Cyclosporiasis is an illness characterised by watery diarrhoea caused by the food-borne parasite Cyclospora cayetanensis. The increase in annual US cyclosporiasis cases led public health agencies to develop genotyping tools that aid outbreak investigations. A team at the Centers for Disease Control and Prevention (CDC) developed a system based on deep amplicon sequencing and machine learning, for detecting genetically-related clusters of cyclosporiasis to aid epidemiologic investigations. An evaluation of this system during 2018 supported its robustness, indicating that it possessed sufficient utility to warrant further evaluation. However, the earliest version of CDC's system had some limitations from a bioinformatics standpoint. Namely, reliance on proprietary software, the inability to detect novel haplotypes and absence of a strategy to select an appropriate number of discrete genetic clusters would limit the system's future deployment potential. We recently introduced several improvements that address these limitations and the aim of this study was to reassess the system's performance to ensure that the changes introduced had no observable negative impacts. Comparison of epidemiologically-defined cyclosporiasis clusters from 2019 to analogous genetic clusters detected using CDC's improved system reaffirmed its excellent sensitivity (90%) and specificity (99%), and confirmed its high discriminatory power. This C. cayetanensis genotyping system is robust and with ongoing improvement will form the basis of a US-wide C. cayetanensis genotyping network for clinical specimens. 8Joel Barratt et al.

Bourbon virus (Family Orthomyxoviridae: Genus Thogotovirus) was first isolated from a human case-patient residing in Bourbon County, Kansas, who subsequently died. Before becoming ill in late spring of 2014, the patient reported several tick bites. In response, we initiated tick surveillance in Bourbon County and adjacent southern Linn County during spring and summer of 2015. We collected 20,639 host-seeking ticks representing four species from 12 sites. Amblyomma americanum (L.) (Acari: Ixodidae) and Dermacentor variabilis (Say) (Acari: Ixodidae) accounted for nearly all ticks collected (99.99%). Three tick pools, all composed of adult A. americanum ticks collected in Bourbon County, were virus positive. Two pools were Heartland virus (Family Bunyaviridae: Genus Phlebovirus) positive, and one was Bourbon virus positive. The Bourbon virus positive tick pool was composed of five adult females collected on a private recreational property on June 5. Detection of Bourbon virus in the abundant and aggressive human-biting tick A. americanum in Bourbon County supports the contention that A. americanum is a vector of Bourbon virus to humans. The current data combined with virus detections in Missouri suggest that Bourbon virus is transmitted to humans by A. americanum ticks, including both the nymphal and adult stages, that ticks of this species become infected as either larvae, nymphs or both, perhaps by feeding on viremic vertebrate hosts, by cofeeding with infected ticks, or both, and that Bourbon virus is transstadially transmitted. Multiple detections of Heartland virus and Bourbon virus in A. americanum ticks suggest that these viruses share important components of their transmission cycles.

Approximately 67% of U.S. households have pets. Limited data are available on SARS-CoV-2 in pets. We assessed SARS-CoV-2 infection in pets during a COVID-19 household transmission investigation. Pets from households with ≥1 person with laboratory-confirmed COVID-19 were eligible for inclusion from April–May 2020. We enrolled 37 dogs and 19 cats from 34 households. All oropharyngeal, nasal, and rectal swabs tested negative by rRT-PCR; one dog’s fur swabs (2%) tested positive by rRT-PCR at the first sampling. Among 47 pets with serological results, eight (17%) pets (four dogs, four cats) from 6/30 (20%) households had detectable SARS-CoV-2 neutralizing antibodies. In households with a seropositive pet, the proportion of people with laboratory-confirmed COVID-19 was greater (median 79%; range: 40–100%) compared to households with no seropositive pet (median 37%; range: 13–100%) (p = 0.01). Thirty-three pets with serologic results had frequent daily contact (≥1 h) with the index patient before the person’s COVID-19 diagnosis. Of these 33 pets, 14 (42%) had decreased contact with the index patient after diagnosis and none were seropositive; of the 19 (58%) pets with continued contact, four (21%) were seropositive. Seropositive pets likely acquired infection after contact with people with COVID-19. People with COVID-19 should restrict contact with pets and other animals.