Culturing of SARS-CoV-2 from patient samples: Protocol for optimal virus recovery and assessment of infectious viral load

Optimal sampling, preservation, and culturing of SARS-CoV-2 from COVID-19 patients are critical for successful recovery of virus isolates and to accurately estimate contagiousness of the patient. In this study, we investigated the influence of the type of sampling media, storage time, freezing conditions, sterile filtration, and combinations of these to determine the optimal pre-analytic conditions for virus recovery and estimation of infectious viral load in COVID-19 patients. Further, we investigated the viral shedding kinetics and mucosal antibody response in 38 COVID-19 hospitalized patients. We found Universal Transport Medium (Copan) to be the most optimal medium for preservation of SARS-CoV-2 infectivity. Our data showed that the probability of a positive viral culture was strongly correlated to Ct values, however some samples did not follow the general trend. We found a significant correlation between plaque forming units and levels of mucosal antibodies and found that high levels of mucosal antibodies correlated with reduced chance of isolating the virus. Our data reveals essential parameters to consider from specimen collection over storage to culturing technique for optimal chance of isolating SARS-CoV-2 and accurately estimating patient contagiousness.

Omicron Variant-Specific Serological Imprinting Following BA.1 or BA.4/5 Bivalent Vaccination and Previous SARS-CoV-2 Infection: A Cohort Study

BACKGROUND

Continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outpaces monovalent vaccine cross-protection to new viral variants. Consequently, bivalent coronavirus disease 2019 (COVID-19) vaccines including Omicron antigens were developed. The contrasting immunogenicity of the bivalent vaccines and the impact of prior antigenic exposure on new immune imprinting remains to be clarified.

METHODS

In the large prospective ENFORCE cohort, we quantified spike-specific antibodies to 5 Omicron variants (BA.1 to BA.5) before and after BA.1 or BA.4/5 bivalent booster vaccination to compare Omicron variant-specific antibody inductions. We evaluated the impact of previous infection and characterized the dominant antibody responses.

RESULTS

Prior to the bivalent fourth vaccine, all participants (N = 1697) had high levels of Omicron-specific antibodies. Antibody levels were significantly higher in individuals with a previous polymerase chain reaction positive (PCR+) infection, particularly for BA.2-specific antibodies (geometric mean ratio [GMR] 6.79, 95% confidence interval [CI] 6.05-7.62). Antibody levels were further significantly boosted in all individuals by receiving either of the bivalent vaccines, but greater fold inductions to all Omicron variants were observed in individuals with no prior infection. The BA.1 bivalent vaccine generated a dominant response toward BA.1 (adjusted GMR 1.31, 95% CI 1.09-1.57) and BA.3 (1.32, 1.09-1.59) antigens in individuals with no prior infection, whereas the BA.4/5 bivalent vaccine generated a dominant response toward BA.2 (0.87, 0.76-0.98), BA.4 (0.85, 0.75-0.97), and BA.5 (0.87, 0.76-0.99) antigens in individuals with a prior infection.

CONCLUSIONS

Vaccination and previous infection leave a clear serological imprint that is focused on the variant-specific antigen. Importantly, both bivalent vaccines induce high levels of Omicron variant-specific antibodies, suggesting broad cross-protection of Omicron variants.

Humoral antibody response following mRNA vaccines against SARS-CoV-2 in solid organ transplant recipients; a status after a fifth and bivalent vaccine dose

Background

In solid organ transplant (SOT) recipients, the humoral response following COVID-19 vaccination is reduced, as a result of their immunosuppressed treatment. In this study, we investigated antibody concentrations after booster vaccinations until the fifth dose, the latter by monovalent or bivalent BA1 or BA4/5 vaccines. In addition, we evaluated the efficacy of vaccination by recording breakthrough infections, hospitalizations, and deaths.

Method

This prospective cohort study included 438 SOT recipients (>18 years) vaccinated with mRNA vaccines against COVID-19 from January 2021 until March 2023. Blood samples were drawn before and after each vaccination and tested for SARS-CoV-2 spike RBD IgG antibodies with the lowest and highest cut-off at 7.1 and 5,680 BAU/mL, respectively. Vaccine information, breakthrough infections, and hospitalizations were collected from the medical records.

Results

Most participants received BNT162b2 and 61.4% received five vaccine doses. The response proportion in SOT recipients increased from 86.7% after the fourth dose to 93.0% following the fifth dose. Antibody concentration decreased with 142.7 BAU/mL between the third and fourth dose (median 132 days, Quartile 1: 123, Quartile 3: 148) and 234.3 BAU/mL between the fourth and fifth (median 250 days, Quartile 1: 241, Quartile 3: 262) dose among those without breakthrough infection (p=0.34). When comparing the Omicron BA.1 or Omicron BA.4/BA.5 adapted vaccines, no significant differences in antibody concentration were found, but 20.0% of SOT recipients receiving a monovalent fifth vaccine dose had a breakthrough infection compared to 4.0% and 7.9% among those who received BA.1 and BA.4/BA.5 adapted vaccines, respectively (p=0.04). Since January 2021, 240 (54.8%) participants had a breakthrough infection, and 22 were hospitalized, but no deaths were observed.

Conclusions

The fifth COVID-19 vaccine dose raised antibody response to 93.0% of the study population. Additional booster doses, as well as bivalent vaccines, led to higher levels of antibody concentration in SOT recipients. We found a lower incidence of breakthrough infections among SOT recipients after receiving a bivalent vaccine as a fifth dose compared to those receiving a monovalent dose. Antibody concentrations did not wane when the time between doses was prolonged from four to eight months.

SARS-CoV-2 vaccine-induced antibodies protect against Omicron breakthrough infection

SARS-CoV-2 Omicron quickly spread globally, also in regions with high vaccination coverage, emphasizing the importance of exploring the immunological requirements for protection against Omicron breakthrough infection. The test-negative matched case-control study (N = 964) characterized Omicron breakthrough infections in triple-vaccinated individuals from the ENFORCE cohort. Within 60 days before a PCR test spike-specific IgG levels were significantly lower in cases compared to controls (GMR [95% CI] for BA.2: 0.83 [0.73-0.95], p = 0.006). Multivariable logistic regression showed significant associations between high antibody levels and lower odds of infection (aOR [95% CI] for BA.2 spike-specific IgG: 0.65 [0.48-0.88], p = 0.006 and BA.2 ACE2-blocking antibodies: 0.46 [0.30-0.69], p = 0.0002). A sex-stratified analysis showed more pronounced associations for females than males. High levels of vaccine-induced antibodies provide partial protection against Omicron breakthrough infections. This is important knowledge to further characterize a threshold for protection against new variants and to estimate the necessity and timing of booster vaccination.

Viral dynamics of SARS-CoV-2 in immunocompromised patients

OBJECTIVES

Immunocompromised patients infected with SARS-CoV-2 have been shown to shed replicable virus for a prolonged period of time, and the duration of isolation can therefore be difficult to estimate. The objective of this study was to evaluate the viral load dynamic in non-hospitalized immunocompromised patients infected with SARS-CoV-2 and treated with monoclonal antibodies (mAbs) or antivirals.

METHODS

Oropharyngeal swabs for RT-PCR and viral culture were collected from 29 immunocompromised patients before treatment with mAbs or antivirals and at days 5 and 15 after treatment. Overall, 12 patients were infected with the subvariant Omicron BA.1, 12 with Omicron BA.2, two with the Delta variant and for three patients determination of the variant were inconclusive.

RESULTS

Before treatment with mAbs or antivirals, 22 of 29 patients (76% [95% CI, 56-90]) shed replicative SARS-CoV-2. At day 5, 21 patients (72% [95% CI, 53-87]) still tested RT-PCR-positive, but for 14 patients (48% [95% CI, 29-67]) there were no replicative virus in culture. At day 15, 16 patients (55% [95% CI, 36-74%]) tested positive but only two patients (7% [95%CI, 1-23]) had replicative virus.

DISCUSSION

Half of the patients in this cohort had no viable virus after 5 days and only two patients had replicative virus after 15 days. This could indicate that the current CDC recommendations of an isolation period of 20 days for immunocompromised patients infected with SARS-CoV-2 could be reduced, but larger studies are needed to estimate the isolation duration for immunocompromised patients.

Serum Neutralization of SARS-CoV-2 Omicron BA.1 and BA.2 after BNT162b2 Booster Vaccination

The SARS-CoV-2 Omicron variant BA.2 sublineage is rapidly replacing earlier Omicron lineages, suggesting BA.2 has increased vaccine evasion properties. We measured neutralization titers of authentic BA.1 and BA.2 isolates in serum samples from persons who received the BNT162b2 booster vaccine. All samples neutralized BA.1 and BA.2 at equal median values.

Inferior cure rate in pilot study of 4-week glecaprevir/pibrentasvir treatment with or without ribavirin of chronic hepatitis C

BACKGROUND & AIMS

Shortening the treatment duration for chronic hepatitis C may increase feasibility and reduce the cost of cure. The aims of this study were to compare 4 weeks of glecaprevir/pibrentasvir (GLE/PIB) treatment with and without ribavirin for patients with chronic hepatitis C and favourable baseline characteristics and to monitor the development of resistance-associated substitutions (RAS) and re-treatment outcomes if treatment failed.

METHODS

We performed an open-label single-centre randomized controlled trial, in which patients with chronic hepatitis C were randomized 1:1 to GLE/PIB ± ribavirin, stratified by genotype 3. The main inclusion criteria were treatment-naive patients, aged 18-49 with all genotypes accepted, and absence of liver fibrosis, determined by liver stiffness measurement less than 8 kPa. Viral genome sequences were determined by deep sequencing at baseline and at the time of relapse.

RESULTS

A total of 32 patients started treatment. Sustained virological response at week 12 (SVR12) was 59% (10/17) for GLE/PIB without ribavirin and 73% (11/15) for GLE/PIB with ribavirin. Drug target-specific NS5A RAS were detected at baseline for 45% (5/11) of patients with treatment failure and for 14% (3/21) of patients who achieved SVR12. Ten failure patients were retreated 12 weeks with sofosbuvir-based regimens; all have been cured.

CONCLUSIONS

In this pilot study of 4-week treatment with GLE/PIB with and without ribavirin, we found that baseline RAS were more frequent in patients with virological failure. Development of RAS did occur after short treatment but did not result in retreatment failure with a different regimen. EudraCT no: 2017-005179-21.

Characterization of a Novel Hepatitis C Virus Genotype 1 Subtype from a Patient Failing 4 Weeks of Glecaprevir-Pibrentasvir Treatment

Limited information is available in relation to surveillance, genotyping, genome sequences, and treatment outcomes for rare hepatitis C virus variants. Here, we have characterized a novel subtype of major hepatitis C virus genotype 1, which was deep sequenced before and after treatment failure with 4 weeks of glecaprevir and pibrentasvir.

Growth differences of male and female Göttingen minipigs during ad libitum feeding: a pilot study

Even though minipigs have been used in biomedical research for nearly half a century now, no specific nutrient requirements are available. For that reason a series of studies into the nutrient requirements of Göttingen minipigs were carried out. Firstly, a pilot study was carried out to determine the ad libitum feed intake (FI) during growth, as a reference for later feed restriction studies. Four male and four female minipigs were fed two types of diet, one standard pig diet (20.6% crude protein; 11.7% crude fat; 13.5 mJ/kg DM metabolizable energy) and one diet specially designed for minipigs (12.0% crude protein; 2.9% crude fat; 11.9 MJ/kg DM metabolizable energy). When fed ad libitum for 13 weeks, female Göttingen minipigs developed a significantly ( P <0.05) higher body weight (BW) than males (27.4 vs 16.6 kg) on either diet. The large difference in growth between male and female Göttingen minipigs did not appear to be the result from differences in metabolizable energy intake. Metabolizable energy intake of male and female Göttingen minipigs could be predicted by ME = 1877 kJ × BW0.61. Both male and female Göttingen minipigs became obese when fed ad libitum, defined by relative backfat thickness. Relative backfat thickness ranged from 5 to 13 cm/100 kg. Females had thicker relative backfat layers than males. Remarkably, no large changes in haematology and clinical chemistry occurred in ad libitum fed Göttingen minipigs as compared to reference values, and no abnormalities other than enlarged fat reserves were observed at necropsy. Apparently, Göttingen minipigs do not restrain FI voluntarily, and restricted feeding is therefore indicated to prevent obesity.

Depressive symptoms are frequent among drug users, but not associated with hepatitis C infection

AIM

To compare the prevalence and severity of depressive symptoms among drug users with and without hepatitis C virus (HCV) infection.

METHODS

This was a cross-sectional survey study carried out at the 2 major drug treatment centres on the island of Funen, Denmark. Participants were drug users presenting to the 2 treatment centres. Individuals with chronic hepatitis B virus or HIV infection were excluded. Participants completed the Major Depression Inventory (MDI) questionnaire when presenting at the centres. Patients with MDI scores indicating severe depression (total MDI score ≥ 35) were referred for treatment evaluation. Hepatitis C status was classified by the presence of anti-HCV as a marker of HCV exposure and HCV-RNA as a marker of ongoing infection.

RESULTS

Two hundred and sixty-eight patients were included, of whom 235 (88%) had complete serological testing; 100 (43%, 95% confidence interval (CI) 36-49%) had chronic hepatitis C. The median MDI score was 22 (interquartile range 12-33); 32% (95% CI 26-39%) had a score compatible with depression and 14% (95% CI 10-19%) were rated as severe depression. Depression was not associated with hepatitis C (HCV-infected 29%, non-infected 35%; p = 0.25). Forty-one percent (11/27) of the evaluated participants started antidepressant treatment.

CONCLUSIONS

Our study demonstrated a high prevalence of depressive symptoms among drug users, but this was not more frequent among HCV-infected patients. The high overall prevalence of depression underlines the relevance of screening for depression in patients who are drug users.

Immune complex-associated thrombocytopenic purpura syndrome in sexually mature Göttingen minipigs

Eleven cases of thrombocytopenic purpura (TP) in sexually mature male or female Göttingen minipigs occurred sporadically over 3 1/2 years in a closed breeding colony protected by strict barrier conditions. Typical clinical signs of TP, including extensive subcutaneous haemorrhages, were seen in all affected animals. Haematological abnormalities included marked thrombocytopenia and anaemia. A consistent histopathological finding was the presence of membranoproliferative lesions in the renal glomeruli. Immunohistochemically, glomerular deposits were positively labelled for complement factor C1q and often also for immunoglobulins. Bone marrow findings consisting of increased numbers of immature and apoptotic megakaryocytes were compatible with a state of increased platelet consumption. Based on the combined presence of thrombocytopenia and renal immune complexes, it is suggested that the syndrome was related to a type III hypersensitivity reaction. However, further studies are needed to verify this hypothesis.

Bacterial colonization and invasion in pigs experimentally exposed to Streptococcus suis serotype 2 in aerosol

A recently developed porcine model for aerogenous infection with Streptococcus suis serotype 2 was applied in a study of the phases of bacterial colonization and initial invasion. Eighteen pigs were exposed to aerosolized S. suis serotype 2 after pre-exposure to mild acetic acid in aerosol. The animals were killed consecutively within the first six days after challenge. After death, all animals were necropsied and examined by bacteriology, histopathology, and immunohistochemistry. Systemic infection was established in four out of 18 animals exposed to S. suis serotype 2. All systemically infected animals developed clinical signs and lesions typical of the infection. In four additional animals, subclinical infection was demonstrated by re-isolation of S. suis from the palatine tonsil. However, in all 18 challenged animals, immunohistochemistry demonstrated S. suis serotype 2 antigen in the palatine and/or nasopharyngeal tonsils. In all four systemically infected animals, S. suis serotype 2 antigen was also found in the mandibular lymph node. These observations point towards the tonsils as possible portals of entry for S. suis serotype 2 with subsequent lymphogenous spread. Thus, the present findings parallel the proposed pathogenesis for S. suis serotype 1 infection in pigs.

Streptococcus suis serotype 2 infection in pigs: new diagnostic and pathogenetic aspects

In a study aimed at improving the diagnosis and elucidating the pathogenesis of Streptococcus suis serotype 2 infection in pigs, a combination of bacterial culture and histopathological and immunohistochemical examination was applied to a range of tissues from 42 naturally infected pigs with typical macroscopical lesions. By culture, 21 pigs (50%) were shown to be systemically infected with S. suis serotype 2; seven (17%) were infected with S. suis serotype 7, two with other bacteria, and 12 yielded no bacterial pathogens. The highest isolation rate for S. suis serotype 2 was obtained from the lateral cerebral ventricles and other regions of the brain, whereas the bacterium was only rarely isolated from the liver or spleen. Immunohistochemically, a diagnosis of S. suis serotype 2 infection was obtained in two of 12 (17%) animals from which no pathogens had been cultured. Moreover, immunohistochemistry differed from culture in revealing a greater number of positive tissue specimens. The microanatomical distribution of bacteria pointed toward the pharyngeal and palatine tonsils as principal portals of entry. Furthermore, S. suis serotype 2 bacteria were frequently identified immunohistochemically in the regional lymph nodes of the upper respiratory tract, possibly reflecting primary lymphogenous spread from the tonsils.

An enzyme-based in situ hybridisation method for the identification of Streptococcus suis

A method for enzyme-based in situ hybridisation of Streptococcus suis was developed. It enables the light microscopic localization of bacterial ribosomal RNA (rRNA) in formalin-fixed paraffin-embedded tissues. A unique sequence in the 16S rRNA of S. suis was targeted. Different pretreatment protocols were applied to facilitate probe penetration and multiple detection systems were tested. The results were compared to those obtained by immunohistochemistry. Pretreatment was necessary to obtain a signal by in situ hybridisation. The use of proteinase-K pretreatment was optimal regarding sensitivity and preservation of tissue morphology. A strong specific in situ hybridisation signal was achieved in tissue sections containing S. suis in microcolonies and the microanatomy of the surrounding tissue was easily assessed. However, the signal distribution differed from that found immunohistochemically and low-grade infection could not be detected by in situ hybridisation. These findings were interpreted as reflecting the physiological state of the bacteria. Thus, this method could prove useful in future studies of the infection pathogenesis.

Aerogenous infection of microbiologically defined minipigs with Streptococcus suis serotype 2. A new model

Streptococcus suis serotype 2 is the cause of serious infections in animals and humans, but certain aspects of the infection pathogenesis still remain unclear. In this study an experimental model of aerogenous infection and induction of septicemia with S. suis serotype 2 was established in microbiologically defined Göttingen minipigs. Ten animals were exposed to aerosolized S. suis after previous exposure to mild acetic acid in aerosol. Six of the animals were immunosuppressed with prednisolone acetate on different days. All the animals were monitored clinically until euthanasia on days 6 to 13 after exposure. Necropsy was performed and samples were taken for microbiology, histopathology, and immunohistochemistry Three out of four animals immunosuppressed on days 5 to 7 after exposure developed S. suis septicemia, and S. suis could be detected in the tonsil of the soft palate and/or the nasal cavity of all exposed animals. Thus, using the presented model, local as well as systemic infection with S. suis serotype 2 was established in the Göttingen minipig. Since this breed is defined as free of S. suis and a range of other endemic porcine pathogens, the experimental model could prove useful in the study of this infection.

Otitis interna is a frequent sequela to Streptococcus suis meningitis in pigs

Twenty-eight histologically confirmed cases of porcine leptomeningitis were examined retrospectively, with focus on the pathology of the inner and middle ear, brain, and vestibulocochlear nerve. Tissues were evaluated by histology and immunohistochemistry for Streptococcus suis serotype 2 antigen, and the bacteriologic results were recorded. Exudative otitis interna was diagnosed in 20/28 pigs (71%). The lesions primarily affected the perilymphatic ducts, with consistent involvement of the scala tympani. Perineuritis of the vestibulocochlear nerve was seen in all but four of the ears affected with otitis interna. Immunohistochemically, S. suis serotype 2 antigen was demonstrated in the leptomeningeal, perineural, and labyrinthine exudates in 11 cases. Otitis media was diagnosed in 10/28 pigs (34%), but evidence of extension to the inner ear was not observed. The findings were highly similar to descriptions of meningogenic labyrinthitis in humans and in laboratory animal models. Otitis interna in pigs can also develop via the meningogenic route and is not always, as generally stated, tympanogenic.