Emergence of an early SARS-CoV-2 epidemic in the United States.

The emergence of the COVID-19 epidemic in the United States (U.S.) went largely undetected due to inadequate testing. New Orleans experienced one of the earliest and fastest accelerating outbreaks, coinciding with Mardi Gras. To gain insight into the emergence of SARS-CoV-2 in the U.S. and how large-scale events accelerate transmission, we sequenced SARS-CoV-2 genomes during the first wave of the COVID-19 epidemic in Louisiana. We show that SARS-CoV-2 in Louisiana had limited diversity compared to other U.S. states and that one introduction of SARS-CoV-2 led to almost all of the early transmission in Louisiana. By analyzing mobility and genomic data, we show that SARS-CoV-2 was already present in New Orleans before Mardi Gras, and the festival dramatically accelerated transmission. Our study provides an understanding of how superspreading during large-scale events played a key role during the early outbreak in the U.S. and can greatly accelerate epidemics.

Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades.

Lassa fever is a severe viral hemorrhagic fever caused by a zoonotic virus that repeatedly spills over to humans from its rodent reservoirs. It is currently not known how climate and land use changes could affect the endemic area of this virus, currently limited to parts of West Africa. By exploring the environmental data associated with virus occurrence using ecological niche modelling, we show how temperature, precipitation and the presence of pastures determine ecological suitability for virus circulation. Based on projections of climate, land use, and population changes, we find that regions in Central and East Africa will likely become suitable for Lassa virus over the next decades and estimate that the total population living in ecological conditions that are suitable for Lassa virus circulation may drastically increase by 2070. By analysing geotagged viral genomes using spatially-explicit phylogeography and simulating virus dispersal, we find that in the event of Lassa virus being introduced into a new suitable region, its spread might remain spatially limited over the first decades.

Regional connectivity drove bidirectional transmission of SARS-CoV-2 in the Middle East during travel restrictions.

Regional connectivity and land travel have been identified as important drivers of SARS-CoV-2 transmission. However, the generalizability of this finding is understudied outside of well-sampled, highly connected regions. In this study, we investigated the relative contributions of regional and intercontinental connectivity to the source-sink dynamics of SARS-CoV-2 for Jordan and the Middle East. By integrating genomic, epidemiological and travel data we show that the source of introductions into Jordan was dynamic across 2020, shifting from intercontinental seeding in the early pandemic to more regional seeding for the travel restrictions period. We show that land travel, particularly freight transport, drove introduction risk during the travel restrictions period. High regional connectivity and land travel also drove Jordan's export risk. Our findings emphasize regional connectedness and land travel as drivers of transmission in the Middle East.

Emergence of an early SARS-CoV-2 epidemic in the United States.

The emergence of the early COVID-19 epidemic in the United States (U.S.) went largely undetected, due to a lack of adequate testing and mitigation efforts. The city of New Orleans, Louisiana experienced one of the earliest and fastest accelerating outbreaks, coinciding with the annual Mardi Gras festival, which went ahead without precautions. To gain insight into the emergence of SARS-CoV-2 in the U.S. and how large, crowded events may have accelerated early transmission, we sequenced SARS-CoV-2 genomes during the first wave of the COVID-19 epidemic in Louisiana. We show that SARS-CoV-2 in Louisiana initially had limited sequence diversity compared to other U.S. states, and that one successful introduction of SARS-CoV-2 led to almost all of the early SARS-CoV-2 transmission in Louisiana. By analyzing mobility and genomic data, we show that SARS-CoV-2 was already present in New Orleans before Mardi Gras and that the festival dramatically accelerated transmission, eventually leading to secondary localized COVID-19 epidemics throughout the Southern U.S.. Our study provides an understanding of how superspreading during large-scale events played a key role during the early outbreak in the U.S. and can greatly accelerate COVID-19 epidemics on a local and regional scale.

Tissue hemoglobin index: a non-invasive optical measure of total tissue hemoglobin.

INTRODUCTION: The tissue hemoglobin index (THI) is a hemoglobin signal strength metric provided on the InSpectra StO2 Tissue Oxygenation Monitor, Model 650. There is growing interest regarding the physiologic meaning of THI and whether a clinically useful correlation between THI and blood hemoglobin concentration exists. A series of in vitro and in vivo experiments was performed to evaluate whether THI has potential utility beyond its primary purpose of helping InSpectra device users optimally position a StO2 sensor over muscle tissue. METHODS: The THI and tissue hemoglobin oxygen saturation (StO2) were measured using the InSpectra StO2 Tissue Oxygenation Monitor, Model 650, with a 15 mm optical sensor. A THI normal reference range was established in the thenar eminence (hand) for 434 nonhospitalized human volunteers. In 30 subjects, the thenar THI was also evaluated during 5-minute arterial and venous blood flow occlusions, and with blood volume exsanguination in the hand induced with an Esmarch bandage. In addition, correlation of the THI to blood total hemoglobin concentration (Hbt) was studied in five pigs whose Hbt was isovolumetrically diluted from 13 to 4 g/dl systemically and 0.5 g/dl locally in the hind limb. The sensitivity and specificity of the THI to measure tissue hemoglobin concentration (THC) were characterized in vitro using isolated blood tissue phantoms. RESULTS: In human thenar tissue, the average THI was 14.1 +/- 1.6 (mean +/- standard deviation). The THI extrapolated to 100% blood volume exsanguination was 3.7 +/- 2.0 units presumably from myoglobin. On average, the THI increased 1.5 +/- 1.0 units with venous occlusion and decreased 4.0 +/- 2.0 units with arterial occlusion. In porcine hind limbs, the THI weakly correlated with Hbt (r2 = 0.26) while DeltaTHI during venous occlusion had a stronger correlation (r2 = 0.62). In vitro tests indicated that THI strongly correlated (r2 > 0.99) to phantom THC and was insensitive to StO2 changes. CONCLUSIONS: Steady-state THI values do not reliably indicate Hbt. The THI is a reproducible quantitative index for THC, and THI trends can discriminate between arterial or venous blood flow occlusions. The THI magnitude permits the estimation of myoglobin's contribution to StO2.

Near-infrared spectroscopy in patients with severe sepsis: correlation with invasive hemodynamic measurements.

BACKGROUND: Clinicians have begun using near-infrared spectroscopy (NIRS) to monitor tissue perfusion in hemorrhagic shock, as the technique allows continuous noninvasive monitoring of tissue hemoglobin oxygen saturation (StO(2)) and the tissue hemoglobin index (THI). We hypothesized that StO(2) measurements in patients with severe sepsis would be associated with the severity of their illness and would correlate with invasive hemodynamic measurements. METHODS: We measured mean arterial pressure (MAP), serum lactate concentration, blood hemoglobin concentration, StO(2), and THI in nine healthy volunteers and ten patients with septic shock in a surgical intensive care unit (ICU). Enrolled patients had a pulmonary artery catheter, and had family able to give informed consent. The average Acute Physiology and Chronic Health Evaluation (APACHE) II score at enrollment for the patients was 19 +/- 5 (standard deviation) points. Volunteers and patients were similar with respect to age and sex. To collect NIRS data, we used the InSpectra Tissue Spectrometer, Model 325 (Hutchinson Technology, Inc., Hutchinson, MN). For three consecutive days, we obtained invasive hemodynamic measurements three times daily, simultaneously with NIRS measurements, and metabolic cart measurements once daily. RESULTS: Patients with severe sepsis had significantly lower thenar muscle StO(2) values (p = 0.031) than healthy volunteers. Near-infrared spectroscopy-derived mixed venous oxygen saturation (NIRSvO(2)) and StO(2) measured from the thenar eminence in patients with severe sepsis correlated with SvO(2) from the pulmonary artery catheter (p < 0.05). In this group of patients, StO(2) did not correlate significantly with lactate concentration, base deficit, or APACHE II score. CONCLUSIONS: Near-infrared spectroscopic measurements of StO(2) correlated with invasive hemodynamic measurements in patients with severe sepsis but did not correlate with severity of illness. These findings suggest that NIRStO(2) may be a clinically useful measurement in monitoring patients with severe sepsis. Further study of this device in early resuscitation of patients with sepsis is necessary.