COVID-19 Epidemiology during Delta Variant Dominance Period in 45 High-Income Countries, 2020-2021.

The SARS-CoV-2 Delta variant, first identified in October 2020, quickly became the dominant variant worldwide. We used publicly available data to explore the relationship between illness and death (peak case rates, death rates, case-fatality rates) and selected predictors (percentage vaccinated, percentage of the population >65 years, population density, testing volume, index of mitigation policies) in 45 high-income countries during the Delta wave using rank-order correlation and ordinal regression. During the Delta-dominant period, most countries reported higher peak case rates (57%) and lower peak case-fatality rates (98%). Higher vaccination coverage was protective against peak case rates (odds ratio 0.95, 95% CI 0.91-0.99) and against peak death rates (odds ratio 0.96, 95% CI 0.91-0.99). Vaccination coverage was vital to preventing infection and death from COVID-19 during the Delta wave. As new variants emerge, public health authorities should encourage the uptake of COVID-19 vaccination and boosters.

Performance Characteristics of the Abbott BinaxNOW SARS-CoV-2 Antigen Test in Comparison to Real-Time Reverse Transcriptase PCR and Viral Culture in Community Testing Sites during November 2020.

Point-of-care antigen tests are an important tool for SARS-CoV-2 detection. Antigen tests are less sensitive than real-time reverse transcriptase PCR (rRT-PCR). Data on the performance of the BinaxNOW antigen test compared to rRT-PCR and viral culture by symptom and known exposure status, timing during disease, or exposure period and demographic variables are limited. During 3 to 17 November 2020, we collected paired upper respiratory swab specimens to test for SARS-CoV-2 by rRT-PCR and Abbott BinaxNOW antigen test at two community testing sites in Pima County, Arizona. We administered a questionnaire to capture symptoms, known exposure status, and previous SARS-CoV-2 test results. Specimens positive by either test were analyzed by viral culture. Previously we showed overall BinaxNOW sensitivity was 52.5%. Here, we showed BinaxNOW sensitivity increased to 65.7% among currently symptomatic individuals reporting a known exposure. BinaxNOW sensitivity was lower among participants with a known exposure and previously symptomatic (32.4%) or never symptomatic (47.1%) within 14 days of testing. Sensitivity was 71.1% in participants within a week of symptom onset. In participants with a known exposure, sensitivity was highest 8 to 10 days postexposure (75%). The positive predictive value for recovery of virus in cell culture was 56.7% for BinaxNOW-positive and 35.4% for rRT-PCR-positive specimens. Result reporting time was 2.5 h for BinaxNOW and 26 h for rRT-PCR. Point-of-care antigen tests have a shorter turnaround time than laboratory-based nucleic acid amplification tests, which allows for more rapid identification of infected individuals. Antigen test sensitivity limitations are important to consider when developing a testing program.

Time from Start of Quarantine to SARS-CoV-2 Positive Test Among Quarantined College and University Athletes - 17 States, June-October 2020.

To safely resume sports, college and university athletic programs and regional athletic conferences created plans to mitigate transmission of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19). Mitigation measures included physical distancing, universal masking, and maximizing outdoor activity during training; routine testing; 10-day isolation of persons with COVID-19; and 14-day quarantine of athletes identified as close contacts* of persons with confirmed COVID-19. Regional athletic conferences created testing and quarantine policies based on National Collegiate Athletic Association (NCAA) guidance (1); testing policies varied by conference, school, and sport. To improve compliance with quarantine and reduce the personal and economic burden of quarantine adherence, the quarantine period has been reduced in several countries from 14 days to as few as 5 days with testing (2) or 10 days without testing (3). Data on quarantined athletes participating in NCAA sports were used to characterize COVID-19 exposures and assess the amount of time between quarantine start and first positive SARS-CoV-2 test result. Despite the potential risk for transmission from frequent, close contact associated with athletic activities (4), more athletes reported exposure to COVID-19 at social gatherings (40.7%) and from roommates (31.7%) than they did from exposures associated with athletic activities (12.7%). Among 1,830 quarantined athletes, 458 (25%) received positive reverse transcription-polymerase chain reaction (RT-PCR) test results during the 14-day quarantine, with a mean of 3.8 days from quarantine start (range = 0-14 days) until the positive test result. Among athletes who had not received a positive test result by quarantine day 5, the probability of having a positive test result decreased from 27% after day 5 to <5% after day 10. These findings support new guidance from CDC (5) in which different options are provided to shorten quarantine for persons such as collegiate athletes, especially if doing so will increase compliance, balancing the reduced duration of quarantine against a small but nonzero risk for postquarantine transmission. Improved adherence to mitigation measures (e.g., universal masking, physical distancing, and hand hygiene) at all times could further reduce exposures to SARS-CoV-2 and disruptions to athletic activities because of infections and quarantine (1,6).

SARS-CoV-2 Transmission Associated with High School Wrestling Tournaments - Florida, December 2020-January 2021.

On December 7, 2020, local public health officials in Florida county A were notified of a person with an antigen-positive SARS-CoV-2 test* result who had attended two high school wrestling tournaments held in the county on December 4 and 5. The tournaments included 10 participating high schools from three counties. The host school (school A in county A) participated in the tournaments on both days; five high school teams from two counties participated the first day only; four additional high school teams from the three counties participated the second day. A total of 130 wrestlers, coaches, and referees attended the tournaments (Table). During December 8-9, 13 wrestlers from school A received positive SARS-CoV-2 test results (Figure), including nine who were symptomatic, two who were asymptomatic, and two for whom symptom status at time of specimen collection was unknown. Local public health officials in the three counties initiated an investigation† and tested specimens from an additional 40 attendees from nine of the 10 participating schools. A total of 54 (41.5%) of the 130 tournament attendees received testing, and 38 cases of SARS-CoV-2 infection were identified; the minimum attack rate was 30.2% (38 of 126§), and 70.4% (38 of 54) of tests had a positive result. Among contacts of the 38 COVID-19 patients, 446 were determined by investigators to meet the CDC definition of a close contact,¶ including 62 who were household contacts and 384 who were in-school contacts (classmates, teachers, noncompeting wrestling team members, and other school athletic team members). Among these 446 contacts, five had received a diagnosis of COVID-19 during June-November and were excluded from attack rate calculations. Among 95 (21.3%) contacts who received SARS-CoV-2 testing, 41 (43.2%) received a positive test result (minimum attack rate = 9.3% [41 of 441]); 21 (51.2%) persons with positive test results were symptomatic, eight (19.5%) were asymptomatic, and symptom status for 12 (29.3%) was unknown at the time of specimen collection. Among contacts, attack rates were highest among household members (30.0%) and wrestling team members who did not attend the tournament (20.3%), as were the percentages of positive test results (60.0% among household members and 54.2% among team members). Among all contacts, the odds of receiving a positive test result were highest among household contacts (odds ratio = 2.7; 95% confidence interval = 1.2-6.0). Local health authorities reported the death of one adult contact aged >50 years.

Evaluation of Abbott BinaxNOW Rapid Antigen Test for SARS-CoV-2 Infection at Two Community-Based Testing Sites - Pima County, Arizona, November 3-17, 2020.

Rapid antigen tests, such as the Abbott BinaxNOW COVID-19 Ag Card (BinaxNOW), offer results more rapidly (approximately 15-30 minutes) and at a lower cost than do highly sensitive nucleic acid amplification tests (NAATs) (1). Rapid antigen tests have received Food and Drug Administration (FDA) Emergency Use Authorization (EUA) for use in symptomatic persons (2), but data are lacking on test performance in asymptomatic persons to inform expanded screening testing to rapidly identify and isolate infected persons (3). To evaluate the performance of the BinaxNOW rapid antigen test, it was used along with real-time reverse transcription-polymerase chain reaction (RT-PCR) testing to analyze 3,419 paired specimens collected from persons aged ≥10 years at two community testing sites in Pima County, Arizona, during November 3-17, 2020. Viral culture was performed on 274 of 303 residual real-time RT-PCR specimens with positive results by either test (29 were not available for culture). Compared with real-time RT-PCR testing, the BinaxNOW antigen test had a sensitivity of 64.2% for specimens from symptomatic persons and 35.8% for specimens from asymptomatic persons, with near 100% specificity in specimens from both groups. Virus was cultured from 96 of 274 (35.0%) specimens, including 85 (57.8%) of 147 with concordant antigen and real-time RT-PCR positive results, 11 (8.9%) of 124 with false-negative antigen test results, and none of three with false-positive antigen test results. Among specimens positive for viral culture, sensitivity was 92.6% for symptomatic and 78.6% for asymptomatic individuals. When the pretest probability for receiving positive test results for SARS-CoV-2 is elevated (e.g., in symptomatic persons or in persons with a known COVID-19 exposure), a negative antigen test result should be confirmed by NAAT (1). Despite a lower sensitivity to detect infection, rapid antigen tests can be an important tool for screening because of their quick turnaround time, lower costs and resource needs, high specificity, and high positive predictive value (PPV) in settings of high pretest probability. The faster turnaround time of the antigen test can help limit transmission by more rapidly identifying infectious persons for isolation, particularly when used as a component of serial testing strategies.

Investigation of Ebolavirus exposure in pigs presented for slaughter in Uganda.

In 2008, an outbreak of Reston ebolavirus (RESTV) in pigs in the Philippines expanded our understanding of the host range of ebolaviruses. Subsequent experimental infections with the human-pathogenic species Zaire ebolavirus (EBOV) confirmed that pigs are susceptible to African species of ebolaviruses. Pig keeping has become an increasingly important livelihood strategy throughout parts of sub-Saharan Africa, driven by increasing demand for pork. The growth in pig keeping is particularly rapid in Uganda, which has the highest per capita pork consumption in East Africa and a history of sporadic human outbreaks of Ebola virus disease (EVD). Using a systematic sampling protocol, we collected sera from 658 pigs presented for slaughter in Uganda between December 2015 and October 2016. Forty-six pigs (7%) were seropositive based on ELISA tests at two different institutions. Seropositive pigs had antibodies that bound to Sudan NP (n = 27), Zaire NP (Kikwit; n = 8) or both NPs (n = 11). Sera from 4 of the ELISA-positive pigs reacted in Western blot (EBOV NP = 1; RESTV NP = 2; both NPs = 2), and one sample had full neutralizing antibody against Sudan ebolavirus (SUDV) in virus neutralization tests. Pigs sampled in June 2016 were significantly more likely to be seropositive than pigs sampled in October 2016 (p = .03). Seropositive pigs were sourced from all regions except Western region. These observed temporal and spatial variations are suggestive of multiple introductions of ebolaviruses into the pig population in Uganda. This is the first report of exposure of pigs in Uganda to ebolaviruses and the first to employ systematic abattoir sampling for ebolavirus surveillance during a non-outbreak period. Future studies will be necessary to further define the role pigs play (if any) in ebolavirus maintenance and transmission so that potential risks can be mitigated.

Selected Endemic Zoonoses in Pigs Presenting for Slaughter in Kampala, Uganda.

Leptospirosis, brucellosis, and Q fever (coxiellosis) are bacterial zoonoses that cause acute febrile illness in people as well as reproductive losses in pigs. Pig keeping is an increasingly important livelihood to millions of smallholder farmers in Uganda because of exponential increases in demand for pork. The prevalence of leptospirosis and Q fever in pigs is unknown, and the few studies of porcine brucellosis have estimated a range of seroprevalence. Therefore, we undertook a prevalence survey of leptospirosis, brucellosis, and Q fever in pigs using quantitative real-time PCR to determine the potential importance of these zoonoses to the growing pig sector in Uganda. Six hundred forty-nine pigs were sampled in 2015-2016 at an urban pork slaughterhouse. Ten percent of pigs (n = 68) had leptospiral DNA in either their kidney or reproductive tissue. In adjusted analyses, variables predictive of leptospiral status included female sex (odds ratio [OR]: 2.37, P < 0.01) and pigs sampled in March 2016 (OR: 2.23, P = 0.02) and October 2016 (OR: 0.30, P = 0.04). DNA fingerprinting revealed circulation of at least four distinct serovars in these pigs. Brucella spp. and Coxiella burnetii DNA were not detected in any sampled pig. This is the first report of widespread circulation of pathogenic Leptospira spp. in pigs in Uganda, suggesting that leptospirosis likely has a greater impact on the health of pigs than was previously recognized. Pig farmers, pig traders, and slaughterhouse workers may be at greatest occupational risk because of their direct contact with infective leptospires in aborted fetuses, bodily fluids, and other tissues.

Evidence of exposure to henipaviruses in domestic pigs in Uganda.

Hendra virus (HeV) and Nipah virus (NiV), belonging to the genus Henipavirus, are among the most pathogenic of viruses in humans. Old World fruit bats (family Pteropodidae) are the natural reservoir hosts. Molecular and serological studies found evidence of henipavirus infection in fruit bats from several African countries. However, little is known about the potential for spillover into domestic animals in East Africa, particularly pigs, which served as amplifying hosts during the first outbreak of NiV in Malaysia and Singapore. We collected sera from 661 pigs presented for slaughter in Uganda between December 2015 and October 2016. Using HeV G and NiV G indirect ELISAs, 14 pigs (2%) were seroreactive in at least one ELISA. Seroprevalence increased to 5.4% in October 2016, when pigs were 9.5 times more likely to be seroreactive than pigs sampled in December 2015 (p = 0.04). Eight of the 14 ELISA-positive samples reacted with HeV N antigen in Western blot. None of the sera neutralized HeV or NiV in plaque reduction neutralization tests. Although we did not detect neutralizing antibodies, our results suggest that pigs in Uganda are exposed to henipaviruses or henipa-like viruses. Pigs in this study were sourced from many farms throughout Uganda, suggesting multiple (albeit rare) introductions of henipaviruses into the pig population. We postulate that given the widespread distribution of Old World fruit bats in Africa, spillover of henipaviruses from fruit bats to pigs in Uganda could result in exposure of pigs at multiple locations. A higher risk of a spillover event at the end of the dry season might be explained by higher densities of bats and contact with pigs at this time of the year, exacerbated by nutritional stress in bat populations and their reproductive cycle. Future studies should prioritize determining the risk of spillover of henipaviruses from pigs to people, so that potential risks can be mitigated.

Serological Evidence for the Circulation of Ebolaviruses in Pigs From Sierra Leone.

Many human ebolavirus outbreaks have been linked to contact with wildlife including nonhuman primates and bats, which are assumed to serve as host species. However, it is largely unknown to what extent other animal species, particularly livestock, are involved in the transmission cycle or act as additional hosts for filoviruses. Pigs were identified as a susceptible host for Reston virus with subsequent transmission to humans reported in the Philippines. To date, there is no evidence of natural Ebola virus (EBOV) infection in pigs, although pigs were shown to be susceptible to EBOV infection under experimental settings. To investigate the potential role of pigs in the ecology of EBOV, we analyzed 400 porcine serum samples from Sierra Leone for the presence of ebolavirus-specific antibodies. Three samples reacted with ebolavirus nucleoproteins but had no neutralizing antibodies. Our results (1) suggest the circulation of ebolaviruses in swine in Sierra Leone that are antigenically related but not identical to EBOV and (2) could represent undiscovered ebolaviruses with unknown pathogenic and/or zoonotic potential.

Seroprevalence of Leptospira hardjo in cattle and African buffalos in southwestern Uganda.

Leptospirosis, caused by the spirochete bacterium Leptospira spp. is a zoonosis, distributed worldwide and classified as an emerging infectious disease. Fatal outcomes to leptospiral infection do occur and the disease can cause abortion and other reproductive problems in cattle, goats, and pigs. In humans the symptoms range from subclinical infection to acute febrile illness, pulmonary hemorrhage and renal failure. Leptospirosis has never been officially reported to the World Health Organization (WHO) or the World Animal Health Organization in animals or humans in Uganda. However, favorable ecological conditions and suitable animal hosts can be found within the country. A commercially available enzyme-linked immunosorbent (ELISA) kit was used to screen sera samples from domesticated cattle and African buffalo (Syncerus caffer) at two locations in southwestern Uganda, collected over a 4-year period. Positive samples were found in both cattle and African buffalo samples, from both locations and across the sampling period. Overall seroprevalence was 42.39% in African buffalo and 29.35% in cattle.