Coronavirus Disease among Workers in Food Processing, Food Manufacturing, and Agriculture Workplaces.

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.

COVID-19 in a Correctional Facility Employee Following Multiple Brief Exposures to Persons with COVID-19 - Vermont, July-August 2020.

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.

COVID-19 in Correctional and Detention Facilities - United States, February-April 2020.

An estimated 2.1 million U.S. adults are housed within approximately 5,000 correctional and detention facilities† 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.

Genetic Evidence of Focal Plasmodium falciparum Transmission in a Pre-elimination Setting in Southern Province, Zambia.

BACKGROUND: Southern Province, Zambia has experienced a dramatic decline in Plasmodium falciparum malaria transmission in the past decade and is targeted for elimination. Zambia's National Malaria Elimination Program recommends reactive case detection (RCD) within 140 m of index households to enhance surveillance and eliminate remaining transmission foci. METHODS: To evaluate whether RCD captures local transmission, we genotyped 26 microsatellites from 106 samples collected from index (n = 27) and secondary (n = 79) cases detected through RCD in the Macha Hospital catchment area between January 2015 and April 2016. RESULTS: Participants from the same RCD event harbored more genetically related parasites than those from different RCD events, suggesting that RCD captures, at least in part, infections related through local transmission. Related parasites clustered in space and time, up to at least 250 m from index households. Spatial analysis identified a putative focal transmission hotspot. CONCLUSIONS: The current RCD strategy detects focal transmission events, although programmatic guidelines to screen within 140 m of index households may fail to capture all secondary cases. This study highlights the utility of parasite genetic data in assessing programmatic interventions, and similar approaches may be useful to malaria elimination programs seeking to tailor intervention strategies to the underlying transmission epidemiology.

High Plasmodium falciparum genetic diversity and temporal stability despite control efforts in high transmission settings along the international border between Zambia and the Democratic Republic of the Congo.

BACKGROUND: While the utility of parasite genotyping for malaria elimination has been extensively documented in low to moderate transmission settings, it has been less well-characterized in holoendemic regions. High malaria burden settings have received renewed attention acknowledging their critical role in malaria elimination. Defining the role for parasite genomics in driving these high burden settings towards elimination will enhance future control programme planning. METHODS: Amplicon deep sequencing was used to characterize parasite population genetic diversity at polymorphic Plasmodium falciparum loci, Pfama1 and Pfcsp, at two timepoints in June-July 2016 and January-March 2017 in a high transmission region along the international border between Luapula Province, Zambia and Haut-Katanga Province, the Democratic Republic of the Congo (DRC). RESULTS: High genetic diversity was observed across both seasons and in both countries. No evidence of population structure was observed between parasite populations on either side of the border, suggesting that this region may be one contiguous transmission zone. Despite a decline in parasite prevalence at the sampling locations in Haut-Katanga Province, no genetic signatures of a population bottleneck were detected, suggesting that larger declines in transmission may be required to reduce parasite genetic diversity. Analysing rare variants may be a suitable alternative approach for detecting epidemiologically important genetic signatures in highly diverse populations; however, the challenge is distinguishing true signals from potential artifacts introduced by small sample sizes. CONCLUSIONS: Continuing to explore and document the utility of various parasite genotyping approaches for understanding malaria transmission in holoendemic settings will be valuable to future control and elimination programmes, empowering evidence-based selection of tools and methods to address pertinent questions, thus enabling more efficient resource allocation.

Correctional-Facility-Outbreak-Associated COVID-19 Cases Among Asymptomatic Persons Identified Through Universal Testing: Vermont, 2020.

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.

Genetic Diversity of Anopheles coustani (Diptera: Culicidae) in Malaria Transmission Foci in Southern and Central Africa.

Despite ongoing malaria control efforts implemented throughout sub-Saharan Africa, malaria remains an enormous public health concern. Current interventions such as indoor residual spraying with insecticides and use of insecticide-treated bed nets are aimed at targeting the key malaria vectors that are primarily endophagic and endophilic. Anopheles coustani s.l., an understudied vector of malaria, is a species previously thought to exhibit mostly zoophilic behavior. Like many of these understudied species, An. coustani has greater anthropophilic tendencies than previously appreciated, is often both endophagic and exophagic, and carries Plasmodium falciparum sporozoites. The aim of this study was to explore genetic variation of An. coustani mosquitoes and the potential of this species to contribute to malaria parasite transmission in high transmission settings in Zambia and the Democratic Republic of the Congo (DRC). Morphologically identified An. coustani specimens that were trapped outdoors in these study sites were analyzed by PCR and sequencing for species identification and bloodmeal sources, and malaria parasite infection was determined by ELISA and qPCR. Fifty An. coustani s.s. specimens were confirmed by analysis of mitochondrial DNA cytochrome c oxidase subunit I (COI) and ribosomal internal transcribed spacer region 2 (ITS2). Maximum likelihood phylogenetic analysis of COI and ITS2 sequences revealed two distinct phylogenetic groups within this relatively small regional collection. Our findings indicate that both An. coustani groups have anthropophilic and exophagic habits and come into frequent contact with P. falciparum, suggesting that this potential alternative malaria vector might elude current vector control measures in northern Zambia and southern DRC.

Therapeutic Efficacy of Artemether-Lumefantrine for Uncomplicated Falciparum Malaria in Northern Zambia.

Artemether-lumefantrine (AL) is a first-line agent for uncomplicated malaria caused by Plasmodium falciparum. The WHO recommends periodic therapeutic efficacy studies of antimalarial drugs for the detection of malaria parasite drug resistance and to inform national malaria treatment policies. We conducted a therapeutic efficacy study of AL in a high malaria transmission region of northern Zambia from December 2014 to July 2015. One hundred children of ages 6 to 59 months presenting to a rural health clinic with uncomplicated falciparum malaria were admitted for treatment with AL (standard 6-dose regimen) and followed weekly for 5 weeks. Parasite counts were taken every 6 hours during treatment to assess parasite clearance. Recurrent episodes during follow-up (n = 14) were genotyped to distinguish recrudescence from reinfection and to identify drug resistance single nucleotide polymorphisms (SNPs) and multidrug resistance protein 1 (mdr1) copy number variation. Day 7 lumefantrine concentrations were measured for correspondence with posttreatment reinfection. All children who completed the parasite clearance portion of the study (n = 94) were microscopy-negative by 72 hours. The median parasite elimination half-life was 2.7 hours (interquartile range: 2.1-3.3). Genotype-corrected therapeutic efficacy was 98.8% (95% CI: 97.6-100). Purported artemisinin and lumefantrine drug resistance SNPs in atp6, 3D7_1451200, and mdr1 were detected but did not correlate with parasite recurrence, nor did day 7 lumefantrine concentrations. In summary, AL was highly effective for the treatment of uncomplicated falciparum malaria in northern Zambia during the study period. The high incidence of recurrent parasitemia was consistent with reinfection due to high, perennial malaria transmission.

Sustained Malaria Transmission despite Reactive Screen-and-Treat in a Low-Transmission Area of Southern Zambia.

Malaria elimination strategies are designed to more effectively identify and treat infected individuals to interrupt transmission. One strategy, reactive screen-and-treat, starts with passive detection of symptomatic cases at health facilities. Individuals residing within the index case and neighboring households are screened with a malaria rapid diagnostic test (RDT) and treated if positive. However, it is unclear to what extent this strategy is effective in reducing transmission. Reactive screen-and-treat was implemented in Choma district, Southern Province, Zambia, in 2013, in which residents of the index case and neighboring households within 140 m were screened with an RDT. From March 2016 to July 2018, the screening radius was extended to 250-m, and additional follow-up visits at 30 and 90 days were added to evaluate the strategy. Plasmodium falciparum parasite prevalence was measured using an RDT and by quantitative PCR (qPCR). A 24-single nucleotide polymorphism molecular bar-code assay was used to genotype parasites. Eighty-four index case households with 676 residents were enrolled between March 2016 and March 2018. Within each season, parasite prevalence declined significantly in index households at the 30-day visit and remained low at the 90-day visit. However, parasite prevalence was not reduced to zero. Infections identified by qPCR persisted between study visits and were not identified by RDT. Parasites identified within the same household were most genetically related; however, overall parasite relatedness was low and similar across time and space. Thus, despite implementation of a reactive screen-and-treat program, parasitemia was not eliminated, and persisted in targeted households for at least 3 months.

Complete Anopheles funestus mitogenomes reveal an ancient history of mitochondrial lineages and their distribution in southern and central Africa.

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.

RTS,S/AS01 malaria vaccine mismatch observed among Plasmodium falciparum isolates from southern and central Africa and globally.

The RTS,S/AS01 malaria vaccine encompasses the central repeats and C-terminal of Plasmodium falciparum circumsporozoite protein (PfCSP). Although no Phase II clinical trial studies observed evidence of strain-specific immunity, recent studies show a decrease in vaccine efficacy against non-vaccine strain parasites. In light of goals to reduce malaria morbidity, anticipating the effectiveness of RTS,S/AS01 is critical to planning widespread vaccine introduction. We deep sequenced C-terminal Pfcsp from 77 individuals living along the international border in Luapula Province, Zambia and Haut-Katanga Province, the Democratic Republic of the Congo (DRC) and compared translated amino acid haplotypes to the 3D7 vaccine strain. Only 5.2% of the 193 PfCSP sequences from the Zambia-DRC border region matched 3D7 at all 84 amino acids. To further contextualize the genetic diversity sampled in this study with global PfCSP diversity, we analyzed an additional 3,809 Pfcsp sequences from the Pf3k database and constructed a haplotype network representing 15 countries from Africa and Asia. The diversity observed in our samples was similar to the diversity observed in the global haplotype network. These observations underscore the need for additional research assessing genetic diversity in P. falciparum and the impact of PfCSP diversity on RTS,S/AS01 efficacy.

Beyond the entomological inoculation rate: characterizing multiple blood feeding behavior and Plasmodium falciparum multiplicity of infection in Anopheles mosquitoes in northern Zambia.

BACKGROUND: A commonly used measure of malaria transmission intensity is the entomological inoculation rate (EIR), defined as the product of the human biting rate (HBR) and sporozoite infection rate (SIR). The EIR excludes molecular parameters that may influence vector control and surveillance strategies. The purpose of this study was to investigate Anopheles multiple blood feeding behavior (MBF) and Plasmodium falciparum multiplicity of infection (MOI) within the mosquito host in Nchelenge District, northern Zambia. Mosquitoes were collected from light traps and pyrethroid spray catch in Nchelenge in the 2013 wet season. All anophelines were tested for blood meal host, P. falciparum, and MOI using PCR. Circumsporozoite (CSP) ELISA and microsatellite analysis were performed to detect parasites in the mosquito and MBF, respectively. Statistical analyses used regression models to assess MBF and MOI and exact binomial test for human sex bias. Both MBF and MOI can enhance our understanding of malaria transmission dynamics beyond what is currently understood through conventional EIR estimates alone. RESULTS: The dominant malaria vectors collected in Nchelenge were Anopheles funestus (sensu stricto) and An. gambiae (s.s.) The EIRs of An. funestus (s.s.) and An. gambiae (s.s.) were 39.6 infectious bites/person/6 months (ib/p/6mo) and 5.9 ib/p/6mo, respectively, and took multiple human blood meals at high rates, 23.2 and 25.7% respectively. There was no bias in human host sex preference in the blood meals. The SIR was further characterized for parasite genetic diversity. The overall P. falciparum MOI was 6.4 in infected vectors, exceeding previously reported average MOIs in humans in Africa. CONCLUSIONS: Both Anopheles MBF rates and P. falciparum MOI in Nchelenge were among some of the highest reported in sub-Saharan Africa. The results suggest an underestimation of the EIR and large numbers of circulating parasite clones. Together, the results describe important molecular aspects of transmission excluded from the traditional EIR measurement. These elements may provide more sensitive measures with which to assess changes in transmission intensity and risk in vector and parasite surveillance programs.

Detection of Plasmodium falciparum Infection in Anopheles squamosus (Diptera: Culicidae) in an Area Targeted for Malaria Elimination, Southern Zambia.

Southern Zambia is the focus of strategies to create malaria-free zones. Interventions being rolled out include test and treat strategies and distribution of insecticide-treated bed nets that target vectors that host-seek indoors and late at night. In Macha, Choma District, collections of mosquitoes were made outdoors using barrier screens within homesteads or UV bulb light traps set next to goats, cattle, or chickens during the rainy season of 2015. Anopheline mosquitoes were identified to species using molecular methods and Plasmodium falciparum infectivity was determined by ELISA and real-time qPCR methods. More than 40% of specimens caught were identified as Anopheles squamosus Theobald, 1901 of which six were found harboring malaria parasites. A single sample, morphologically identified as Anopheles coustani Laveran, 1900, was also found to be infectious. All seven specimens were caught outdoors next to goat pens. Parasite-positive specimens as well as a subset of An. squamosus specimens from either the same study or archive collections from the same area underwent sequencing of the mitochondrial cytochrome oxidase subunit I gene. Maximum parsimony trees constructed from the aligned sequences indicated presence of at least two clades of An. squamosus with infectious specimens falling in each clade. The single infectious specimen identified morphologically as An. coustani could not be matched to reference sequences. This is the first report from Zambia of infections in An. squamosus, a species which is described in literature to display exophagic traits. The bionomic characteristics of this species needs to be studied further to fully evaluate the implications for indoor-targeted vector control.

Spatio-temporal heterogeneity of malaria vectors in northern Zambia: implications for vector control.

BACKGROUND: Despite large reductions in malaria burden across Zambia, some regions continue to experience extremely high malaria transmission. In Nchelenge District, Luapula Province, northern Zambia, almost half the human population carries parasites. Intervention coverage has increased substantially over the past decade, but comprehensive district-wide entomological studies to guide delivery of vector control measures are lacking. This study describes the bionomics and spatio-temporal patterns of malaria vectors in Nchelenge over a two and a half year period, investigates what household factors are associated with high vector densities and determines why vector control may not have been effective in the past to better guide future control efforts. METHODS: Between April 2012 and September 2014, twenty-seven households from across Nchelenge District were randomly selected for monthly light trap collections of mosquitoes. Anopheline mosquitoes were identified morphologically and molecularly to species. Foraging rates were estimated and sporozoite rates were determined by circumsporozoite ELISAs to calculate annual entomological inoculation rates. Blood feeding rates and host preference were determined by PCR. Zero-inflated negative binomial models measured environmental and household factors associated with mosquito abundance at study households such as season, proximity to the lake, and use of vector control measures. RESULTS: The dominant species in Nchelenge was An. funestus (s.s.) with An. gambiae (s.s.) as a secondary vector. Both vectors were found together in large numbers across the district and the combined EIRs of the two vectors exceeded 80 infectious bites per person per annum. An. funestus household densities increased in the dry season whilst An. gambiae surged during the rains. Presence of insecticide treated nets (ITNs) and closed eaves in the houses were found to be associated with fewer numbers of An. gambiae but not An. funestus. There was no association with indoor residual spraying (IRS). CONCLUSION: In Nchelenge, the co-existence of two highly anthropophagic vectors, present throughout the year, is likely to be driving the high malaria transmission evident in the district. The vectors here have been shown to be highly resistant to pyrethroids used for IRS during the study. Vector control interventions in this area would have to be multifaceted and district-wide for effective control of malaria.