Global Container Port Network Linkages and Topology in 2021.

The maritime transport of containers between ports accounts for the bulk of global trade by weight and value. Transport impedance among ports through transit times and port infrastructures can, however, impact accessibility, trade performance, and the attractiveness of ports. Assessments of the transit routes between ports based on performance and attractiveness criteria can provide a topological liner shipping network that quantifies the performance profile of ports. Here, we constructed a directed global liner shipping network (GLSN) of the top six liner shipping companies between the ports of Africa, Asia, North/South America, Europe, and Oceania. Network linkages and community groupings were quantified through a container port accessibility evaluation model, which quantified the performance of the port using betweenness centrality, the transport impedance among ports with the transit time, and the performance of ports using the Port Liner Shipping Connectivity Index. The in-degree and out-degree of the GLSN conformed to the power-law distribution, respectively, and their R-square fitting accuracy was greater than 0.96. The community partition illustrated an obvious consistence with the actual trading flow. The accessibility evaluation result showed that the ports in Asia and Europe had a higher accessibility than those of other regions. Most of the top 30 ports with the highest accessibility are Asian (17) and European (10) ports. Singapore, Port Klang, and Rotterdam have the highest accessibility. Our research may be helpful for further studies such as species invasion and the planning of ports.

Global Fisheries Responses to Culture, Policy and COVID-19 from 2017 to 2020

Global Fishing Watch (GFW) provides global open-source data collected via automated monitoring of vessels to help with sustainable management of fisheries. Limited previous global fishing effort analyses, based on Automatic Identification System (AIS) data (2017–2020), suggest economic and environmental factors have less influence on fisheries than cultural and political events, such as holidays and closures, respectively. As such, restrictions from COVID-19 during 2020 provided an unprecedented opportunity to explore added impacts from COVID-19 restrictions on fishing effort. We analyzed global fishing effort and fishing gear changes (2017–2019) for policy and cultural impacts, and then compared impacts of COVID-19 lockdowns across several countries (i.e., China, Spain, the US, and Japan) in 2020. Our findings showed global fishing effort increased from 2017 to 2019 but decreased by 5.2% in 2020. We found policy had a greater impact on monthly global fishing effort than culture, with Chinese longlines decreasing annually. During the lockdown in 2020, trawling activities dropped sharply, particularly in the coastal areas of China and Spain. Although Japan did not implement an official lockdown, its fishing effort in the coastal areas also decreased sharply. In contrast, fishing in the Gulf of Mexico, not subject to lockdown, reduced its scope of fishing activities, but fishing effort was higher. Our study demonstrates, by including the dimensions of policy and culture in fisheries, that large data may materially assist decision-makers to understand factors influencing fisheries’ efforts, and encourage further marine interdisciplinary research. We recommend the lack of data for small-scale Southeast Asian fisheries be addressed to enable future studies of fishing drivers and impacts in this region.

Genomic Epidemiology of SARS-CoV-2 in Pakistan.

COVID-19 has swept globally and Pakistan is no exception. To investigate the initial introductions and transmissions of the SARS-CoV-2 in Pakistan, we performed the largest genomic epidemiology study of COVID-19 in Pakistan and generated 150 complete SARS-CoV-2 genome sequences from samples collected from March 16 to June 1, 2020. We identified a total of 347 mutated positions, 31 of which were over-represented in Pakistan. Meanwhile, we found over 1000 intra-host single-nucleotide variants (iSNVs). Several of them occurred concurrently, indicating possible interactions among them or coevolution. Some of the high-frequency iSNVs in Pakistan were not observed in the global population, suggesting strong purifying selections. The genomic epidemiology revealed five distinctive spreading clusters. The largest cluster consisted of 74 viruses which were derived from different geographic locations of Pakistan and formed a deep hierarchical structure, indicating an extensive and persistent nation-wide transmission of the virus that was probably attributed to a signature mutation (G8371T in ORF1ab) of this cluster. Furthermore, 28 putative international introductions were identified, several of which are consistent with the epidemiological investigations. In all, this study has inferred the possible pathways of introductions and transmissions of SARS-CoV-2 in Pakistan, which could aid ongoing and future viral surveillance and COVID-19 control.

Dynamics of the Upper Respiratory Tract Microbiota and Its Association with Mortality in COVID-19.

Rationale: Alteration of human respiratory microbiota had been observed in coronavirus disease (COVID-19). How the microbiota is associated with the prognosis in COVID-19 is unclear. Objectives: To characterize the feature and dynamics of the respiratory microbiota and its associations with clinical features in patients with COVID-19. Methods: We conducted metatranscriptome sequencing on 588 longitudinal oropharyngeal swab specimens collected from 192 patients with COVID-19 (including 39 deceased patients) and 95 healthy controls from the same geographic area. Meanwhile, the concentration of 27 cytokines and chemokines in plasma was measured for patients with COVID-19. Measurements and Main Results: The upper respiratory tract (URT) microbiota in patients with COVID-19 differed from that in healthy controls, whereas deceased patients possessed a more distinct microbiota, both on admission and before discharge/death. The alteration of URT microbiota showed a significant correlation with the concentration of proinflammatory cytokines and mortality. Specifically, Streptococcus-dominated microbiota was enriched in recovered patients, and showed high temporal stability and resistance against pathogens. In contrast, the microbiota in deceased patients was more susceptible to secondary infections and became more deviated from the norm after admission. Moreover, the abundance of S. parasanguinis on admission was significantly correlated with prognosis in nonsevere patients (lower vs. higher abundance, odds ratio, 7.80; 95% CI, 1.70-42.05). Conclusions: URT microbiota dysbiosis is a remarkable manifestation of COVID-19; its association with mortality suggests it may reflect the interplay between pathogens, symbionts, and the host immune status. Whether URT microbiota could be used as a biomarker for diagnosis and prognosis of respiratory diseases merits further investigation.

Rapid greening response of China's 2020 spring vegetation to COVID-19 restrictions: Implications for climate change.

The 2019 novel coronavirus pandemic (COVID-19) negatively affected global public health and socioeconomic development. Lockdowns and travel restrictions to contain COVID-19 resulted in reduced human activity and decreased anthropogenic emissions. However, the secondary effects of these restrictions on the biophysical environment are uncertain. Using remotely sensed big data, we investigated how lockdowns and traffic restrictions affected China's spring vegetation in 2020. Our analyses show that travel decreased by 58% in the first 18 days following implementation of the restrictions across China. Subsequently, atmospheric optical clarity increased and radiation levels on the vegetation canopy were augmented. Furthermore, the spring of 2020 arrived 8.4 days earlier and vegetation 17.45% greener compared to 2015-2019. Reduced human activity resulting from COVID-19 restrictions contributed to a brighter, earlier, and greener 2020 spring season in China. This study shows that short-term changes in human activity can have a relatively rapid ecological impact at the regional scale.

Dynamics of severe acute respiratory syndrome coronavirus 2 genome variants in the feces during convalescence.

In response to the current coronavirus disease 2019 (COVID-19) pandemic, it is crucial to understand the origin, transmission, and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which relies on close surveillance of genomic diversity in clinical samples. Although the mutation at the population level had been extensively investigated, how the mutations evolve at the individual level is largely unknown. Eighteen time-series fecal samples were collected from nine patients with COVID-19 during the convalescent phase. The nucleic acids of SARS-CoV-2 were enriched by the hybrid capture method. First, we demonstrated the outstanding performance of the hybrid capture method in detecting intra-host variants. We identified 229 intra-host variants at 182 sites in 18 fecal samples. Among them, nineteen variants presented frequency changes > 0.3 within 1-5 days, reflecting highly dynamic intra-host viral populations. Moreover, the evolution of the viral genome demonstrated that the virus was probably viable in the gastrointestinal tract during the convalescent period. Meanwhile, we also found that the same mutation showed a distinct pattern of frequency changes in different individuals, indicating a strong random drift. In summary, dramatic changes of the SARS-CoV-2 genome were detected in fecal samples during the convalescent period; whether the viral load in feces is sufficient to establish an infection warranted further investigation.

Genomic Diversity of Severe Acute Respiratory Syndrome-Coronavirus 2 in Patients With Coronavirus Disease 2019.

BACKGROUND: A novel coronavirus (CoV), severe acute respiratory syndrome (SARS)-CoV-2, has infected >75 000 individuals and spread to >20 countries. It is still unclear how fast the virus evolved and how it interacts with other microorganisms in the lung. METHODS: We have conducted metatranscriptome sequencing for bronchoalveolar lavage fluid samples from 8 patients with SARS-CoV-2, and also analyzed data from 25 patients with community-acquired pneumonia (CAP), and 20 healthy controls for comparison. RESULTS: The median number of intrahost variants was 1-4 in SARS-CoV-2-infected patients, ranged from 0 to 51 in different samples. The distribution of variants on genes was similar to those observed in the population data. However, very few intrahost variants were observed in the population as polymorphisms, implying either a bottleneck or purifying selection involved in the transmission of the virus, or a consequence of the limited diversity represented in the current polymorphism data. Although current evidence did not support the transmission of intrahost variants in a possible person-to-person spread, the risk should not be overlooked. Microbiotas in SARS-CoV-2-infected patients were similar to those in CAP, either dominated by the pathogens or with elevated levels of oral and upper respiratory commensal bacteria. CONCLUSION: SARS-CoV-2 evolves in vivo after infection, which may affect its virulence, infectivity, and transmissibility. Although how the intrahost variant spreads in the population is still elusive, it is necessary to strengthen the surveillance of the viral evolution in the population and associated clinical changes.