We report a time course of SARS-CoV-2 RNA concentrations in primary sewage sludge during the Spring COVID-19 outbreak in a northeastern U.S. metropolitan area. SARS-CoV-2 RNA was detected in all environmental samples, and when adjusted for the time lag, the virus RNA concentrations tracked the COVID-19 epidemiological curve. SARS-CoV-2 RNA concentrations were a leading indicator of community infection ahead of compiled COVID-19 testing data and local hospital admissions. Decisions to implement or relax public health measures and restrictions require timely information on outbreak dynamics in a community.

The emergence and spread of SARS-CoV-2 lineage B.1.1.7, first detected in the United Kingdom, has become a national public health concern in the United States because of its increased transmissibility. Over 500 COVID-19 cases associated with this variant have been detected since December 2020, but its local establishment and pathways of spread are relatively unknown. Using travel, genomic, and diagnostic testing data, we highlight the primary ports of entry for B.1.1.7 in the US and locations of possible underreporting of B.1.1.7 cases. New York, which receives the most international travel from the UK, is likely one of the key hubs for introductions and domestic spread. Finally, we provide evidence for increased community transmission in several states. Thus, genomic surveillance for B.1.1.7 and other variants urgently needs to be enhanced to better inform the public health response.

There is an urgent need to expand testing for SARS-CoV-2 and other respiratory pathogens as the global community struggles to control the COVID-19 pandemic. Current diagnostic methods can be affected by supply chain bottlenecks and require the assistance of medical professionals, impeding the implementation of large-scale testing. Self-collection of saliva may solve these problems because it can be completed without specialized training and uses generic materials. In this study, we observed thirty individuals who self-collected saliva using four different collection devices and analyzed their feedback. These devices enabled the safe collection of saliva that was acceptable for SARS-CoV-2 diagnostic testing.

BackgroundClinical and virologic characteristics of COVID-19 infections in veterans in New England have not been described.ObjectivesTo evaluate clinical and virologic factors impacting COVID-19 outcomes.Study DesignWe reviewed charts and sequenced virus from nasopharyngeal specimens with confirmed SARS-CoV-2 from 426 veterans in six New England states between April and September, 2020. Peak disease severity, hospitalization, and mortality were correlated to clinical, demographic, and virologic factors.ResultsOf 426 veterans, 274 had complete and accessible charts. 92.7% were men, 83.2% White, with mean age 63 years. On multivariate regression, significant predictors of hospitalization were age (OR: 1.05) and non-white race (OR: 2.39). Mortality and peak disease severity varied by age (OR 1.06 and 1.07 respectively) and oxygen requirement on admission (OR6.74 and 45.7). Dementia (OR: 3.44) was also associated with mortality. Most (97.3%) of our samples were dominated by the spike protein D614G substitution, and were from SARS-CoV-2 B.1 lineage or one of 37 different B.1 sub-lineages, with none representing more than 8.7% of the cases.ConclusionsIn an older cohort of veterans from the six New England states with a high comorbidity burden, age was the largest predictor of hospitalization, peak disease severity, and mortality. Non-white veterans were more likely to be hospitalized, and patients who required oxygen on admission were more likely to have severe disease and higher rates of mortality. Multiple SARS-CoV-2 lineages were distributed in patients in New England early in the COVID-19 era, mostly related to viruses from New York with D614G mutation.

Many viruses infect circulating mononuclear cells thereby facilitating infection of diverse organs. Blood monocytes (PBMC) are being intensively studied as immunologic and pathologic responders to the new SARS-CoV-2 virus (CoV19) but direct evidence showing CoV19 in monocytes is lacking. Circulating myeloid cells that take up residence in various organs can harbor viral genomes for many years in lymphatic tissues and brain, and act as a source for re-infection and/or post-viral organ pathology. Because nucleocapsid (NC) proteins protect the viral genome we tested PBMC from acutely ill patients for the diagnostic 72bp NC RNA plus adjacent longer (301bp) transcripts. In 2/11 patient PBMC, but no uninfected controls, long NCs were positive as early as 2-6 days after hospital admission as validated by sequencing. Pathogenic viral fragments, or the infectious virus, are probably disseminated by rare myeloid migratory cells that incorporate CoV19 by several pathways. Predictably, these cells carried CoV19 to heart and brain educing the late post-viral pathologies now evident.