Context dependent substitution biases vary within the human genome

Background: Models of sequence evolution typically assume that different nucleotide positions evolve independently. This assumption is widely appreciated to be an over-simplification. The best known violations involve biases due to adjacent nucleotides. There have also been suggestions that biases exist at larger scales, however this possibility has not been systematically explored. Results: To address this we have developed a method which identifies over- and under-represented substitution patterns and assesses their overall impact on the evolution of genome composition. Our method is designed to account for biases at smaller pattern sizes, removing their effects. We used this method to investigate context bias in the human lineage after the divergence from chimpanzee. We examined bias effects in substitution patterns between 2 and 5 bp long and found significant effects at all sizes. This included some individual three and four base pair patterns with relatively large biases. We also found that bias effects vary across the genome, differing between transposons and non-transposons, between different classes of transposons, and also near and far from genes. Conclusions: We found that nucleotides beyond the immediately adjacent one are responsible for substantial context effects, and that these biases vary across the genome

Severe acute respiratory syndrome coronavirus 2, primary varicella zoster virus coinfection, and a polymicrobial ventilator-associated tracheobronchitis in an adult immunocompetent male: a case report

BACKGROUND: The spectrum of clinical manifestations and differential diagnosis associated with coronavirus disease 2019 is broad, ranging from fever and cutaneous eruptions to respiratory distress or even neurological disorders. Coexisting multipathogen infections significantly increase the complexity of the proper diagnostic and therapeutic approach and correlate with the rate of intensive care unit admissions and in-hospital mortality. CASE PRESENTATION: We present a case of multipathogen respiratory infection with severe acute respiratory syndrome coronavirus 2, varicella zoster virus, and polymicrobial tracheobronchitis in a 48-year-old Caucasian male hospitalized after traumatic brain injury. The patient tested positive for severe acute respiratory syndrome coronavirus 2 infection upon admission. During his stay in the intensive care unit, the patient developed a vesicular exanthema along with respiratory failure and signs of septic shock. CONCLUSION: This case of an adult presenting with severe acute respiratory syndrome coronavirus 2 infection and simultaneous primary varicella zoster virus infection illustrates the importance of considering coinfections in patients with coronavirus disease 2019 with unusual clinical manifestations

Quantitation of norovirus-specific IgG before and after infection in immunocompromised patients.

Noroviruses (NoV) cause the majority of non-bacterial gastroenteritis cases worldwide, with genotype II.4 being the most common. The aim of our study was to quantitate norovirus-specific IgG in immunocompromised patients before and after laboratory-confirmed norovirus infection. A quantitative ELISA was developed by coating ELISA plates with recombinantly expressed P domain of GII.1 capsid protein. After testing mouse sera drawn before and after immunization with GII.1- and GII.4 P domain, sera from GII.1- and GII.4 infected patients were tested. The assay reliably detected preexisting NoV-specific IgG antibodies. Sera drawn after infection showed increased antibody concentrations. Antibodies elicited by GII.1- and GII.4 infections could be detected with coated GII.1 capsid protein. IgG levels remained constant during the first week and then increased in the second week after laboratory diagnosis. The results show that immunocompromised patients elicited IgG responses to NoV infections that could be reliably detected with our quantitative ELISA