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Since its outbreak in 2019, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) keeps surprising the medical community by evolving diverse immune escape mutations in a rapid and effective manner. To gain deeper insight into mutation frequency and dynamics, we isolated ten ancestral strains of SARS-CoV-2 and performed consecutive serial incubation in ten replications in a suitable and common cell line and subsequently analysed them using RT-qPCR and whole genome sequencing. Along those lines we hoped to gain fundamental insights into the evolutionary capacity of SARS-CoV-2 in vitro. Our results identified a series of adaptive genetic changes, ranging from unique convergent substitutional mutations and hitherto undescribed insertions. The region coding for spike proved to be a mutational hotspot, evolving a number of mutational changes including the already known substitutions at positions S:484 and S:501. We discussed the evolution of all specific adaptations as well as possible reasons for the seemingly inhomogeneous potential of SARS-CoV-2 in the adaptation to cell culture. The combination of serial passage in vitro with whole genome sequencing uncovers the immense mutational potential of some SARS-CoV-2 strains. The observed genetic changes of SARS-CoV-2 in vitro could not be explained solely by selectively neutral mutations but possibly resulted from the action of directional selection accumulating favourable genetic changes in the evolving variants, along the path of increasing potency of the strain. Competition among a high number of quasi-species in the SARS-CoV-2 in vitro population gene pool may reinforce directional selection and boost the speed of evolutionary change.

We studied a unique case of prolonged viral shedding in an immunocompromised patient that generated a series of SARS-CoV-2 immune escape mutations over a period of seven months. During the persisting SARS-CoV-2 infection seventeen non-synonymous mutations were observed, thirteen (13/17; 76.5%) of which occurred in the genomic region coding for spike. Fifteen (15/17; 88.2%) of these mutations have already been described in the context of variants of concern and include the prominent immune escape mutations S:E484K, S:D950N, S:P681H, S:N501Y, S:del(9), N:S235F and S:H655Y. Fifty percent of all mutations acquired by the investigated strain (11/22) are found in similar form in the Omicron variant of concern. The study shows the chronology of the evolution of intra-host mutations, which can be seen as the straight mutational response of the virus to specific antibodies and should therefore be given special attention in the rating of immune escape mutations of SARS-CoV-2.

Different scenarios explaining the emergence of novel variants of concern (VOC) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been reported, including their evolution in scarcely monitored populations, in animals as alternative hosts, or in immunocompromised individuals. Here we report SARS-CoV-2 immune escape mutations over a period of seven months in an immunocompromised patient with prolonged viral shedding. Signs of infection, viral shedding and mutation events are periodically analyzed using RT-PCR and next-generation sequencing based on naso-pharyngeal swabs, with the results complemented by immunological diagnostics to determine humoral and T cell immune responses. Throughout the infection course, 17 non-synonymous intra-host mutations are noted, with 15 (88.2%) having been previously described as prominent immune escape mutations (S:E484K, S:D950N, S:P681H, S:N501Y, S:del(9), N:S235F and S:H655Y) in VOCs. The high frequency of these non-synonymous mutations is consistent with multiple events of convergent evolution. Thus, our results suggest that specific mutations in the SARS-CoV-2 genome may represent positions with a fitness advantage, and may serve as targets in future vaccine and therapeutics development for COVID-19.

Knowledge of the level and duration of protective immunity against SARS‐CoV‐2 after primary infection is of crucial importance for preventive approaches. Currently, there is a lack of evidence on the persistence of specific antibodies. We investigated the generation and maintenance of neutralizing antibodies of convalescent SARS‐CoV‐2‐afflicted patients over a ten‐month period post‐primary infection using an immunofluorescence assay, a commercial chemiluminescent immunoassay and an in‐house enzyme‐linked neutralization assay. We present the successful application of an improved version of the plaque‐reduction neutralization assay which can be analysed optometrically to simplify data interpretation. Based on the results of the enzyme‐linked neutralization assay, neutralizing antibodies were maintained in 77.4% of convalescent individuals without relevant decay over ten months. Furthermore, a positive correlation between severity of infection and antibody titre was observed. In conclusion, SARS‐CoV‐2‐afflicted individuals have been proven to be able to develop and maintain neutralizing antibodies over a period of ten months after primary infection. Findings suggest long‐lasting presumably protective humoral immune responses after wild‐type infection.

Background At the beginning of the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), little was known about its actual rate of infectivity and any COVID-19 patient positive in laboratory testing was supposed to be highly infective and a public health risk factor. Methods One hundred oropharyngeal samples were obtained during routine work flow of testing symptomatic persons by quantitative polymerase chain reaction (qPCR) and were inoculated onto cell culture of VeroB4 cells to study the degree of infectivity of SARS-CoV-2 in vitro. Quantification by virus titration and an external standard using synthetic RNA gave the breaking point of infectivity in SARS-CoV-2 in vitro. Results A clear negative correlation (r = − 0.76; p Conclusions This study showed that only the 21% of samples with the highest viral load were infectious enough to transmit the virus in vitro and determined that the dispersion rate in vitro is surprisingly close to those calculated in large retrospective epidemiological studies for SARS-CoV-2. This raises the question of whether this simple in vitro model is suitable to give first insights in dispersion characters of novel or neglected viral pathogens. The statement that SARS-CoV-2 needs at least 40,000 copies to reliably induce infection in vitro is an indication of its transmissibility in Public Health decisions. Applying quantitative PCR systems in diagnosis of SARS-CoV2 can distinguish between patients providing a high risk of transmission and those, where the risk of transmission is probably limited to close and long-lasting contacts.

A cohort of the first 50 COVID-19 patients in East Tyrol, a region in the southwest of Austria, were monitored in home quarantine. Specific viral ribonucleic acid was detected in throat swabs and stool samples. Analysis indicated a median virus shedding duration of 13 days; however, statistical outliers highlight the importance of consequent testing. This underlines the need of negative throat swabs prior to removing quarantine. We monitored the disease's characteristics via an in-house score called Corona Severity Index, in order to predict an aggravation of the disease. Special attention was paid to early symptoms, such as headache, which appeared to be significantly more common in younger patients (p=0.019). Anosmia and ageusia showed a predominance in female patients (p=0.028). Investigation revealed seven relapses and viral shedding fluctuation in four cases. A follow-up examination shed light on seroconversion which could be observed in 35 of 40 participants. This further clarifies the necessity of establishing discharge standards and follow-up management for COVID-19 patients.

Level and duration of protective immunity against SARS-CoV-2 after primary infection is of crucial importance for preventive approaches. In order to provide evidence for the longevity of specific antibodies, we investigated the generation and maintenance of neutralizing antibodies of convalescent SARS-CoV-2-afflicted patients over a five month period post primary infection using an immunofluorescence assay, a commercial chemiluminescent immunoassay and an in-house enzyme-linked plaque-reduction neutralization assay. We present the successful application of an improved version of the plaque-reduction neutralization assay, which can be analyzed optometrically, significantly simplifying the interpretation of the results. Based on the results of the plaque-reduction neutralization assay, neutralizing antibodies were maintained in 85.3% of convalescent individuals without significant decay over five months. Furthermore, a positive correlation between severity of infection and neutralizing titer was shown. In conclusion, SARS-CoV-2-afflicted individuals have been proven to be able to establish and maintain neutralizing antibodies over a five months’ period after primary infection which allows to hope for long-lasting presumably protective humoral immunity after wild-type infection or even after vaccination.

Background After malaria, babesiosis is the second most common transfusion-transmitted parasitic disease in the United States. In Europe, one reported transfusion case, concerning Babesia microti, occurred in Germany. Study Design and Methods Due to the fact that Babesia spp. are present in Tyrolean ticks, the aim of this study is to assess the occurrence of immunoglobulin (Ig)G antibodies against the Babesia divergens complex, including B. divergens and Babesia venatorum (EU1), as well as B. microti by screening a representative collective of 988 blood donors from North and East Tyrol (Austria) with indirect immunofluorescence antibody test. Additionally, we investigated 206 local ixodid ticks for the presence of babesial DNA by polymerase chain reaction. Results Seroprevalence data resulted in rates of 2.1% for IgG antibodies against the B. divergens complex and 0.6% against B. microti in Tyrolean blood donors. All sera could be confirmed by independent retesting. Our data indicate that cross-reactivity is high between B. divergens and B. venatorum and lower than 19.8% between B. divergens and B. microti. Conclusions This study shows that Babesia spp. are present in the Tyrols, which blood donors come into serologic contact with, and that we have to consider how to sustain blood product safety concerning this new challenge. Additionally, it is the first description of B. venatorum in the Tyrols, found in one Ixodes ricinus at the Italian border.

Summary The aim of our study was to assess the occurrence of Rickettsia in the inner-alpine valleys of the Eastern Alps and to determine the amount of seroreaction among the local human population. Ticks were investigated by PCR and the percentage of seropositives was determined among local blood donors by an in-house immunofluorescence assay. The local cut-off titre for screening of IgG was set at 1 : 128 with a well-characterised low-risk collective according to WHO-guidelines. Positive sera were confirmed by independent re-testing. Rickettsia is present in ticks north and south of the continental divide. Of 259 ticks investigated, 12.4% are positive for Rickettsia. Of over 1200 blood donors tested so far, 7.7% bear IgG at a titre of 1 : 128 or higher against R. helvetica. R. helvetica is present in the study area, causes immunoreaction among local residents and is associated with anamnestic erythema. Furthermore, screening with a second Spotted Fever Group Rickettsia indicates that significant parts of the Tyrolean population are exposed to a Rickettsia other than R. helvetica.

West Nile virus and Usutu virus are spreading over Europe. The last confirmed outbreaks of West Nile virus took place in Greece in 2011 and Northern Italy, 2012. A serious outbreak of Usutu virus in birds occurred in Germany in 2010 and 2011, indicating an increased risk of Usutu virus infections in humans. Sera of 1,607 healthy blood donors in the Tyrols (Austria and Italy) were investigated for the presence of IgG antibodies for tick-borne encephalitis virus and West Nile virus by ELISA as well as for Usutu virus by in-house immunofluorescence assay. Furthermore, 2,571 mosquitoes were trapped in the study area and screened for flaviviral and West Nile-specific RNA by RT-PCR. Initial results indicated seroprevalence rates of 46.2% for West Nile virus in North Tyrol and 0.5% in South Tyrol as well as 16.5% and 0.3% for Usutu virus, respectively, which turned out to be false positive cross-reactions with antibodies against tick-borne encephalitis virus or other vaccine-associated flaviviral antibodies by adjacent neutralization assays. Actually, neutralizing antibodies against West Nile virus were found in five sera (0.5% seroprevalence), against Usutu virus in one serum (0.1% seroprevalence). This study shows that the Tyrolean population does not come into immunoreactive contact with West Nile virus or Usutu virus and that no flavivirus could be detected in trapped mosquitoes. Furthermore, the study provides cross-reactivities of up to 58.8% (460 of 782) of flaviviral antibodies in ELISA-testing and up to 21.5% (168 of 782) in immunofluorescence assay and that cross-reactivity increases with increasing number of vaccinations against Flaviviruses. This study illuminates the degree of cross-reactivities of flaviviral antibodies in a healthy blood donor collective and shows the difficulties in the differentiation of flaviviral antibodies in serologic diagnostics.

Seroprevalence rates for immunoglobulin G (IgG) antibodies to Tahyna virus (TAHV) and Inkoo virus (INKV) were determined in sera of 1630 blood donors from North, East, and South Tyrol by immunofluorescence assays (IFAs) and confirmatory serum neutralization tests (SNTs). Ten sera (0.6%) reacted positive by TAHV IFA, five of which (0.3%) were confirmed by SNT. Eleven sera (0.7%) reacted positive in the INKV IFA; only one thereof (0.06%) was verified by subsequent SNT. To identify the source of infections, mosquitoes were trapped at 18 sampling sites in the study area, resulting in the collection of 2571 adult mosquitoes: 1254 individuals of the genus Aedes (48.8% of total) including A. albopictus, 640 Culex (24.9%), 303 Coquillettidia (11.8%), 252 Ochlerotatus (9.8%), 49 Anopheles (1.9%), and 73 mosquitoes of the genus Culiseta (2.8%). The mosquitoes were pooled according to species, trapping site, and time, and were tested by RT-PCR for the presence of California serogroup orthobunyavirus nucleic acids. PCR amplification products were obtained in five of 195 pools (2.6%), and all were identified as TAHVs by subsequent sequencing. This represents the first evidence of TAHV circulation and human exposure in the Tyrols and in the alpine region in general. Interestingly, all TAHV sequences were identified in Culex pipiens/torrentium mosquitoes. Whether other California serogroup orthobunyaviruses such as INKV are also circulating in this area is subject of further investigations on larger numbers of mosquitoes.

After malaria, babesiosis is the second most common transfusion-transmitted parasitic disease in the United States. In Europe, one reported transfusion case, concerning Babesia microti, occurred in Germany.Due to the fact that Babesia spp. are present in Tyrolean ticks, the aim of this study is to assess the occurrence of immunoglobulin (Ig)G antibodies against the Babesia divergens complex, including B. divergens and Babesia venatorum (EU1), as well as B. microti by screening a representative collective of 988 blood donors from North and East Tyrol (Austria) with indirect immunofluorescence antibody test. Additionally, we investigated 206 local ixodid ticks for the presence of babesial DNA by polymerase chain reaction.Seroprevalence data resulted in rates of 2.1% for IgG antibodies against the B. divergens complex and 0.6% against B. microti in Tyrolean blood donors. All sera could be confirmed by independent retesting. Our data indicate that cross-reactivity is high between B. divergens and B. venatorum and lower than 19.8% between B. divergens and B. microti.This study shows that Babesia spp. are present in the Tyrols, which blood donors come into serologic contact with, and that we have to consider how to sustain blood product safety concerning this new challenge. Additionally, it is the first description of B. venatorum in the Tyrols, found in one Ixodes ricinus at the Italian border.

Seroprevalences were determined by testing sera of 1607 blood donors from North, East, and South Tyrol. In the Tyrols, the continental divide delimitates areas with high seroprevalences of IgG antibodies against Borrelia burgdorferi sensu lato in the North (7.2%) from areas with low seroprevalences in the South (1.5%). To determine Borrelia prevalences in unfed Ixodes ricinus ticks, 755 questing ticks were tested by PCR. Prevalences in nymphal and adult ticks were found to be 19.7% (n=132) and 21.5% (n=205) in North Tyrol and 23% (n=43) and 23.7% (n=376) in South Tyrol, respectively. Sequencing of 46 Borrelia-positive ticks yielded 74% Borrelia (B.) afzelii, 11% B. garinii, 7% B. lusitaniae, 7% B. burgdorferi sensu stricto, and 2% B. valaisiana infections. Distinct genetic clusters could not be delimitated on either side of the continental divide. This study describes occurrence and geographic dispersion of Borrelia spp. in the Tyrols, discusses possible reasons for significant differences in human seroprevalence, and indicates that prevalence of Borrelia in vector ticks is not a direct predictive factor for the local seroprevalence in humans.

In the last several years, West Nile virus (WNV) was proven to be present especially in the neighboring countries of Austria, such as Italy, Hungary, and the Czech Republic, as well as in eastern parts of Austria, where it was detected in migratory and domestic birds. In summer 2010, infections with WNV were reported from Romania and northern Greece with about 150 diseased and increasingly fatal cases. We tested the sera of 1,607 blood donors from North Tyrol (Austria) and South Tyrol (Italy) for antibodies against WNV by using IgG enzyme-linked immunosorbent assay (ELISA). Initial results of the ELISA tests showed seroprevalence rates of 46.2% in North Tyrol and 0.5% in South Tyrol, which turned out to be false-positive cross-reactions with antibodies against tick-borne encephalitis virus (TBEV) by adjacent neutralization assays. These results indicate that seropositivity against WNV requires confirmation by neutralization assays, as cross-reactivity with TBEV is frequent and because, currently, WNV is not endemic in the study area.