2021, 13, 996 .
AMA StyleJenni Virtanen, Ruut Uusitalo, Essi Korhonen, Kirsi Aaltonen, Teemu Smura, Suvi Kuivanen, Sari Pakkanen, Sointu Mero, Anu Patjas, Marianna Riekkinen, Anu Kantele, Visa Nurmi, Klaus Hedman, Jussi Hepojoki, Tarja Sironen, Eili Huhtamo, Olli Vapalahti. Kinetics of Neutralizing Antibodies of COVID-19 Patients Tested Using Clinical D614G, B.1.1.7, and B 1.351 Isolates in Microneutralization Assays. Viruses. 2021; 13 (6):996.
Chicago/Turabian StyleJenni Virtanen; Ruut Uusitalo; Essi Korhonen; Kirsi Aaltonen; Teemu Smura; Suvi Kuivanen; Sari Pakkanen; Sointu Mero; Anu Patjas; Marianna Riekkinen; Anu Kantele; Visa Nurmi; Klaus Hedman; Jussi Hepojoki; Tarja Sironen; Eili Huhtamo; Olli Vapalahti. 2021. "Kinetics of Neutralizing Antibodies of COVID-19 Patients Tested Using Clinical D614G, B.1.1.7, and B 1.351 Isolates in Microneutralization Assays." Viruses 13, no. 6: 996.
Background: Hantavirus pulmonary syndrome (HPS) is well-known in South and North America; however, not enough data exist for the Caribbean. The first report of clinical orthohantavirus infection was obtained in Barbados, but no other evidence of clinical orthohantavirus infections among adults in the Caribbean has been documented. Methods: Using enzyme linked immunosorbent assay (ELISA) tests followed by confirmatory testing with immunofluorescent assays (IFA), immunochromatographic (ICG) tests, and pseudotype focus reduction neutralization tests (pFRNT), we retrospectively and prospectively detected orthohantavirus-specific antibodies among patients with febrile illness in Barbados. Results: The orthohantavirus prevalence rate varied from 5.8 to 102.6 cases per 100,000 persons among febrile patients who sought medical attention annually between 2008 and 2016. Two major orthohantavirus epidemics occurred in Barbados during 2010 and 2016. Peak orthohantavis infections were observed observed during the rainy season (August) and prevalence rates were significantly higher in females than males and in patients from urban parishes than rural parishes. Conclusions: Orthohantavirus infections are still occurring in Barbados and in some patients along with multiple pathogen infections (CHIKV, ZIKV, DENV and Leptospira). Orthohantavirus infections are more prevalent during periods of high rainfall (rainy season) with peak transmission in August; females are more likely to be infected than males and infections are more likely among patients from urban rather than rural parishes in Barbados.
Kirk Douglas; Thelma Samuels; Rommel Iheozor-Ejiofor; Olli Vapalahti; Tarja Sironen; Marquita Gittens-St. Hilaire. Serological Evidence of Human Orthohantavirus Infections in Barbados, 2008 to 2016. Pathogens 2021, 10, 571 .
AMA StyleKirk Douglas, Thelma Samuels, Rommel Iheozor-Ejiofor, Olli Vapalahti, Tarja Sironen, Marquita Gittens-St. Hilaire. Serological Evidence of Human Orthohantavirus Infections in Barbados, 2008 to 2016. Pathogens. 2021; 10 (5):571.
Chicago/Turabian StyleKirk Douglas; Thelma Samuels; Rommel Iheozor-Ejiofor; Olli Vapalahti; Tarja Sironen; Marquita Gittens-St. Hilaire. 2021. "Serological Evidence of Human Orthohantavirus Infections in Barbados, 2008 to 2016." Pathogens 10, no. 5: 571.
Tuberculosis (TB) is an airborne communicable disease with high morbidity and mortality rates, especially in developing countries. The causal agents of TB belong to the complex Mycobacterium tuberculosis (MTBc), which is composed of different human and animal TB associated species. Some animal associated species have zoonotic potential and add to the burden of TB management. The BCG (“Bacillus Calmette-Guérin”) vaccine is widely used for the prevention against TB, but its use is limited in immunocompromised patients and animals due to the adverse effects and disseminated life-threatening complications. In this study, we aimed to carry out a comparative genome analysis between the human adapted species including BCG vaccine strains to identify and pinpoint the conserved genes related to the virulence across all the species, which could add a new value for vaccine development. For this purpose, the sequences of 183 Mycobacterium tuberculosis (MTB) strains were retrieved from the freely available WGS dataset at NCBI. The species included: 168 sensu stricto MTB species with other human MTB complex associated strains: M. tuberculosis var. africanum (3), M. tuberculosis var. bovis (2 draft genomes) and 10 BCG species, which enabled the analysis of core genome which contains the conserved genes and some virulence factor determinants. Further, a phylogenetic tree was constructed including the genomes of human (183); animals MTB adapted strains (6) and the environmental Mycobacterium strain “M. canettii”. Our results showed that the core genome consists of 1166 conserved genes among these species, which represents a small portion of the pangenome (7036 genes). The remaining genes in the pangenome (5870) are accessory genes, adding a high inter-species diversity. Further, the core genome includes several virulence-associated genes and this could explain the rare infectiousness potential of some attenuated vaccine strains in some patients. This study reveals that low number of conserved genes in human adapted MTBc species and high inter-species diversity of the pan-genome could be considered for vaccine candidate development.
Fathiah Zakham; Tarja Sironen; Olli Vapalahti; Ravi Kant. Pan and Core Genome Analysis of 183 Mycobacterium tuberculosis Strains Revealed a High Inter-Species Diversity among the Human Adapted Strains. Antibiotics 2021, 10, 500 .
AMA StyleFathiah Zakham, Tarja Sironen, Olli Vapalahti, Ravi Kant. Pan and Core Genome Analysis of 183 Mycobacterium tuberculosis Strains Revealed a High Inter-Species Diversity among the Human Adapted Strains. Antibiotics. 2021; 10 (5):500.
Chicago/Turabian StyleFathiah Zakham; Tarja Sironen; Olli Vapalahti; Ravi Kant. 2021. "Pan and Core Genome Analysis of 183 Mycobacterium tuberculosis Strains Revealed a High Inter-Species Diversity among the Human Adapted Strains." Antibiotics 10, no. 5: 500.
In order to plan and execute proper preventative measures against COVID-19, we need to understand how SARS-CoV-2 is transmitted. It has been shown to remain infectious on surfaces from hours to days depending on surface type and environmental factors. The possibility of transmission through fur animals and contaminated pelts, along with the safety of those working with them, is a major concern. SARS-CoV-2 can infect minks and raccoon dogs and has spread to mink farms in numerous countries. Here, we studied the stability of SARS-CoV-2 on blue fox, Finn raccoon, and American mink pelt, fake fur, cotton, plastic, faux leather, and polyester and tested its inactivation by UV light and heat treatment. We detected infectious virus up to 5 days on plastic, up to 1 day on fake fur, less than a day on cotton, polyester, and faux leather, and even 10 days on mink fur. UV light failed to inactivate SARS-CoV-2 on pelts, most likely due to the mechanical protection by the fur. Hence, it should not be used to inactivate the virus on fur products, and its use for other surfaces should also be considered carefully. Heat treatment at 60°C for 1 h inactivated the virus on all surfaces and is a promising method to be applied in practice. This study helps prevent further spread of COVID-19 by increasing our understanding about risks of SARS-CoV-2 spread through contaminated clothing materials and giving important information needed to improve safety of those working in the production line as well as people using the products.
Jenni Virtanen; Kirsi Aaltonen; Ilkka Kivistö; Tarja Sironen. Survival of SARS-CoV-2 on Clothing Materials. Advances in Virology 2021, 2021, 1 -5.
AMA StyleJenni Virtanen, Kirsi Aaltonen, Ilkka Kivistö, Tarja Sironen. Survival of SARS-CoV-2 on Clothing Materials. Advances in Virology. 2021; 2021 ():1-5.
Chicago/Turabian StyleJenni Virtanen; Kirsi Aaltonen; Ilkka Kivistö; Tarja Sironen. 2021. "Survival of SARS-CoV-2 on Clothing Materials." Advances in Virology 2021, no. : 1-5.
Every day, new information is presented with respect to how to best combat the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This manuscript sheds light on such recent findings, including new co-factors (i.e., neuropilin-1) and routes (i.e., olfactory transmucosal) allowing cell entry of SARS-CoV-2 and induction of neurological symptoms, as well as the new SARS-CoV-2 variants. We highlight the SARS-CoV-2 human–animal interfaces and elaborate containment strategies using the same vaccination (i.e., nanoparticle “NP” formulations of the BNT162b2 and mRNA-1273 vaccines) for humans, minks, raccoon dogs, cats, and zoo animals. We investigate the toxicity issues of anti-CoV NPs (i.e., plasmonic NPs and quantum dots) on different levels. Namely, nano–bio interfaces (i.e., protein corona), in vitro (i.e., lung cells) and in vivo (i.e., zebrafish embryos) assessments, and impacts on humans are discussed in a narrative supported by original figures. Ultimately, we express our skeptical opinion on the comprehensive administration of such antiviral nanotheranostics, even when integrated into facemasks, because of their reported toxicities and the different NP parameters (e.g., size, shape, surface charge, and purity and chemical composition of NPs) that govern their end toxicity. We believe that more toxicity studies should be performed and be presented, clarifying the odds of the safe administration of nanotoxocological solutions and the relief of a worried public.
Dina Mosselhy; Jenni Virtanen; Ravi Kant; Wei He; Mady Elbahri; Tarja Sironen. COVID-19 Pandemic: What about the Safety of Anti-Coronavirus Nanoparticles? Nanomaterials 2021, 11, 796 .
AMA StyleDina Mosselhy, Jenni Virtanen, Ravi Kant, Wei He, Mady Elbahri, Tarja Sironen. COVID-19 Pandemic: What about the Safety of Anti-Coronavirus Nanoparticles? Nanomaterials. 2021; 11 (3):796.
Chicago/Turabian StyleDina Mosselhy; Jenni Virtanen; Ravi Kant; Wei He; Mady Elbahri; Tarja Sironen. 2021. "COVID-19 Pandemic: What about the Safety of Anti-Coronavirus Nanoparticles?" Nanomaterials 11, no. 3: 796.
The COVID-19 pandemic caused by SARS-CoV-2 started in fall 2019. A range of different mammalian species, including farmed mink, have been confirmed as susceptible to infection with this virus. We report here the spillover of mink-adapted SARS-CoV-2 from farmed mink to humans after extensive adaptation that lasted at least 3 months. We found the presence of four mutations in the S gene (that gave rise to variant: G75V, M177T, Y453F and C1247F) and others in an isolate obtained from SARS-CoV-2 positive patient.
Lukasz Rabalski; Maciej Kosinski; Natalia Mazur-Panasiuk; Boguslaw Szewczyk; Krystyna Bienkowska-Szewczyk; Ravi Kant; Tarja Sironen; Krysztof Pyrć; Maciej Grzybek. Zoonotic spillover of SARS-CoV-2: mink-adapted virus in humans. 2021, 1 .
AMA StyleLukasz Rabalski, Maciej Kosinski, Natalia Mazur-Panasiuk, Boguslaw Szewczyk, Krystyna Bienkowska-Szewczyk, Ravi Kant, Tarja Sironen, Krysztof Pyrć, Maciej Grzybek. Zoonotic spillover of SARS-CoV-2: mink-adapted virus in humans. . 2021; ():1.
Chicago/Turabian StyleLukasz Rabalski; Maciej Kosinski; Natalia Mazur-Panasiuk; Boguslaw Szewczyk; Krystyna Bienkowska-Szewczyk; Ravi Kant; Tarja Sironen; Krysztof Pyrć; Maciej Grzybek. 2021. "Zoonotic spillover of SARS-CoV-2: mink-adapted virus in humans." , no. : 1.
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.
Phuoc Truong Nguyen; Ilya Plyusnin; Tarja Sironen; Olli Vapalahti; Ravi Kant; Teemu Smura. HaVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences. 2021, 1 .
AMA StylePhuoc Truong Nguyen, Ilya Plyusnin, Tarja Sironen, Olli Vapalahti, Ravi Kant, Teemu Smura. HaVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences. . 2021; ():1.
Chicago/Turabian StylePhuoc Truong Nguyen; Ilya Plyusnin; Tarja Sironen; Olli Vapalahti; Ravi Kant; Teemu Smura. 2021. "HaVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences." , no. : 1.
Staphylococcus aureus is a notorious pathogen that colonizes implants (orthopedic and breast implants) and wounds with a vicious resistance to antibiotic therapy. Methicillin-resistant S. aureus (MRSA) is a catastrophe mainly restricted to hospitals and emerged to community reservoirs, acquiring resistance and forming biofilms. Treating biofilms is problematic except via implant removal or wound debridement. Nanoparticles (NPs) and nanofibers could combat superbugs and biofilms and rapidly diagnose MRSA. Nanotheranostics combine diagnostics and therapeutics into a single agent. This comprehensive review is interpretative, utilizing mainly recent literature (since 2016) besides the older remarkable studies sourced via Google Scholar and PubMed. We unravel the molecular S. aureus resistance and complex biofilm. The diagnostic properties and detailed antibacterial and antibiofilm NP mechanisms are elucidated in exciting stories. We highlight the challenges of bacterial infections nanotheranostics. Finally, we discuss the literature and provide “three action appraisals”. (i) The first appraisal consists of preventive actions (two wings), avoiding unnecessary hospital visits, hand hygiene, and legislations against over-the-counter antibiotics as the general preventive wing. Our second recommended preventive wing includes preventing the adverse side effects of the NPs from resistance and toxicity by establishing standard testing procedures. These standard procedures should provide breakpoints of bacteria’s susceptibility to NPs and a thorough toxicological examination of every single batch of synthesized NPs. (ii) The second appraisal includes theranostic actions, using nanotheranostics to diagnose and treat MRSA, such as what we call “multifunctional theranostic nanofibers. (iii) The third action appraisal consists of collaborative actions.
Dina A. Mosselhy; Mhd Assad; Tarja Sironen; Mady Elbahri. Nanotheranostics: A Possible Solution for Drug-Resistant Staphylococcus aureus and their Biofilms? Nanomaterials 2021, 11, 82 .
AMA StyleDina A. Mosselhy, Mhd Assad, Tarja Sironen, Mady Elbahri. Nanotheranostics: A Possible Solution for Drug-Resistant Staphylococcus aureus and their Biofilms? Nanomaterials. 2021; 11 (1):82.
Chicago/Turabian StyleDina A. Mosselhy; Mhd Assad; Tarja Sironen; Mady Elbahri. 2021. "Nanotheranostics: A Possible Solution for Drug-Resistant Staphylococcus aureus and their Biofilms?" Nanomaterials 11, no. 1: 82.
SARS-CoV-2 is the aetiological agent of COVID-19 disease and has been spreading worldwide since December 2019. The virus has been shown to infect different animal species under experimental conditions. Also, minks have been found to be susceptible to SARS-CoV-2 infection in fur farms in Europe and the USA. Here we investigated 91 individual minks from a farm located in Northern Poland. Using RT-PCR, antigen detection and NGS, we confirmed 15 animals positive for SARS-CoV-2. The result was verified by sequencing of full viral genomes, confirming SARS-CoV-2 infection in Polish mink. Country-scale monitoring conducted by veterinary inspection so far has not detected the presence of SARS-CoV-2 on other mink farms. Taking into consideration that Poland has a high level of positive diagnostic tests among its population, there is a high risk that more Polish mink farms become a source for SARS-CoV-2. Findings reported here and from other fur producing countries urge the assessment of SARS-CoV-2 prevalence in animals bred in Polish fur farms.
Lukasz Rabalski; Maciej Kosinski; Teemu Smura; Kirsi Aaltonen; Ravi Kant; Tarja Sironen; Boguslaw Szewczyk; Maciej Grzybek. Detection and molecular characterisation of SARS-CoV-2 in farmed mink (Neovision vision) in Poland. 2020, 1 .
AMA StyleLukasz Rabalski, Maciej Kosinski, Teemu Smura, Kirsi Aaltonen, Ravi Kant, Tarja Sironen, Boguslaw Szewczyk, Maciej Grzybek. Detection and molecular characterisation of SARS-CoV-2 in farmed mink (Neovision vision) in Poland. . 2020; ():1.
Chicago/Turabian StyleLukasz Rabalski; Maciej Kosinski; Teemu Smura; Kirsi Aaltonen; Ravi Kant; Tarja Sironen; Boguslaw Szewczyk; Maciej Grzybek. 2020. "Detection and molecular characterisation of SARS-CoV-2 in farmed mink (Neovision vision) in Poland." , no. : 1.
Emerging zoonotic viruses are one of the greatest threats to human health and security, as evidenced by the increasing frequency of disease outbreaks.1Morens DM Fauci AS Emerging pandemic diseases: how we got to COVID-19.Cell. 2020; 182: 1077-1092Summary Full Text Full Text PDF PubMed Scopus (0) Google Scholar To date, the main pre-emptive response to these outbreaks has been extensive, cost-heavy efforts to document virus diversity in wildlife (eg, PREDICT and the Global Virome Projects).2Morse SS Mazet JAK Woolhouse M et al.Prediction and prevention of the next pandemic zoonosis.Lancet. 2012; 380: 1956-1965Summary Full Text Full Text PDF PubMed Scopus (349) Google Scholar, 3Carroll D Daszak P Wolfe ND et al.The Global Virome Project.Science. 2018; 359: 872-874Crossref PubMed Scopus (96) Google Scholar Although these efforts have resulted in the identification of thousands of novel viruses, fewer than 1% are described to date, substantial challenges remain around access and benefit sharing from viral discovery programmes, and—perhaps most problematic for public health application—the spillover hazard of these viruses can only be coarsely inferred at present.4Rourke M Viruses for sale – all viruses are subject to access and benefit sharing obligations under the convention on biological diversity. Griffith University Law School Research Paper No. 17-14.https://papers.ssrn.com/sol3/papers.cfm?abstract_id=2984046Date: June 17, 2017Date accessed: November 30, 2020Google Scholar, 5Carlson CJ Zipfel CM Garnier R Bansal S Global estimates of mammalian viral diversity accounting for host sharing.Nat Ecol Evol. 2019; 3: 1070-1075Crossref PubMed Scopus (11) Google Scholar, 6Carlson CJ From PREDICT to prevention, one pandemic later.Lancet Microbe. 2020; 1: e6-e7Summary Full Text Full Text PDF Google Scholar
Kristian M Forbes; Omu Anzala; Colin J Carlson; Alyson A Kelvin; Krutika Kuppalli; Eric M Leroy; Gael D Maganga; Moses M Masika; Illich M Mombo; Dufton M Mwaengo; Roch F Niama; Julius Nziza; Joseph Ogola; Brad S Pickering; Angela L Rasmussen; Tarja Sironen; Olli Vapalahti; Paul W Webala; Jason Kindrachuk. Towards a coordinated strategy for intercepting human disease emergence in Africa. The Lancet Microbe 2020, 2, e51 -e52.
AMA StyleKristian M Forbes, Omu Anzala, Colin J Carlson, Alyson A Kelvin, Krutika Kuppalli, Eric M Leroy, Gael D Maganga, Moses M Masika, Illich M Mombo, Dufton M Mwaengo, Roch F Niama, Julius Nziza, Joseph Ogola, Brad S Pickering, Angela L Rasmussen, Tarja Sironen, Olli Vapalahti, Paul W Webala, Jason Kindrachuk. Towards a coordinated strategy for intercepting human disease emergence in Africa. The Lancet Microbe. 2020; 2 (2):e51-e52.
Chicago/Turabian StyleKristian M Forbes; Omu Anzala; Colin J Carlson; Alyson A Kelvin; Krutika Kuppalli; Eric M Leroy; Gael D Maganga; Moses M Masika; Illich M Mombo; Dufton M Mwaengo; Roch F Niama; Julius Nziza; Joseph Ogola; Brad S Pickering; Angela L Rasmussen; Tarja Sironen; Olli Vapalahti; Paul W Webala; Jason Kindrachuk. 2020. "Towards a coordinated strategy for intercepting human disease emergence in Africa." The Lancet Microbe 2, no. 2: e51-e52.
Exposure, risks and immunity of healthcare workers (HCWs), a vital resource during the SARS-CoV-2 pandemic, warrant special attention. HCWs at Helsinki University Hospital, Finland, filled in questionnaires and provided serum samples for SARS-CoV-2-specific antibody screening by Euroimmun IgG assay in March–April 2020. Positive/equivocal findings were confirmed by Abbott and microneutralization tests. Positivity by two of the three assays or RT-PCR indicated a Covid-19 case (CoV+). The rate of CoV(+) was 3.3% (36/1095) and seropositivity 3.0% (33/1095). CoV(+) was associated with contact with a known Covid-19 case, and working on a Covid-19-dedicated ward or one with cases among staff. The rate in the Covid-19-dedicated ICU was negligible. Smoking and age <55 years were associated with decreased risk. CoV(+) was strongly associated with ageusia, anosmia, myalgia, fatigue, fever, and chest pressure. Seropositivity was recorded for 89.3% of those with prior documented RT-PCR-positivity and 2.4% of those RT-PCR-negative. The rate of previously unidentified cases was 0.7% (8/1067) and asymptomatic ones 0% (0/36). Undiagnosed and asymptomatic cases among HCWs proved rare. An increased risk was associated with Covid-19-dedicated wards. Particularly high rates were seen for wards with liberal HCW-HCW contacts, highlighting the importance of social distancing also among HCWs.
Anu Kantele; Tinja Lääveri; Lauri Kareinen; Sari H. Pakkanen; Karin Blomgren; Sointu Mero; Anu Patjas; Jenni Virtanen; Ruut Uusitalo; Maija Lappalainen; Asko Järvinen; Satu Kurkela; Anne J. Jääskeläinen; Olli Vapalahti; Tarja Sironen. SARS-CoV-2 infections among healthcare workers at Helsinki University Hospital, Finland, spring 2020: Serosurvey, symptoms and risk factors. Travel Medicine and Infectious Disease 2020, 39, 101949 -101949.
AMA StyleAnu Kantele, Tinja Lääveri, Lauri Kareinen, Sari H. Pakkanen, Karin Blomgren, Sointu Mero, Anu Patjas, Jenni Virtanen, Ruut Uusitalo, Maija Lappalainen, Asko Järvinen, Satu Kurkela, Anne J. Jääskeläinen, Olli Vapalahti, Tarja Sironen. SARS-CoV-2 infections among healthcare workers at Helsinki University Hospital, Finland, spring 2020: Serosurvey, symptoms and risk factors. Travel Medicine and Infectious Disease. 2020; 39 ():101949-101949.
Chicago/Turabian StyleAnu Kantele; Tinja Lääveri; Lauri Kareinen; Sari H. Pakkanen; Karin Blomgren; Sointu Mero; Anu Patjas; Jenni Virtanen; Ruut Uusitalo; Maija Lappalainen; Asko Järvinen; Satu Kurkela; Anne J. Jääskeläinen; Olli Vapalahti; Tarja Sironen. 2020. "SARS-CoV-2 infections among healthcare workers at Helsinki University Hospital, Finland, spring 2020: Serosurvey, symptoms and risk factors." Travel Medicine and Infectious Disease 39, no. : 101949-101949.
Previously identified only in Sierra Leone, Guinea, and southeastern Kenya, Bombali virus–infected Mops condylurus bats were recently found »750 km away in western Kenya. This finding supports the role of M. condylurus bats as hosts and the potential for Bombali virus circulation across the bats’ range in sub-Saharan Africa.
Lauri Kareinen; Joseph Ogola; Ilkka Kivistö; Teemu Smura; Kirsi Aaltonen; Anne J. Jääskeläinen; Sospeter Kibiwot; Moses M. Masika; Philip Nyaga; Dufton Mwaengo; Omu Anzala; Olli Vapalahti; Paul W. Webala; Kristian M. Forbes; Tarja Sironen. Range Expansion of Bombali Virus in Mops condylurus Bats, Kenya, 2019. Emerging Infectious Diseases 2020, 26, 3007 -3010.
AMA StyleLauri Kareinen, Joseph Ogola, Ilkka Kivistö, Teemu Smura, Kirsi Aaltonen, Anne J. Jääskeläinen, Sospeter Kibiwot, Moses M. Masika, Philip Nyaga, Dufton Mwaengo, Omu Anzala, Olli Vapalahti, Paul W. Webala, Kristian M. Forbes, Tarja Sironen. Range Expansion of Bombali Virus in Mops condylurus Bats, Kenya, 2019. Emerging Infectious Diseases. 2020; 26 (12):3007-3010.
Chicago/Turabian StyleLauri Kareinen; Joseph Ogola; Ilkka Kivistö; Teemu Smura; Kirsi Aaltonen; Anne J. Jääskeläinen; Sospeter Kibiwot; Moses M. Masika; Philip Nyaga; Dufton Mwaengo; Omu Anzala; Olli Vapalahti; Paul W. Webala; Kristian M. Forbes; Tarja Sironen. 2020. "Range Expansion of Bombali Virus in Mops condylurus Bats, Kenya, 2019." Emerging Infectious Diseases 26, no. 12: 3007-3010.
Acute febrile neurological infection cases in southern Iraq (N = 212) were screened for lymphocytic choriomeningitis virus (LCMV). Two LCMV IgM-positive serum samples and 2 cerebrospinal fluid samples with phylogenetically distinct LCMV strains were found. The overall LCMV seroprevalence was 8.8%. LCMV infections are common and associated with acute neurological disease in Iraq.
Hussein Alburkat; Anne J. Jääskeläinen; Ali M. Barakat; Hassan J. Hasony; Tarja Sironen; Haider Al-Hello; Teemu Smura; Olli Vapalahti. Lymphocytic Choriomeningitis Virus Infections and Seroprevalence, Southern Iraq. Emerging Infectious Diseases 2020, 26, 3002 -3006.
AMA StyleHussein Alburkat, Anne J. Jääskeläinen, Ali M. Barakat, Hassan J. Hasony, Tarja Sironen, Haider Al-Hello, Teemu Smura, Olli Vapalahti. Lymphocytic Choriomeningitis Virus Infections and Seroprevalence, Southern Iraq. Emerging Infectious Diseases. 2020; 26 (12):3002-3006.
Chicago/Turabian StyleHussein Alburkat; Anne J. Jääskeläinen; Ali M. Barakat; Hassan J. Hasony; Tarja Sironen; Haider Al-Hello; Teemu Smura; Olli Vapalahti. 2020. "Lymphocytic Choriomeningitis Virus Infections and Seroprevalence, Southern Iraq." Emerging Infectious Diseases 26, no. 12: 3002-3006.