High diversity, close genetic relatedness, and favorable living conditions benefit species co-occurrence of gut microbiota in Brandt's vole.

Introduction: Revealing factors and mechanisms in determining species co-existence are crucial to community ecology, but studies using gut microbiota data are still lacking. Methods: Using gut microbiota data of 556 Brandt's voles from 37 treatments in eight experiments, we examined the relationship of species co-occurrence of gut microbiota in Brandt's voles (Lasiopodomys brandtii) with genetic distance (or genetic relatedness), community diversity, and several environmental variables. Results: We found that the species co-occurrence index (a larger index indicates a higher co-occurrence probability) of gut microbiota in Brandt's voles was negatively associated with the genetic distance between paired ASVs and the number of cohabitating voles in the experimental space (a larger number represents more crowding social stress), but positively with Shannon diversity index, grass diets (representing natural foods), and non-physical contact within an experimental space (representing less stress). Discussion: Our study demonstrated that high diversity, close genetic relatedness, and favorable living conditions would benefit species co-occurrence of gut microbiota in hosts. Our results provide novel insights into factors and mechanisms that shape the community structure and function of gut microbiota and highlight the significance of preserving the biodiversity of gut microbiota.

Reconstructing early transmission networks of SARS-CoV-2 using a genomic mutation model.

The coronavirus disease 2019 (COVID-19) pandemic has greatly damaged human society, but the origins and early transmission patterns of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogen remain unclear. Here, we reconstructed the transmission networks of SARS-CoV-2 during the first three and six months since its first report based on ancestor-offspring relationships using BANAL-52-referenced mutations. We explored the position (i.e., root, middle, or tip) of early detected samples in the evolutionary tree of SARS-CoV-2. In total, 6 799 transmission chains and 1 766 transmission networks were reconstructed, with chain lengths ranging from 1-9 nodes. The root node samples of the 1 766 transmission networks were from 58 countries or regions and showed no common ancestor, indicating the occurrence of many independent or parallel transmissions of SARS-CoV-2 when first detected (i.e., all samples were located at the tip position of the evolutionary tree). No root node sample was found in any sample ( n=31, all from the Chinese mainland) collected in the first 15 days from 24 December 2019. Results using six-month data or RaTG13-referenced mutation data were similar. The reconstruction method was verified using a simulation approach. Our results suggest that SARS-CoV-2 may have already been spreading independently worldwide before the outbreak of COVID-19 in Wuhan, China. Thus, a comprehensive global survey of human and animal samples is essential to explore the origins of SARS-CoV-2 and its natural reservoirs and hosts.

Transmission rate and control efficiency of COVID-19 was lower in warm and wet climate.

COVID-19 has caused huge damage to public health around the world, revealing the influencing factors are essential to take effective control. By using a global dataset covering 617 time series over the world, we estimated the transmission parameters and modeled human and climate effects on COVID-19 transmission. We found that the average transmission rate was lower in warm climate over the world and in wet climate (more precipitation) in Europe. The maximum transmission rate was lower in warm climate in the world, China and USA, and in wet climate in China. The control efficiency in the world, China, and USA was lower in warm and wet condition. In general, our results indicate that warm and wet climate do not favor transmission and human intervention of COVID-19, and COVID-19 transmission rate would be lower in warm and wet seasons or regions than in dry and cold ones.

Host and geographic barriers shape the competition, coexistence, and extinction patterns of influenza A (H1N1) viruses.

The influenza virus mutates and spreads rapidly, making it suitable for studying evolutionary and ecological processes. The ecological factors and processes by which different lineages of influenza compete or coexist within hosts through time and across geographical space are poorly known. We hypothesized that competition would be stronger for influenza viruses infecting the same host compared to different hosts (the Host Barrier Hypothesis), and for those with a higher cross-region transmission intensity (the Geographic Barrier Hypothesis). Using available sequences of the influenza A (H1N1) virus in GenBank, we identified six lineages, twelve clades, and several replacement events. We found that human-hosted lineages had a higher cross-region transmission intensity than swine-hosted lineages. Co-occurrence probabilities of lineages infecting the same host were lower than those infecting different hosts, and human-hosted lineages had lower co-occurrence probabilities and genetic diversity than swine-hosted lineages. These results show that H1N1 lineages infecting the same host or with high cross-region transmission rates experienced stronger competition and extinction pressures than those infecting different hosts or with low cross-region transmission. Our study highlights how host and geographic barriers shape the competition, extinction, and coexistence patterns of H1N1 lineages and clades.

Rapid Spread of Severe Fever with Thrombocytopenia Syndrome Virus by Parthenogenetic Asian Longhorned Ticks.

Severe fever with thrombocytopenia syndrome virus (SFTSV) is spreading rapidly in Asia. This virus is transmitted by the Asian longhorned tick (Haemaphysalis longicornis), which has parthenogenetically and sexually reproducing populations. Parthenogenetic populations were found in ≥15 provinces in China and strongly correlated with the distribution of severe fever with thrombocytopenia syndrome cases. However, distribution of these cases was poorly correlated with the distribution of populations of bisexual ticks. Phylogeographic analysis suggested that the parthenogenetic population spread much faster than bisexual population because colonization is independent of sexual reproduction. A higher proportion of parthenogenetic ticks was collected from migratory birds captured at an SFTSV-endemic area, implicating the contribution to the long-range movement of these ticks in China. The SFTSV susceptibility of parthenogenetic females was similar to that of bisexual females under laboratory conditions. These results suggest that parthenogenetic Asian longhorned ticks, probably transported by migratory birds, play a major role in the rapid spread of SFTSV.

Modeling analysis reveals the transmission trend of COVID-19 and control efficiency of human intervention.

BACKGROUND: A novel coronavirus disease (COVID-19) has caused huge damage to public health around the world. Revealing the transmission dynamics of COVID-19 and control efficiency is important for containing the spread of the virus. METHODS: By using a logistic growth model, we estimated the transmission parameters of COVID-19 in China and six other countries (Republic of Korea, Iran, Italy, Spain, France and Germany). The transmission parameters represent the maximum daily increase rate in the early stages of the epidemic and the control efficiency under human intervention. The control efficiency was determined by the significant decrease of the daily increase rate in time and cumulative cases. RESULTS: We found the daily increase rate of cumulative cases of COVID-19 decreased significantly in both time and cumulative cases in all countries, but the decreasing trend was not further reduced in other countries except for China and Republic of Korea. The response of the daily increase rate to control measures was much earlier than the number of new cases. CONCLUSIONS: Our results suggested that lockdown at the epicenter and social distancing effectively reduced the spread of COVID-19 in the early stage, but identification and isolation of patients, suspected cases and people with close contact at a community level is essential in further reduction of the daily increase rate of COVID-19.

Modeling analysis revealed the distinct global transmission patterns of influenza A viruses and their influencing factors.

Influenza A virus has caused huge damage to human health and poultry production worldwide, but its global transmission patterns and influencing factors remain unclear. Here, by using the Nearest Genetic Distance Approach with genetic sequences data, we reconstructed the global transmission patterns of 4 most common subtypes of influenza A virus (H1N1, H3N2, H5N1, and H7N9) and analyzed associations of transmission velocity of these influenza viruses with environmental factors. We found that the transmission patterns of influenza viruses and their associations with environmental factors were closely related to their host properties. H1N1 and H3N2, which are mainly held by humans, are transmitted between regions at high velocity and over long distances, which may be due to human transportation via airplane; while H5N1 and H7N9, which are mainly carried by animals, are transmitted locally at short distances and at low velocity, which may be facilitated by poultry transportation via railways or high ways. H1N1 and H3N2 spread faster in cold seasons, while H5N1 spread faster in both cold and warm seasons, and H7N9 spread faster in wet seasons. H1N1, H3N2, and H5N1 spread faster in places with both high and low human densities. Our study provided novel insights into the global transmission patterns, processes, and management strategies for influenza under accelerated global change.

More invaders do not result in heavier impacts: The effects of non-native bullfrogs on native anurans are mitigated by high densities of non-native crayfish.

With accelerating species introductions in an era of globalization, co-occurring alien species have become increasingly common. Understanding the combined ecological impacts of multiple invaders is not only crucial for wildlife managers attempting to ameliorate biodiversity loss, but also provides key insights into invasion success and species coexistence mechanisms in natural ecosystems. Compared with much attentions given to single-invader impacts, little is known about the impacts of multiple co-occurring invaders. The American bullfrog (Lithobates catesbeianus = Rana catesbeiana) and the red swamp crayfish (Procambarus clarkii) are two aquatic invasive species in many different areas of the globe. They coexist with native anurans in a variety of permanent lentic waters, which provide an ideal model system to explore the combined effects of multiple invaders from different trophic levels on native species. Based on a global diet analysis covering 34 native and invasive bullfrog populations, and data from 10-year field surveys across 157 water bodies in the Zhoushan Archipelago, China, we observed a reduced impact of bullfrogs on native anurans at high crayfish densities when the two invaders co-occurred. The global diet analysis showed that crayfish occurrence reduced the number of native anuran prey consumed by bullfrogs in both native and invasive populations. After accounting for pseudoreplication of different observations among water bodies, islands, and survey time, model averaging analyses based on GLMMs showed a negative relationship between bullfrog density and native anuran densities for field observations of invasive bullfrogs alone and co-invaded observations with low crayfish density. However, this negative relationship disappeared when the two invaders co-occurred with high crayfish density. Structural equation modelling (SEM) analyses further validated that the impacts of bullfrogs on native frogs were mitigated by the negative interactions between crayfish and bullfrogs. Our results provide novel evidence of a density-dependent antagonistic effect of two sympatric invaders from different trophic levels on native species. This study highlights the importance of considering complex interactions among co-invaders and native species when prioritizing conservation and management actions and will facilitate the development of a more precise framework to predict invasion impacts.