Isolation of SARS-CoV-2 from the air in a car driven by a COVID patient with mild illness

Objective: To determine if viable virus could be isolated from the air within a car driven by a patient infected with SARS-CoV-2, and to assess the size range of the infectious particles. Methods: We used a Sioutas personal cascade impactor sampler (PCIS) to screen for SARS-CoV-2 in a car driven by a COVID-19 patient. The patient, who had only mild illness without fever or cough and was not wearing a mask, drove the car for 15 min with the air conditioning turned on and windows closed. The PCIS was clipped to the sun-visor above the front passenger seat and was retrieved from the car two hours after completion of the drive. Results: SARS-CoV-2 was detectable at all PCIS stages by PCR and was cultured from the section of the sampler collecting particles in the 0.25–0.50 μm size range. Conclusions: Our data highlight the potential risk of SARS-CoV-2 transmission by minimally symptomatic persons in the closed space inside of a car and suggest that a substantial component of that risk is via aerosolized virus

Mayaro Virus in Child with Acute Febrile Illness, Haiti, 2015

Mayaro virus has been associated with small outbreaks in northern South America. We isolated this virus from a child with acute febrile illness in rural Haiti, confirming its role as a cause of mosquitoborne illness in the Caribbean region. The clinical presentation can mimic that of chikungunya, dengue, and Zika virus infections

Diagnostic approaches to malaria in Zambia, 2009-2014

Malaria is an important health burden in Zambia with proper diagnosis remaining as one of the biggest challenges. The need for reliable diagnostics is being addressed through the introduction of rapid diagnostic tests (RDTs). However, without sufficient laboratory amenities in many parts of the country, diagnosis often still relies on non-specific, clinical symptoms. In this study, geographical information systems were used to both visualize and analyze the spatial distribution and the risk factors related to the diagnosis of malaria. The monthly reported, district-level number of malaria cases from January 2009 to December 2014 were collected from the National Malaria Control Center (NMCC). Spatial statistics were used to reveal cluster tendencies that were subsequently linked to possible risk factors, using a non-spatial regression model. Significant, spatio-temporal clusters of malaria were spotted while the introduction of RDTs made the number of clinically diagnosed malaria cases decrease by 33% from 2009 to 2014. The limited access to road network(s) was found to be associated with higher levels of malaria, which can be traced by the expansion of health promotion interventions by the NMCC, indicating enhanced diagnostic capability. The capacity of health facilities has been strengthened with the increased availability of proper diagnostic tools and through retraining of community health workers. To further enhance spatial decision support systems, a multifaceted approach is required to ensure mobilization and availability of human, infrastructural and technological resources. Surveillance based on standardized geospatial or other analytical methods should be used by program managers to design, target, monitor and assess the spatio-temporal dynamics of malaria diagnostic resources country-wide

A new "American" subgroup of African-lineage Chikungunya virus detected in and isolated from mosquitoes collected in Haiti, 2016

<div><p>As part of on-going arboviral surveillance activity in a semi-rural region in Haiti, <i>Chikungunya virus</i> (CHIKV)-positive mosquito pools were identified in 2014 (the peak of the Caribbean Asian-clade epidemic), and again in 2016 by RT-PCR. In 2014, CHIKV was only identified in <i>Aedes aegypti</i> (11 positive pools/124 screened). In contrast, in sampling in 2016, CHIKV was not identified in <i>Ae</i>. <i>aegypti</i>, but, rather, in (a) a female <i>Aedes albopictus</i> pool, and (b) a female <i>Culex quinquefasciatus</i> pool. Genomic sequence analyses indicated that the CHIKV viruses in the 2016 mosquito pools were from the East-Central-South African (ECSA) lineage, rather than the Asian lineage. In phylogenetic studies, these ECSA lineage strains form a new ECSA subgroup (subgroup IIa) together with Brazilian ECSA lineage strains from an isolated human outbreak in 2014, and a mosquito pool in 2016. Additional analyses date the most recent common ancestor of the ECSA IIa subgroup around May 2007, and the 2016 Haitian CHIKV genomes around December 2015. Known CHIKV mutations associated with improved <i>Ae</i>. <i>albopictus</i> vector competence were not identified. Isolation of this newly identified lineage from <i>Ae</i>. <i>albopictus</i> is of concern, as this vector has a broader geographic range than <i>Ae</i>. <i>aegypti</i>, especially in temperate areas of North America, and stresses the importance for continued vector surveillance.</p></div

Earliest detection to date of SARS-CoV-2 in Florida: Identification together with influenza virus on the main entry door of a university building, February 2020.

In February and March, 2020, environmental surface swab samples were collected from the handle of the main entry door of a major university building in Florida, as part of a pilot surveillance project screening for influenza. Samples were taken at the end of regular classroom hours, between the dates of February 1-5 and February 19-March 4, 2020. Influenza A(H1N1)pdm09 virus was isolated from the door handle on four of the 19 days sampled. Both SARS-CoV-2 and A(H1N1)pdm09 virus were detected in a sample collected on February 21, 2020. Based on sequence analysis, the Florida SARS-CoV-2 strain (designated UF-11) was identical to strains being identified in Washington state during the same time period, while the earliest similar sequences were sampled in China/Hubei between Dec 30th 2019 and Jan 5th 2020. The first human case of COVID-19 was not officially reported in Florida until March 1st. In an analysis of sequences from COVID-19 patients in this region of Florida, there was only limited evidence of subsequent dissemination of the UF-11 strain. Identical or highly similar strains, possibly related through a common transmission chain, were detected with increasing frequency in Washington state between end of February and beginning of March. Our data provide further documentation of the rapid early spread of SARS-CoV-2 and underscore the likelihood that closely related strains were cryptically circulating in multiple U.S. communities before the first "official" cases were recognized

Diversity and Genetic Reassortment of Keystone Virus in Mosquito Populations in Florida

International audienceABSTRACT. Keystone orthobunyavirus (KEYV), a member of the genus Orthobunyavirus , was first isolated in 1964 from mosquitoes in Keystone, Florida. Although data on human infections are limited, the virus has been linked to a fever/rash syndrome and, possibly, encephalitis, with early studies suggesting that 20% of persons in the Tampa, Florida, region had antibodies to KEYV. To assess the distribution and diversity of KEYV in other regions of Florida, we collected > 6,000 mosquitoes from 43 sampling sites in St. Johns County between June 2019 and April 2020. Mosquitoes were separated into pools by species and collection date and site. All pools with Aedes spp. (293 pools, 2,171 mosquitoes) were screened with a real-time reverse transcriptase polymerase chain reaction (rRT-PCR) assay that identifies KEYV and other closely related virus species of what was previously designated as the California encephalitis serogroup. In 2020, screening for KEYV was expanded to include 211 pools of Culex mosquitoes from sites where KEYV-positive Aedes spp. had been identified. rRT-PCR–positive samples were inoculated into cell cultures, and five KEYV isolates from Aedes atlanticus pools were isolated and sequenced. Analyses of the KEYV large genome segment sequences revealed two distinct KEYV clades, whereas analyses of the medium and small genome segments uncovered past reassortment events. Our data documented the ongoing seasonal circulation of multiple KEYV clades within Ae. atlanticus mosquito populations along the east coast of Florida, highlighting the need for further studies of the impact of this virus on human health

Isolation of Coronavirus NL63 from Blood from Children in Rural Haiti: Phylogenetic Similarities with Recent Isolates from Malaysia

Human coronavirus (HCoV) NL63 is recognized as a common cause of upper respiratory infections and influenza-like illness. In screening children with acute undifferentiated febrile illness in a school cohort in rural Haiti, we identified HCoV-NL63 in blood samples from four children. Cases clustered over an 11-day period; children did not have respiratory symptoms, but two had gastrointestinal complaints. On phylogenetic analysis, the Haitian HCoV-NL63 strains cluster together in a highly supported monophyletic clade linked most closely with recently reported strains from Malaysia; two respiratory HCoV-NL63 strains identified in north Florida in the same general period form a separate clade, albeit again with close linkages with the Malaysian strains. Our data highlight the variety of presentations that may be seen with HCoV-NL63, and underscore the apparent ease with which CoV strains move among countries, with our data consistent with recurrent introduction of strains into the Caribbean (Haiti and Florida) from Asia

Characteristics of CHIKV-positive mosquito pools, Haiti, 2016.

<p>Characteristics of CHIKV-positive mosquito pools, Haiti, 2016.</p

Collection of SARS-CoV-2 Virus from the Air of a Clinic Within a University Student Health Care Center and Analyses of the Viral Genomic Sequence

The progression of COVID-19 worldwide can be tracked by identifying mutations within the genomic sequence of SARS-CoV-2 that occur as a function of time. Such efforts currently rely on sequencing the genome of SARS-CoV-2 in patient specimens (direct sequencing) or of virus isolated from patient specimens in cell cultures. A pilot SARS-CoV-2 air sampling study conducted at a clinic within a university student health care center detected the virus vRNA, with an estimated concentration of 0.87 virus genomes L(-1) air. To determine whether the virus detected was viable ('live'), attempts were made to isolate the virus in cell cultures. Virus-induced cytopathic effects (CPE) were observed within two days post-inoculation of Vero E6 cells with collection media from air samples; however, rtRT-PCR tests for SARS-CoV-2 vRNA from cell culture were negative. Instead, three other fast-growing human respiratory viruses were isolated and subsequently identified, illustrating the challenge in isolating SARS-CoV-2 when multiple viruses are present in a test sample. The complete SAR-CoV-2 genomic sequence was nevertheless determined by Sanger sequencing and most closely resembles SARS-CoV-2 genomes previously described in Georgia, USA. Results of this study illustrate the feasibility of tracking progression of the COVID-19 pandemic using environmental aerosol samples instead of human specimens. Collection of a positive sample from a distance more than 2 m away from the nearest patient traffic implies the virus was in an aerosol

Pangenomic maximum likelihood phylogenetic inference of CHIKV.

<p>Phylogeny was inferred based on maximum likelihood method using the software IQ-TREE for the complete dataset of publicly available CHIKV genomes. Indian Ocean lineage (IOL), East/Central/South African (ECSA) lineage and Asian lineage are indicated. Branch lengths reflect genetic distances, and diamonds at each node shows strong statistical support based on ultrafast-bootstrap (BB>90%).</p