Vaccination protects against infection with SARS-CoV-2 (the virus that causes COVID-19) and related hospitalizations (1,2), and surviving a previous infection protects against B.1.1.7 (Alpha) and B.1.617.2 (Delta) variant reinfections† (2). Since the SARS-CoV-2 B.1.1.529 (Omicron) variant became predominant in the United States in late December 2021, reported reinfections have increased§ (3). Early reinfections (those occurring within 90 days of previous infection) are not well understood (4). Because some persons have prolonged detection of viral RNA after infection,¶ repeat positive nucleic acid amplification test (NAAT) results within 90 days could reflect prolonged shedding from earlier infection, presenting technical challenges to documenting and characterizing early reinfections. This report describes 10 patients from four states, with whole genome sequencing (WGS)–confirmed Omicron variant infections within 90 days of a previous Delta infection. This activity was reviewed by CDC, approved by respective institutional review boards, and was conducted consistent with applicable federal law and CDC policy.**

On April 6, 2020, a confirmed COVID-19 case in a correctional facility employee (Staff A) was reported to the Vermont Department of Health (VDH). Staff A worked in the facility while symptomatic, without reporting symptoms, for 10 days. VDH and the facility conducted two facility-wide testing events, implemented symptom monitoring, and initiated contact tracing. All 197 incarcerated persons and 115 (71%) staff were tested for SARS-CoV-2; 45 (23%) incarcerated persons and 17 (10%) staff had positive results (confirmed case), of whom 37 (82%) incarcerated persons and 1 (6%) staff had asymptomatic infections. Case detection enabled isolation of incarcerated persons and staff, work exclusion of staff with COVID-19, and quarantine of staff and incarcerated persons who had close contact with persons with COVID-19. Broad-based SARS-CoV-2 testing identified more cases than symptom monitoring.

We describe coronavirus disease (COVID-19) among US food manufacturing and agriculture workers and provide updated information on meat and poultry processing workers. Among 742 food and agriculture workplaces in 30 states, 8,978 workers had confirmed COVID-19; 55 workers died. Racial and ethnic minority workers could be disproportionately affected by COVID-19.

On August 11, 2020, a confirmed case of coronavirus disease 2019 (COVID-19) in a male correctional facility employee (correctional officer) aged 20 years was reported to the Vermont Department of Health (VDH). On July 28, the correctional officer had multiple brief encounters with six incarcerated or detained persons (IDPs)* while their SARS-CoV-2 test results were pending. The six asymptomatic IDPs arrived from an out-of-state correctional facility on July 28 and were housed in a quarantine unit. In accordance with Vermont Department of Corrections (VDOC) policy for state prisons, nasopharyngeal swabs were collected from the six IDPs on their arrival date and tested for SARS-CoV-2, the virus that causes COVID-19, at the Vermont Department of Health Laboratory, using real-time reverse transcription-polymerase chain reaction (RT-PCR). On July 29, all six IDPs received positive test results. VDH and VDOC conducted a contact tracing investigation(†) and used video surveillance footage to determine that the correctional officer did not meet VDH's definition of close contact (i.e., being within 6 feet of infectious persons for ≥15 consecutive minutes)(§)(,)(¶); therefore, he continued to work. At the end of his shift on August 4, he experienced loss of smell and taste, myalgia, runny nose, cough, shortness of breath, headache, loss of appetite, and gastrointestinal symptoms; beginning August 5, he stayed home from work. An August 5 nasopharyngeal specimen tested for SARS-CoV-2 by real-time RT-PCR at a commercial laboratory was reported as positive on August 11; the correctional officer identified two contacts outside of work, neither of whom developed COVID-19. On July 28, seven days preceding his illness onset, the correctional officer had multiple brief exposures to six IDPs who later tested positive for SARS-CoV-2; available data suggests that at least one of the asymptomatic IDPs transmitted SARS-CoV-2 during these brief encounters.

An estimated 2.1 million U.S. adults are housed within approximately 5,000 correctional and detention facilities(dagger) on any given day (1). Many facilities face significant challenges in controlling the spread of highly infectious pathogens such as SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19). Such challenges include crowded dormitories, shared lavatories, limited medical and isolation resources, daily entry and exit of staff members and visitors, continual introduction of newly incarcerated or detained persons, and transport of incarcerated or detained persons in multiperson vehicles for court-related, medical, or security reasons (2,3). During April 22-28, 2020, aggregate data on COVID-19 cases were reported to CDC by 37 of 54 state and territorial health department jurisdictions. Thirty-two (86%) jurisdictions reported at least one laboratory-confirmed case from a total of 420 correctional and detention facilities. Among these facilities, COVID-19 was diagnosed in 4,893 incarcerated or detained persons and 2,778 facility staff members, resulting in 88 deaths in incarcerated or detained persons and 15 deaths among staff members. Prompt identification of COVID-19 cases and consistent application of prevention measures, such as symptom screening and quarantine, are critical to protecting incarcerated and detained persons and staff members.

Anopheles funestus s.s. is a primary vector of malaria in sub-Saharan Africa. Despite its important role in human Plasmodium transmission, evolutionary history, genetic diversity, and population structure of An. funestus in southern and central Africa remains understudied. We deep sequenced, assembled, and annotated the complete mitochondrial genome of An. funestus s.s. for the first time, providing a foundation for further genetic research of this important malaria vector species. We further analyzed the complete mitochondrial genomes of 43 An. funestus s.s. from three sites in Zambia, Democratic Republic of the Congo, and Tanzania. From these 43 mitogenomes we identified 41 unique haplotypes that comprised 567 polymorphic sites. Bayesian phylogenetic reconstruction confirmed the co-existence of two highly divergent An. funestus maternal lineages, herein defined as lineages I and II, in Zambia and Tanzania. The estimated coalescence time of these two mitochondrial lineages is ~500,000 years ago (95% HPD 426,000-594,000 years ago) with subsequent independent diversification. Haplotype network and phylogenetic analysis revealed two major clusters within lineage I, and genetic relatedness of samples with deep branching in lineage II. At this time, data suggest that the lineages are partially sympatric. This study illustrates that accurate retrieval of full mitogenomes of Anopheles vectors enables fine-resolution studies of intraspecies genetic relationships, population differentiation, and demographic history. Further investigations on whether An. funestus mitochondrial lineages represent biologically meaningful populations and their potential implications for malaria vector control are warranted.