The burden of ticks and the pathogens they carry is increasing worldwide. Powassan virus (POWV, Flaviviridae: Flavivirus), the only known North American tick-borne flavivirus, is of particular concern due to rising cases and the severe morbidity of POWV encephalitis. Here, we use a multifaceted approach to evaluate the emergence of lineage II POWV, known as deer tick virus (DTV), in parts of North America where human cases occur. We detected DTV-positive ticks from eight of twenty locations in the northeastern United States with an average infection rate of 1.4%. High-depth whole genome sequencing of eighty-four POWV and DTV samples allowed us to assess geographic and temporal phylodynamics. We observed both stable infection in the northeastern United States and patterns of geographic dispersal within and between regions. Bayesian skyline analysis demonstrated DTV population expansion over the last fifty years. This is concordant with the documented expansion of I. scapularis tick populations and suggests increasing risk of human exposure as the vector spreads. Finally, we isolated sixteen novel viruses in cell culture and demonstrated limited genetic change after passage, a valuable resource for future studies investigating this emerging virus.

SARS-CoV-2 escape from combination monoclonal antibody treatment is rarely reported. We describe an immunocompromised individual with HIV and persistent SARS-CoV-2 infection, in whom substantial SARS-CoV-2 evolution occurred, including the emergence of two mutations associated with escape from the monoclonal antibody cocktail received.

Objectives Viral infections of the central nervous system can be challenging to diagnose because of the wide range of causative agents and nonspecific histologic features. We sought to determine whether detection of double-stranded RNA (dsRNA), produced during active RNA and DNA viral infections, could be used to select cases for metagenomic next-generation sequencing (mNGS) from formalin-fixed, paraffin-embedded brain tissue. Methods Eight commercially available anti-dsRNA antibodies were optimized for immunohistochemistry (IHC) and the top antibody tested in a series of cases with confirmed viral infections (n = 34) and cases with inflammatory brain lesions of unclear etiology (n = 62). Results Among known positives, anti-dsRNA IHC produced a strong cytoplasmic or nuclear staining pattern for Powassan virus, West Nile virus, rabies virus, JC polyoma virus, and adenovirus while failing to detect Eastern equine encephalitis virus, Jamestown Canyon virus, or any herpesvirus. All the unknown cases were negative by anti-dsRNA IHC, while mNGS detected rare viral reads (0.3-1.3 reads per million total reads) in 2 cases (3%), with only 1 having potential clinical significance. Conclusions Anti-dsRNA IHC can effectively identify a subset of clinically relevant viral infections but not all. The absence of staining should not exclude cases from mNGS if sufficient clinical and histologic suspicion exists.

Background Professional soccer athletes are at risk of acquiring SARS-CoV-2 when traveling or through domestic community transmission. The U.S. Major League Soccer (MLS) league uses protocol-based SARS-CoV-2 testing for identification of individuals with COVID-19. Methods Per MLS protocol, fully vaccinated players underwent SARS-CoV-2 RT-PCR testing weekly; unvaccinated players were tested every other day. Demographic and epidemiologic data (e.g., travel history) were collected from individuals who tested positive, and contact tracing was performed. Whole genome sequencing (WGS) was performed on positive specimens, and phylogenetic analyses were used to identify potential transmission patterns. Results In the fall of 2021, all 30 players from one MLS team underwent SARS-CoV-2 testing per protocol; 27 (90%) were vaccinated. One player who recently traveled to Africa tested positive for SARS-CoV-2; within the following two weeks, 10 additional players and 1 staff member without recent international travel history tested positive. WGS yielded full genome sequences for 10 samples, including one from the traveler. The traveler’s sample was Delta sublineage AY.36 and was closely related to a sequence from Africa. Nine samples yielded other Delta sublineages including AY.4 (n = 7), AY.39 (n = 1), and B.1.617.2 (n = 1). The seven AY.4 sequences clustered together; five were identical, suggesting a common source of infection. Transmission from a family member visiting from England to an MLS player was identified as the potential index case. The other two AY.4 sequences differed from this group by 1-3 nucleotides, as did a partial genome sequence from an additional team member. Conclusions WGS is a useful tool for understanding SARS-CoV-2 transmission dynamics in professional sports teams.