Multiplex Reverse Transcription-PCR for Simultaneous Surveillance of Influenza A and B Viruses.

Influenza A and B viruses are the causative agents of annual influenza epidemics that can be severe, and influenza A viruses intermittently cause pandemics. Sequence information from influenza virus genomes is instrumental in determining mechanisms underpinning antigenic evolution and antiviral resistance. However, due to sequence diversity and the dynamics of influenza virus evolution, rapid and high-throughput sequencing of influenza viruses remains a challenge. We developed a single-reaction influenza A/B virus (FluA/B) multiplex reverse transcription-PCR (RT-PCR) method that amplifies the most critical genomic segments (hemagglutinin [HA], neuraminidase [NA], and matrix [M]) of seasonal influenza A and B viruses for next-generation sequencing, regardless of viral type, subtype, or lineage. Herein, we demonstrate that the strategy is highly sensitive and robust. The strategy was validated on thousands of seasonal influenza A and B virus-positive specimens using multiple next-generation sequencing platforms.

Microclimate conditions alter Ixodes scapularis (Acari: Ixodidae) overwinter survival across climate gradients in Maine, United States.

The incidence and geographic range of vector-borne diseases have been expanding in recent decades, attributed in part to global climate change. Blacklegged ticks (Ixodes scapularis), the primary vector for multiple tick-borne pathogens in North America, are spreading rapidly beyond their historic post-colonial range and are thought to be constrained mainly by winter temperature at northern latitudes. Our research explored whether winter climate currently limits the distribution of blacklegged ticks and the pathogens they transmit in Maine, U.S.A., by contributing to overwinter mortality of nymphs. We experimentally tested tick overwinter survival across large-scale temperature and snowfall gradients and assessed factors contributing to winter mortality in locations where blacklegged tick populations are currently established and locations where the blacklegged tick has not yet been detected. We also tested the hypothesis that insulation in the tick microhabitat (i.e., by leaf litter and snowpack) can facilitate winter survival of blacklegged tick nymphs despite inhospitable ambient conditions. Overwinter survival was not significantly different in coastal southern compared to coastal and inland northern Maine, most likely due to sufficient snowpack that protected against low ambient temperatures at high latitudes. Snow cover and leaf litter contributed significantly to overwinter survival at sites in both southern and northern Maine. To further assess whether the current distribution of blacklegged ticks in Maine aligns with patterns of overwinter survival, we systematically searched for and collected ticks at seven sites along latitudinal and coastal-inland climate gradients across the state. We found higher densities of blacklegged ticks in coastal southern Maine (90.2 ticks/1000 m2) than inland central Maine (17.8 ticks/1000 m2) and no blacklegged ticks in inland northern Maine. Our results suggest that overwinter survival is not the sole constraint on the blacklegged tick distribution even under extremely cold ambient conditions and additional mechanisms may limit the continued northward expansion of ticks.

Microbial Composition of the Human Nasopharynx Varies According to Influenza Virus Type and Vaccination Status.

Factors that contribute to enhanced susceptibility to severe bacterial disease after influenza virus infection are not well defined but likely include the microbiome of the respiratory tract. Vaccination against influenza, while having variable effectiveness, could also play a role in microbial community stability. We collected nasopharyngeal samples from 215 individuals infected with influenza A/H3N2 or influenza B virus and profiled the microbiota by target sequencing of the 16S rRNA gene. We identified signature taxonomic groups by performing linear discriminant analysis and effective size comparisons (LEfSe) and defined bacterial community types using Dirichlet multinomial mixture (DMM) models. Influenza infection was shown to be significantly associated with microbial composition of the nasopharynx according to the virus type and the vaccination status of the patient. We identified four microbial community types across the combined cohort of influenza patients and healthy individuals with one community type most representative of the influenza virus-infected group. We also identified microbial taxa for which relative abundance was significantly higher in the unvaccinated elderly group; these taxa include species known to be associated with pneumonia.IMPORTANCE Our results suggest that there is a significant association between the composition of the microbiota in the nasopharynx and the influenza virus type causing the infection. We observe that vaccination status, especially in more senior individuals, also has an association with the microbial community profile. This indicates that vaccination against influenza, even when ineffective to prevent disease, could play a role in controlling secondary bacterial complications.