The late 2019 marked the onset of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that led to the unprecedented COVID-19 pandemic, with profound global health and socioeconomic impacts. This thesis offers a thorough examination of the molecular biology, evolution, and disease-causing mechanisms of SARS-CoV-2, as well as recent advancements in understanding the structural and functional implications of mutations in viral proteins. The prevailing belief is that SARS-CoV-2 originated from a zoonotic transmission involving bats as the natural reservoir hosts, with an unknown intermediate host facilitating transmission to humans. Genomic sequencing and phylogenetic analysis have identified similarities between SARS-CoV-2 and bat coronaviruses, particularly RaTG13, indicating a potential bat origin. However, the exact circumstances and intermediate hosts of the spillover event remain under investigation. In its structure, SARS-CoV-2 is an enveloped virus with a positive-sense single-stranded RNA genome. This genome encodes both structural and non-structural proteins crucial for viral replication and the development of the disease. The spike (S) protein facilitates viral entry by binding to the angiotensin-converting enzyme 2 (ACE2) receptor. Meanwhile, non-structural proteins are involved in viral RNA synthesis, immune evasion, and the assembly of virions. Alterations in the genetic makeup of the SARS-CoV-2 genome, notably within the spike protein, can impact transmission efficiency, viral load, and immune evasion. Notable mutations such as D614G, N501Y, and E484K have been associated with increased transmissibility and reduced neutralization by antibodies. Understanding the effects of these mutations on viral fitness and pathogenicity is crucial for informing public health interventions and vaccine development efforts. The impacts of Non-structural proteins (NSPs) on viral replication and transmission are however understudied. In this study, we focused on mutations in the several NSPs including NSP1, 2, 3, 13,14, and 15 of the early Omicron (BA.1) and XBB 1.5 variants and investigated their impact on structure and the functional implications using bioinformatics tools and protein structure prediction methods. Our analysis focused on potential alterations in NSP1's structure and hence its ability to suppress host gene expression and modulate immune responses, shedding light on the mechanisms by which SARS-CoV-2 evolves to evade host defenses. Overall, this thesis gives insights into the emergence, structure, replication cycle, evolution, and pathogenesis of SARS-CoV-2, highlighting the importance of ongoing research efforts in understanding and combatting this global health threat and provides a detailed structural analysis of mutations in NSPs. / Master of Science / The COVID-19 pandemic, instigated by the virus referred to as SARS-CoV-2, is a novel coronavirus believed to have originated in bats and possibly transmitted to humans via an intermediate host. Its genetic structure and protein interactions play crucial roles in how it spreads and causes illness. We need to understand where the virus came from, how it's built, it's life cycle and how it's changing over time. While the virus has undergone a lot of mutations over time, scientists are actively studying these changes, with a lot of focus on the structural ones, to understand their implications for public health measures and vaccine development. In our study, we focus on the non- structural proteins and aim to investigate the effect of selected mutations on the protein structure and function using bioinformatics. Understanding the virus is essential for effectively combating future pandemics and safeguarding public health.

COVID-19 Patientinnen und Patienten haben ein hohes thrombotisches Risiko. Die Sicherheit und Wirksamkeit verschiedener Antikoagulationsschemata bei COVID-19 Patientinnen und Patienten sind unklar. Acht RCTs mit 5580 Patientinnen und Patienten wurden identifiziert, wovon zwei RCTs Antikoagulation in halbtherapeutischer und sechs RCTs Antikoagulation in therapeutischer Dosierung mit der Standard Thromboembolieprophylaxe verglichen haben. Die halbtherapeutische Antikoagulation kann wenig oder gar keinen Einfluss auf thrombotische Ereignisse oder Todesfälle haben (RR 1,03, 95% KI 0,86-1,24), kann aber schwere Blutungen (RR 1,48, 95% KI 0,53-4,15) bei mittelschweren bis schweren COVID-19 Patientinnen und Patienten verstärken. Therapeutische Antikoagulation kann thrombotische Ereignisse oder den Tod bei Patientinnen und Patienten mit mittelschwerem COVID-19 (RR 0,64, 95% KI 0,38-1,07) verringern, kann aber bei Patientinnen und Patienten mit schwerer Erkrankung (RR 0,98, 95% KI 0,86-1,12) wenig oder keine Wirkung haben. Das Risiko schwerer Blutungen kann unabhängig vom Schweregrad der Erkrankung zunehmen (RR 1,78, 95% KI 1,15-2,74). Die Evidenzsicherheit ist immer noch gering. Mäßig betroffene COVID-19 Patientinnen und Patienten können von einer therapeutischen Antikoagulation profitieren, jedoch ist das Blutungsrisiko erhöht. / COVID-19 patients have a high risk of thrombotic disease. The safety and efficacy of various anticoagulation regimens in COVID-19 patients remains unclear. Eight RCTs with 5580 patients were identified, with two comparing anticoagulation in intermediate doses and six comparing therapeutic doses to standard thromboembolism prophylaxis. Intermediate anticoagulation may have little or no effect on thrombotic events or deaths (RR 1.03, 95% CI 0.86-1.24), but may increase major bleeding (RR 1.48, 95% CI 0.53-4.15) in moderate to severe COVID-19 patients. Therapeutic anticoagulation may reduce thrombotic events or death in patients with moderate COVID-19 (RR 0.64, 95% CI 0.38-1.07), but may have little or no effect in patients with severe disease (RR 0.98, 95% CI 0.86-1.12). The risk of major bleeding may increase regardless of the severity of the disease (RR 1.78, 95% CI 1.15-2.74). The certainty of evidence is still low. Moderately affected COVID-19 patients may benefit from therapeutic anticoagulation, but the risk of bleeding is increased.

Das severe acute respiratory syndrome Coronavirus (SARS-CoV) ist ein hochpathogenes Virus, dessen zoonotischer Eintrag in die Bevölkerung eine substantielle Gesundheitsgefahr darstellt. Die Identifizierung von Wirtszellfaktoren, die für die SARS-CoV-Ausbreitung und Pathogenese wichtig sind, könnte neue Ansatzpunkte für die Therapie liefern. Das SARS-CoV-Oberflächenprotein Spike (S) bindet an den zellulären Rezeptor angiotensin converting Enzyme 2 (ACE2) und vermittelt den viralen Eintritt in Zielzellen. Die Spaltung und Aktivierung des S Proteins durch Wirtszellproteasen ist für den infektiösen, S Protein-vermittelten Zelleintritt von SARS-CoV essentiell. Die Typ II Transmembranserinproteasen (TTSPs) TMPRSS2 und HAT spalten und aktivieren das S Protein, zumindest nach gerichteter Expression in Zelllinien. Ob diese Enzyme in der menschlichen Lunge, den Zielzellen der SARS-CoV-Infektion, exprimiert werden, war jedoch unklar und sollte im Rahmen der vorliegenden Arbeit untersucht werden. TMPRSS2 und HAT spalten auch den viralen Rezeptor ACE2 und es wurde postuliert, dass die ACE2-Spaltung den viralen Eintritt erhöht. Der zugrundeliegende Mechanismus war jedoch nicht bekannt und sollte innerhalb der vorliegenden Arbeit aufgeklärt werden. Es konnte gezeigt werden, dass TMPRSS2 und HAT zusammen mit ACE2 in Epithelzellen des Respirationstrakts exprimiert werden. Die Proteasen könnten daher die Ausbreitung von SARS-CoV im Lungenepithel fördern. Weiterhin wurde eine Aminosäuresequenz in ACE2 identifiziert, die für die Prozessierung durch TMPRSS2 und HAT essentiell ist. Die funktionelle Analyse von ACE2- Mutanten zeigte, dass die Spaltung in diesem Bereich infektionsverstärkend wirkt. Immunfluoreszenz-Studien erbrachten Hinweise darauf, dass die Verstärkung der Infektion auf eine erhöhte Aufnahme von Virus-Partikeln in die Zelle zurückzuführen ist. Schließlich konnte demonstriert werden, dass TMPRSS2 und eine weitere zelluläre Protease, A Disintegrin And Metalloproteinase 17 (ADAM17), um die ACE2-Spaltung konkurrieren und die ADAM17- Spaltstelle in ACE2 konnte kartiert werden. Die ACE2-Spaltung durch ADAM17 war jedoch für den S Protein-getriebenen Zelleintritt verzichtbar. Zusammenfassend zeigen diese Untersuchungen, dass TMPRSS2 und HAT die SARS-CoV-Infektion durch Spaltung von S Protein und Rezeptor fördern. Die Proteasen stellen daher mögliche Angriffspunkte für die antivirale Intervention dar.

Introducción. El COVID-19 y la gestación es una nueva intercurrencia en la valoración de riesgos para la atención de la gestante. Desde el inicio de la pandemia en el país, los casos han ido en aumento. El primer caso atendido en el Hospital San Bartolomé fue el 12 de abril. Desde los primeros reportes de gestantes COVID+ en China, a la fecha, se tiene cada vez mayor información, siendo importante para fines del manejo de la gestante COVID+ que se conozca su epidemiología y los resultados perinatales. Objetivo. Determinar la epidemiología y resultados materno perinatales de COVID-19 en las gestantes del Hospital Nacional Docente Madre Niño San Bartolomé, Lima, Perú. Método. Estudio observacional de corte transversal, en los meses de abril a julio 2020. Se incluyó a todas las gestantes que llegaron a la emergencia obstétrica del Hospital San Bartolomé, a las cuales se les realizó una prueba de inmunocromatografía para IgM/IgG, para determinar la seroprevalencia de COVID-19. Las variables obstétricas y perinatales fueron recolectadas en una ficha de datos al ingreso a la emergencia. Resultados. Se realizó prueba rápida para SARS-CoV-19 a 345 gestantes que se hospitalizaron para atención de parto. La edad promedio fue 27 años, con 10% de adolescentes y 16% de mayores de 35 años; 60% tenía 2 a 4 embarazos, 38% de los partos fue vaginal, 15% de ellos pretérmino; 1,2% de las gestantes fue sintomática y 0,2% ingresó a la unidad de cuidados intensivos. El 61% de los recién nacidos pesó entre 2 500 y 3 500 g, 53% fue sexo masculino, 94% tuvo Apgar mayor de 7 al minuto, 3,3% con hisopado positivo dentro de las primeras 24 horas. Se presentaron 3% de óbitos. El 48% de las gestantes provino del Cono Norte de la ciudad de Lima. Conclusiones. Casi 100% de las gestantes fue asintomática y solo 0,2% tuvo complicaciones respiratorias. La culminación del parto por vía cesárea fue baja en relación a otras publicaciones; el motivo de cesárea fue por indicación obstétrica. Escaso número de neonatos tuvo hisopado positivo. Hubo mayor incidencia de óbitos en julio 2020. El mayor porcentaje de pacientes provino del Cono Norte de Lima. / Introduction: COVID-19 and pregnancy is a new intercurrence in risk assessment for the care of the pregnant woman. Since the beginning of the pandemic in the country, cases have been increasing. The first case attended at the San Bartolomé Hospital was on April 12. Since the first reports of COVID+ pregnant women in China, to date, there is more important information on epidemiology and perinatal results for the management of the COVID+ pregnant woman. Objective: To determine the epidemiology and maternal perinatal outcomes of COVID-19 in pregnant women at the Hospital Nacional Docente Madre Niño San Bartolomé, Lima, Peru. Methods: Observational cross-sectional study, from April to July 2020. All the pregnant women who arrived at the obstetric emergency at Hospital San Bartolomé were included, and they underwent an immunochromatography test for IgM / IgG, to determine the seroprevalence of COVID-19. Obstetric and perinatal variables were collected in a data sheet upon admission to the emergency room. Results: Rapid test for SARS-CoV-19 was performed in 345 pregnant women who were hospitalized for delivery care. The average age was 27 years, with 10% adolescents and 16% over 35 years; 60% had 2 to 4 pregnancies, 38% of deliveries were vaginal, 15% of them preterm; 1.2% of the pregnant women were symptomatic and 0.2% were admitted to the intensive care unit. 61% of the newborns weighed between 2 500 and 3 500 g, 53% were male, 94% had an Apgar score greater than 7 at one minute, 3.3% with a positive swab within the first 24 hours. There were 3% fetal deaths. 48% of the pregnant women came from the Northern Cone of the city of Lima. Conclusions: Almost 100% of the pregnant women were asymptomatic and only 0.2% had respiratory complications. The mode of delivery by cesarean section was low in relation to other publications, all had obstetric indication. A small number of neonates had a positive swab. There was a higher incidence of fetal deaths in July 2020. The highest percentage of patients came from the Northern Cone of Lima.

The aim of this diploma thesis was to describe information about SARS-CoV-2 virus and coronavirus disease (COVID-19), to evaluate the course of the disease in the Home with a special regime in Břevnice, in which the epidemic took place at the beginning of the first wave of COVID-19 pandemic in spring 2020. Another goal was to perform an antibody analysis and evaluate the obtained data. I divided the diploma thesis into three main parts: theoretical, experimental and discussion. In the theoretical part, I worked with the literature and described information related not only to COVID-19, but also to other serious infections caused by human coronaviruses. In the experimental part, which I performed in the immunological laboratory of the Department of Joint Laboratories at Havlíčkův Brod Hospital, I dealt with the issue of the clinical course of the disease, the severity of the disease and possible consequences after the infection. I also dealt with methods for the determination of antibodies, the principles of which are described in Chapter 4.5. The diagnostic methods and procedures used are described in Chapter 5.3 Laboratory Assays. From the obtained data, I prepared graphs and tables and processed data on the clinical course of the infection in the Břevnice Home, both for the clients and the...

Se validó y evaluó un método de RT-PCR en tiempo real usando cebadores y sondas específicas para los genes RdRP de SARS-CoV-2 y GAPDH de humanos; este último fue usado como control endógeno. Se evaluó la especificidad y sensibilidad; además, se evaluó otros parámetros como la robustez, la repetibilidad, reproducibilidad, comparabilidad y el límite de detección. La sensibilidad, especificidad, los valores predictivos positivo y negativo, la robustez, comparabilidad y la repetibilidad-reproducibilidad de la prueba de RT-PCR en tiempo real dúplex fue de 100%, con un límite de detección de 100 copias/μL, de acuerdo con los criterios de aceptación establecidos para validación del protocolo. Esta prueba estandarizada es una buena alternativa para el diagnóstico de COVID-19; además, la prueba fue aplicada de manera exitosa en personas sospechosas de la enfermedad permitiendo controlar el número de falsos negativos.

<div>The papain-like protease (PLP) domain of nonstructural protein 3 (nsp3) of the coronavirus (CoV) genome promotes viral replication by processing the CoV polyprotein (protease) and also antagonize innate immune responses by deubiquitinating (DUB) and deISGylating (deISG) host substrates. Selectively removing the DUB/deISG activities of PLP while keeping the protease activity intact is a potential strategy for designing a live attenuated virus. However, it is unclear in the literature the precise mechanism by which PLPs support CoV evasion of the innate immune system. Deciphering the substrate specificity of PLPs for host ubiquitin (Ub) and interferon stimulated gene 15 (ISG15) can therefore help in the design of PLP mutants that selectively lack one activity for evaluating the DUB and deISG mechanism in CoV pathogenesis and replication. </div><div> In this dissertation, we investigate the structure and function of the single PLP (PLpro) from beta-CoVs, severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), which are dangerous viral pathogens that emerged from a zoonotic source to cause infectious disease in the human population. Additionally, we translate the knowledge gained to the equivalent PLP2 from alpha-CoV porcine epidemic diarrhea virus (PEDV) and feline infectious peritonitis virus (FIPV), which cause fatal disease in suckling piglets on industrial pork farms and household cats, respectively. The primary objective of this work is to rationally design PLP mutants across beta- and alpha-CoVs to help attenuate CoV infection, as no antiviral or vaccine exist for human CoVs and the efficacy of PEDV vaccines are an ongoing research topic. </div><div><br></div><div>In Chapter 1, different human, animal, and the bat origin CoV strains are introduced. The CoV life-cycle and virion structure are outlined, along with the replicase complex for viral replication. The multidomain nsp3 from alpha- and beta-CoV genomes are also described with a focus on the PLP domain and its proposed cleavage sites of the viral polyprotein. The discovery of the first viral protease DUB and the multiple activities of PLPs are defined, which includes a proposed model of how DUB versus deISG activities may act in the innate immune response. This leads into the therapeutic potential of PLP for an antiviral or live attenuated vaccine, which is followed by the introduction of live attenuated vaccines and the reverse genetics system. Next, proof of concept studies on PLP2 mutants are described and the introduction is concluded by stating the ultimate goal for the design of PLP mutants.</div><div><br></div><div>In Chapter 2, we hypothesize that the flanking ubiquitin-like (Ubl2) domain of MERS-CoV PLpro is not required for its enzymatic function. We characterize the specific activity, kinetics, substrate specificity, and inhibition of the PLpro enzyme with and without the Ubl2 domain and reveal that the Ubl2 domain does not significantly alter PLpro function. We determine the structure of the core PLpro, smallest catalytic unit to 1.9 Å resolution and observed no structural changes compared to the wild-type. Additionally, we demonstrate that a purported MERS-CoV PLpro inhibitor is nonselective in non-reducing conditions and should not be pursed for therapeutic use. We show that the core PLpro enzyme i.e. without the Ubl2 domain is a stable and robust construct for crystallization and is also thermally stable based on thermal melting studies with utility for structure-based drug design. </div><div><br></div><div>In Chapter 3, we shed light on the specificity of SARS-CoV PLpro towards Ub versus ISG15 by characterizing the specific activity and kinetic parameters of SARS-CoV PLpro mutants. In addition, the structure of SARS-CoV PLpro in complex with the C-terminal domain of ISG15 is determined and compared with the Ub-bound structure. Based on the structure and kinetic results, the altered specificities of SARS-CoV PLpro mutants Arg167Glu, Met209Ala, and Gln233Glu are compared with the wild-type. Arg167Glu mutant exhibits DUB hyperactivity and is expected to adopt a more favorable interaction with the Arg42 of Ub. At the same time, ARG167GLU contains a shorter side-chain that hinders interaction with the unique Trp123 of ISG15 for deISG activity compared to the wild-type. These results aid in the development of SARS-CoV PLpro mutants that have directed shifts in substrate specificity for Ub versus ISG15. </div><div><br></div><div>In Chapter 4, the process and antiviral activity of ISGylation is reviewed and how viruses can modulate host-derived versus virus-derived machineries to counteract ISGylation for viral infection. MERS-CoV PLpro is cross-reactive for Ub, but less is known about its specificity towards ISG15. In this study, we determine the structure of MERS-CoV PLpro bound with ISG15 to 2.3 Å resolution and reveal a small hydrophobic pocket of ISG15 that consists of P130 and W123, which differs from Ub hydrophobic patch. We design and determine the kinetic parameters for 13 PLpro mutants and reveal that MERS-CoV PLpro only has a single ubiquitin recognition (SUb1) site. Kinetic studies show that removing the charge of the R1649 greatly enhances DUB/protease activity while mutating in an Arg near R42 of Ub or ISG15 hydrophobic region is detrimental to both DUB/deISG activities. Kinetic experiments and probe-reactivity assays showed that Val1691Arg, Val1691Lys, and His1652Arg mutants are drastically reduced DUB/deISG activities compared to the wild-type. Overall, MERS-CoV PLpro mutants with alter kinetic profiles will be useful for discovery tools and DUB/deISG deficient mutants are great candidates for removing host cell antagonism activity by PLpro for live attenuated vaccines.</div><div><br></div><div>In Chapter 5, the goal is to translate the knowledge gained in Chapters 2-4 on beta-CoVs PLpro and evaluate the substrate specificity of alpha-CoVs FIPV and PEDV PLP2 for mutagenesis experiments. First, we design and purify the core PLP2 enzymes for kinetics. PLP2s are efficient DUBs that prefer Ub to ISG15 in vitro, and this preference is conserved in beta-CoV MHV PLP2 as well as alpha-CoV NL63 PLP2. We determine the structure of alpha-CoV PEDV PLP2 to 1.95 Å resolution and reveal the unique Zn-finger coordinating Cys3-His arrangement of the alpha-CoV genus that differs from past beta-CoV PLP crystal structures. To determine residues of the SUb1 site, we generate a homology model of FIPV PLP2 and overlay our PLP2 structures with MERS-CoV PLpro bound with Ub. In addition, we create electrostatic surface maps across coronaviral PLP subfamilies to evaluate the charge distribution of the SUb1 for the rational design of several FIPV and PEDV PLP2 mutants. We evaluate the turnover of PLP mutants for FRET-based substrates and reveal that His101ArgFIPV and Asn101ArgPEDV are drastically reduced in Ub-AMC activity while their peptide activities are within 2-fold of the wild-type. These mutants show delayed reactivity for Ub probes and no longer cleave Ub-chains displaying isopeptide bonds compared to the wild-type. Results from this study reveal a hot spot in both alpha- and beta-CoVs that can be used to selectively remove DUB activity of PLPs for generating a DUB deficient PLP enzyme. </div><div><br></div><div>In this dissertation, we investigate the substrate specificity of PLPs across alpha- and beta-CoVs and develop a fingerprint for Ub and also shed light on ISG15 recognition. Specifically, hot spots were identified in the SUb1 site of different PLPs, which recognize R42 and hydrophobic Ile44 of Ub. Position 97-98 of PLPs can be used to remove DUB activity by substituting an Arg, but usually effect protease function. Substituting an Arg at position 101 and 136 of coronaviral PLPs serve as the best strategy to remove DUB function while not hindering active site functionality. The DUB/deISG deficient mutants described will be useful for inhibiting the ability of PLPs to function in the innate immune response. Ultimately, this work provides a guide for identifying attenuating mutants in existing CoVs for live attenuated vaccines and also a blueprint for engineering PLPs from new emerging CoVs. </div>

El virus SARS-CoV-2 sigue reproduciéndose velozmente y muestra variantes más infecciosas. La segunda ola de la enfermedad va apaciguándose en Europa y Estados Unidos de América del Norte, menos en América del Sur. En el Perú, las cifras de fallecidos han sido sinceradas a más del doble, encontrándose mayor mortandad en los hombres y en los mayores de 70 años. Se ha corroborado en el mundo que la gestante sufre una enfermedad más severa -a veces con un proceso similar a la preeclampsia-, con más posibilidad de muerte que la mujer no gestante y mayor muerte fetal y prematuridad. Las vacunas iniciales elaboradas en los EE UU y Europa están siendo efectivas en disminuir las infecciones, hospitalizaciones y muertes en los países donde la vacunación ha avanzado más rápido. Está siendo administrada en gestantes sin efectos secundarios mayores, recomendándoseles se vacunen para evitar la infección severa. Mientras tanto, no se conoce la duración de la inmunidad dada por la infección COVID-19 y por la vacuna. Se está considerando una tercera dosis de refuerzo y el cambio de marca en los vacunados. Y se está en espera de una tercera ola de infecciones debido a la aparición de las variantes brasilera e india (delta). / The SARS-CoV-2 virus continues to reproduce rapidly and is showing more infectious variants. The second wave of the pandemic is subsiding in Europe and the United States of North America, but not in South America. In Peru, the number of deaths has more than doubled, with a higher mortality rate in men and in those over 70 years of age. It has been corroborated worldwide that pregnant women suffer a more severe disease -sometimes with a process similar to preeclampsia- with a greater possibility of death than non-pregnant women and greater fetal death and prematurity. Initial vaccines developed in the USA and Europe are proving effective in reducing infections, hospitalizations and deaths in countries where vaccination has advanced more rapidly. It is being administered in pregnant women without major side effects, and they are recommended to be vaccinated to avoid severe infection. As of now, the duration of immunity given by COVID-19 infection and by the vaccine is not known. A third booster dose and rebranding of vaccinees is being considered. And a third wave of infe ergence of the Brazilian and Indian (Delta) variants.

Bakgrund: Den pågående pandemin COVID-19 orsakas av viruset SARS-CoV-2. Sedan december 2020 har nya varianter av viruset med betydande genetiska förändringar upptäckts, gemensamt benämnt varianter av särskild betydelse eller variants of concern (VOC). Just nu är det tre VOC som bevakas särskilt; B.1.1.7 (först upptäckt i Storbritannien), B.1.351 (först upptäckt i Sydafrika) respektive P.1 (först upptäckt i Brasilien). Den tidigaste statistiken från Folkhälsomyndigheten om förekomsten av VOC i Region Dalarna är från februari 2021. Förekomsten av VOC innan dess är fortfarande okänd. I regionen delas analysering av prover vid misstanke om COVID-19 in i de olika kategorierna patienter, vårdpersonal, smittspårning och allmänhet. Befintlig statistik om förekomsten av VOC grundar sig nästan enbart på förekomsten bland allmänhetens prover. Syfte: Syftet med denna studie var att undersöka förekomsten av SARS-CoV-2 varianter av särskild betydelse i prover tagna från patienter, vårdpersonal och smittspårningar under december 2020-januari 2021 i Region Dalarna. Studien syftade också till att undersöka när spridningen av respektive VOC kan ha startat i regionen. Metod: Provmaterialet bestod av SARS-CoV-2 positiva prov tagna inom analyskategorierna under tidsperioden. Prover analyserades med RT-PCR och smältkurvsanalys för detektion av VOC-karaktäristiska mutationer. Resultat: Ett fåtal fall av B.1.1.7 detekterades redan i december och en stigande andel av B.1.1.7 påvisades inom analyskategorierna under januari, som tecken på att en regional spridning kan ha startat vid tidpunkten. Endast ett fåtal fall av B.1.351 och/eller P.1 detekterades inom analyskategorierna under tidsperioden, vilket tyder på att en regional spridning av dessa ännu inte hade startat i januari. / Background: The ongoing pandemic COVID-19 is caused by the virus SARS-CoV-2. Since December 2020 new variants of the virus with significant mutations have been discovered, referred to as variants of concern (VOC). At the point, the occurrence of three VOC is especially monitored; B.1.1.7 (discovered in UK), B.1.351 (discovered in South Africa) and P.1 (discovered in Brazil). The earliest statistics about the occurrence of VOC in Region Dalarna, Sweden, is from February 2021 and the occurrence before that is still unknown. In the region analysis of specimen in case of suspected COVID-19 is divided into the different categories patients, healthcare-staff, infection tracing and public. Existing statistics is based almost exclusively on the occurrence of VOC in specimen from the public. Aim: The aim of this study was to examine the occurrence of SARS-CoV-2 VOC among specimens collected from patients, healthcare staff and infection tracing in Region Dalarna during December 2020-January 2021. The study also aimed to examine when the spread of each VOC started in the region. Method: SARS-CoV-2 positive specimen collected within the categories during the time was analyzed with RT-PCR and melting curve analysis for detection of VOC-characteristic mutations. Results: A few cases of B.1.1.7 was detected already in December and an increased percentage of B.1.1.7 was detected within the categories during January, suggesting that a regional spread started at the time. Only a few cases of B.1.351 and/or P.1 was detected within the categories, suggesting that a regional spread of these had not yet started in January.

I mars 2020 drabbades världen av en pandemi kopplat till viruset Covid-19 (SARS-CoV-2). I Sverige som i resten av världen har sjukvårdspersonalen varit tvungna att jobba under hög belastning i stressiga arbetssituationer som resultat av denna pandemi. Syftet med studien var att undersöka vilka faktorer som spelade roll för att vårdpersonalen skulle orka med det stressiga jobbet under en ovanlig situation som covid-19 pandemin. Till denna studie valdes kvalitativ design med en tematisk induktiv analys. Resultatet visade att kollegornas stöd, tydliga instruktioner från närmaste chefer, känslan av stolthet för att kunna klara av situationen tillsammans med andra samt personliga strategier var positiva faktorer som hjälpte vårdpersonalen att kunna klara av arbetet. Medan sjukvårdspersonalen upplevde att stöd från högre ledningen och samhällets ansvar inte var tillräckligt. / In March 2020, the world was hit by a pandemic linked to the Covid-19 (SARS-CoV-2) virus. In Sweden, as in the rest of the world, healthcare professionals had to work under high load in stressful work situations as a result of this pandemic. The purpose of this study was to investigate what factors played a role in the care staff being able to cope with the stressful job during an unusual situation such as the pandemic. For this study, qualitative design with a thematic inductive analysis was chosen. The results showed that the colleagues' support, clear instructions from immediate managers, the feeling of pride in being able to cope with the situation together with others and personal strategies were positive factors that helped the care staff to cope with the work load. While the health care staff felt that support from senior management and the responsibility of society was not enough.