Adults with comorbidities have faced a high risk from COVID-19 infection. However, Western Australia experienced relatively few infections and deaths from 2020 until early 2022 compared with other OECD countries, as hard border policies allowed for wide-scale vaccination before mass infections began. This research investigated the thoughts, feelings, risk perceptions, and practices of Western Australian adults with comorbidities aged 18–60 years in regard to COVID-19 disease and COVID-19 vaccines. We conducted 14 in-depth qualitative interviews between January and April 2022, just as the disease was starting to circulate. We coded results inductively and deductively, combining the Extended Parallel Process Model (EPPM) and vaccine belief models. Non-hesitant participants believed COVID-19 vaccines were safe and effective at mitigating COVID-19′s threat and subsequently got vaccinated. Vaccine hesitant participants were less convinced the disease was severe or that they were susceptible to it; they also did not consider the vaccines to be sufficiently safe. Yet, for some hesitant participants, the exogenous force of mandates prompted vaccination. This work is important to understand how people’s thoughts and feelings about their comorbidities and risks from COVID-19 influence vaccine uptake and how mandatory policies can affect uptake in this cohort. The COVID-19 pandemic has had far-reaching consequences, with some people facing greater risk from the disease than others. Adults with specific comorbid conditions, including obesity and immunocompromising conditions among others, are at increased risk of severe symptoms from COVID-19 infection . HoweverGiven their susceptibility to severe illness from contracting COVID-19 and their prioritisation as a cohort for vaccination, it is important to understand how adults with co-morbidities relate to both the threat of COVID-19 and to COVID-19 vaccination. Increasing global attention and the ever-growing body of literature on vaccine hesitancy, vaccine acceptance, and vaccine refusal point to the complex reasons why people might not get vaccinated. Some of these factors are systemic, such as access barriers or poorly designed services that do not reach certain cohorts . There aacceptors, who had no concerns about COVID-19 vaccine safety, efficacy, or access, (2) cautious acceptors, who had some concerns and preferred a particular vaccine brand but would accept what was offered, (3) wait awhiles, who sought more data, easier access, another brand, a greater perceived COVID-19 threat, or waited for mandates, and (4) refusers, who had no intention to vaccinate due to concerns about safety and/or efficacy . For this particular study of people with comorbidities, recruitment commenced in January 2022, although people could express their interest in participating from March 2021, when recruitment for the larger study commenced using media promotion, word-of-mouth, and snowballing. Those who were interested in participating signed up via an online REDCap survey ,46, whicWe conducted semi-structured interviews to ask participants about their COVID-19 vaccination attitudes and experiences; a detailed question guide can be referenced in the study protocol . Additioacceptors, cautious acceptors, wait awhiles or refusers  illness” rendered long COVID “another disability” which would “exacerbate the conditions I already have, not necessarily viewing it as something completely separate” and “make life harder”.Some participants shared that long COVID post-infection was a key concern. Anna  shared, “Vaccine hesitant participants also held some concerns about contracting COVID-19. However, they often presented this retrospectively. For example, Charlie  said that in the early days of the pandemic, he was quite concerned, whereas Sophie  shared that she was less worried at the time of the interview than she had been previously.over-inflated’, indicating lower levels of fear than the non-hesitant participants. Stewart  shared that despite belonging to the age and lifestyle category that would mean he is at greater risk of dying from COVID, he was not concerned by the virus, “I still can’t be afraid of it. It’s like being afraid of driving down the road”. He further elaborated his reasoning by arguing that deaths from COVID-19 were relatively low when compared with other causes of death: “In a global or country effect of how many people are dying, it’s almost inconsequential”. Sophie  noted that the Omicron strain is less severe than earlier variants and that across the world, deaths and hospitalisations are decreasing, which she did not attribute to vaccination. “The risk factors [of getting severely sick from COVID-19] are becoming more apparent and I don’t think I’ve got many of those. I’m not so worried about it”.However, vaccine hesitant participants often depicted concerns about the virus as ‘The same vaccine hesitant participants were similarly unconcerned about long COVID. Many thought there was not enough information about the condition. As Molly  explained,“The research on long COVID isn’t clear, is it? I don’t think they’re in a position yet because there aren’t any longitudinal studies to be clear about long COVID. So I have no concerns for long COVID more than I do for any other infectious disease.”To summarise, non-hesitant participants held concerns about contracting COVID-19 and the severity of the infection they could have, particularly with their pre-existing conditions. By contrast, although hesitant participants did share some earlier worries, they also believed the risk was far less severe and were not more concerned about COVID-19 than they were about other viruses.“We were isolated from everybody else. We were not going to be probably as affected…We’re doing the right things as well in terms of how we’re managing it by…keeping things closed”.The second element of perceived threat is susceptibility, which Witte (1992) defines as an “individual’s belief about his or her chances of experiencing the threat”. Thus, we wanted to understand how all participants perceived their chances of contracting COVID-19. For non-hesitant participants, even though they were worried about catching COVID-19, they did not feel that they were particularly suspectable to the virus when we interviewed them because WA’s hard border policy was keeping them relatively isolated from the virus. Joan  felt safe and was optimistic that she was not going to be sick, It is coming around quite quickly… I’m bloody scared, you know”. Gillian  further shared how in 2022 things changed for her, “I think I’ve kind of been a little bit more frightened, ‘cause I know it’s more of a possibility [that I’ll contract COVID-19]”.At the time of the interviews, WA’s hard border was being lifted after two years. Participants saw their chance of contracting COVID-19 would be significantly higher once the border was open. As Boris  explained, “However, even though they did not feel particularly at risk at the time, participants felt susceptible to being infected with COVID-19 because they believed it had higher rates of transmissibility compared with other infectious diseases, such as influenza, and that people could pass it on whilst appearing to be asymptomatic. Joan  said,“I think that I’ve got a higher chance of getting COVID than I do flu and pneumonia because I don’t really hang around a lot of people who are sick with the flu. But, COVID is another thing altogether.”“I live in WA… I spend 95% of my life at home, my risk of being exposed to that virus in WA, where up until recently, we basically didn’t have it at all”. These participants did not, however, express concerns about the border opening, and Sophie  expressly declared that it should open.In contrast to the other participants, vaccine hesitant participants minimized their susceptibility to catching COVID-19 by emphasising the protection offered by living in WA. Stewart  explained, Thus, participants had differing levels of concerns about the contracting COVID-19 due to WA’s hard border policy, as prior to 2022, there had been very few cases in the state. However, with the border being lifted and the belief that COVID-19 is more transmissible than other diseases, participants felt more susceptible to contracting COVID. Vaccine hesitant participants did not share the same level of concern.According to the EPPM, after the assessment of the perceived threat, individuals then evaluate the efficacy of the recommend response, which here refers to taking COVID-19 vaccines. In the EPPM, response efficacy refers to an individual’s belief as to whether a response effectively prevents the threat. In this context, this concerns participants’ evaluation of COVID-19 vaccines as being an appropriate way to prevent COVID-19 infection. Vaccines would be appropriate if people saw them as safe, effective, and necessary. If participants saw the disease as a threat, as we have described above, then we took the necessity as a ‘given’. However, the vaccines would also need to be regarded as safe and able to effectively prevent serious illness.We trusted what the doctors told us and what the GPs told us, and that was that it’s safe. I wasn’t scared to take the vaccine. That’s for sure. I just trusted what we were told”.When participants were asked about their thoughts on receiving a COVID-19 vaccination, the majority reported feeling very positive about receiving or having had the vaccination. For some, the decision was a ‘no-brainer,’ and their comorbidities did not make them feel as though they may respond badly to vaccination. The majority of our participants stated that they did not feel more at risk from the vaccines than the general population. They expressed trust in medical professionals, particularly as they interacted with them to manage their conditions. For example, Phoenix  explained, “Some participants did have concerns about the vaccine, including the effect it would have on them and their conditions, how quickly it was produced, and the effectiveness, but all felt reassured by medical professionals. For example, Liz  said,“I did actually speak to my endocrinologist and say, ‘Look, you know, again that thing of knowing what immunity … autoimmune stuff is triggered by viruses. What is the chance that this is gonna trigger something?’ And she said, ‘Oh, it’s possible, but it’s that risk versus, you know, which risk is higher kind of thing’ … But, you know, I’m very vaccine positive so, you know, I’m willing to trust the experts on that.”“kind of” thought she could have an adverse reaction but received reassurance from hearing that other people with type 1 diabetes were fine after receiving the vaccine.Similarly, Gillian  shared she I am worried about catching [COVID] as well, but I’m more worried about the vaccine, with my health issues”.By contrast, vaccine hesitant participants said that the vaccine posed more of a risk to them than COVID-19 disease, despite some also having concerns about contracting the disease. For example, Sophie  explained, ““The risks of having an experimental drug were greater to me than the risks of contracting Coronavirus”. She added, “I don’t see that current strategies for managing COVID actually do provide the level of protection that they claim”. Charlie  linked his reticence to the vaccine’s ‘element of the unknown’, although he did not ‘personally believe that there’s likely to be serious long term adverse consequences’.Others also expressed concerns about vaccine efficacy as well as vaccine safety. Molly  said, In summary, the majority of participants felt the vaccine was safe and effective in mitigating the threat of COVID-19; however, vaccine hesitant participants perceived the vaccine as more of a threat than contracting COVID-19.perceived self-efficacy, which refers to an individual’s ability to perform the recommend response. Non-hesitant participants all saw vaccination as something that they could do and wanted to do, and in fact they described the vaccine as a way of exercising agency and control to prevent the risk of COVID-19 disease.The second component of efficacy is “It was a great relief when I could say that I was fully vaccinated”. Jess  shared, “I was actually pretty excited. It felt like I was able to do something proactive to protect myself and increase my changes of coming through this pandemic alright. It made me feel a lot safer”.For example, Polly  expressed, procrastinated’ about getting the vaccine: “I think part of that was because I was like, ‘I wonder what’s gonna happen? Like is everyone gonna be okay? They haven’t done fifteen years of safety trials. Surely, that’s gonna be an issue’”.However, Gillian  shared that doubts about vaccine safety posed a barrier for her and said that she ‘Coerced Acceptors only chose to get vaccinated because of vaccine mandates. Charlie  was very angry about the mandates, describing them as ‘complete overreach’ and ‘very, very, very offensive’. He identified as someone engaging in ‘civil disobedience in the face of authoritarianism’. Vaccine mandates made Charlie feel much more negatively about being vaccinated, but they also made him take the vaccine; at the time of the interview, Charlie had been placed been on leave without pay for two months and was in the process of getting fully vaccinated so that he could return to his job in WA’s mining sector. Stewart , who had begun a course of Novavax vaccinations, explained the influence of the employment mandates and the consequences of vaccination-related travel restrictions: “I’d already decided a long, long time ago that I would get a Novavax... purely on the basis ‘cause I want to go back to work… I thought the only way I can go and visit my children is if I get vaccinated”. Stewart believed that his adult children, who lived on the other side of the country, had experienced adverse reactions to the vaccines, and so he feared them facing potential booster requirements for travel to visit him. Stewart preferred to get himself vaccinated instead so that he could be the one visiting them. He was more comfortable with Novavax, as he believed it was similar to the influenza vaccination which he had previously had.The two Refusers who chose not to vaccinate and did not share any intention of vaccinating in the future. Thus, the majority of participants in our sample did get vaccinated (or were in the process of doing so) and received booster shots, including two who felt they were coerced into making that decision.The two By tracing each participant through the phases we have described here and laid out in Polly—a quintessential vaccine acceptance storyfears of the disease predisposed her to see the COVID-19 vaccines as necessary. Polly further believed that the vaccines had sufficient levels of safety and effectiveness to orient her towards accepting them. Polly therefore demonstrated response efficacy in believing that the vaccines could address the threat that COVID posed. She also demonstrated self-efficacy in seeing vaccination as a step she could take in addressing that threat. Polly’s journey is illustrative of a straightforward vaccination journey.Polly was afraid of catching COVID because of her comorbidities. She also believed that she had an increased chance of experiencing a severe outcome from COVID-19 and not recovering as well as other people might. These Molly—a quintessential vaccine refusal storynecessary, and more importantly, she did not believe it was sufficiently safe. For Molly, the vaccines failed at the level of response efficacy and self-efficacy. She did not see that they could actually solve the threat of COVID-19, which she believed was not that significant anyway, due to her safety concerns. As a result, Molly refused the vaccines.Molly’s non-vaccination journey was informed by a lower fear of the disease than that shared by Polly and other non-vaccine hesitant participants. Molly’s early fears of the disease had waned during the course of the pandemic, and instead she had come to see the vaccine as the more frightening prospect. Thus, with muted fears of the disease, Molly did not see the vaccine as Charlie—a story of external coercion shaping vaccine decisionsnecessary. He also did not believe they were effective, and although he did not have significant safety concerns, he believed that mandates were inappropriate in the context of novel vaccines. Where Charlie’s journey deviates from that of Molly is that he was compelled to vaccinate because of the WA Government’s mandatory vaccination policy. This policy did not change the way that Charlie thought or felt about any of the factors that drove his preference not to vaccinate: he was still not afraid of COVID-19 and remained somewhat concerned about the vaccines’ safety. However, importantly, Charlie was highly resentful of the policy that required him to choose between his job and his beliefs. However, the mandates exerted a powerful force on Charlie, reorienting his journey and resulting in him becoming vaccinated. We illustrate this in Charlie’s journey generally started out resembling that of Molly. He did not see COVID-19 disease as particularly threatening and therefore did not see vaccines as In this study of people with comorbidities in Western Australia, we have traced the stages of their vaccination journeys using a model informed by the EPPM and the constructs of vaccine safety, efficacy, and necessity.Our analysis of aggregated themes—as well as individual participants’ journeys—demonstrated that fear or lack of fear of the disease was an important shaper of people’s vaccination outcomes, as discussed in previous literature ,24. PartAlthough vaccine hesitant participants had concerns about COVID-19, these concerns were less severe, and some reported them diminishing over time. Vaccine hesitant participants did evaluate COVID-19 as a threat in varying degrees, particularly at the beginning of the pandemic. These concerns may have diminished as participants came to see vaccines as the greater threat.Cautious Acceptors or Wait Awhiles, did worry about the vaccines’ safety, echoing the findings of Kaufman et al. [A similar divergence occurred between hesitant and non-hesitant participants regarding the perceived efficacy of the COVID-19 vaccinations for mitigating the threat of the disease. The participants who believed that the threat of disease was severe thought the vaccines were necessary, believed they were effective at preventing serious illness, and had confidence in their safety. They consequently took the vaccines. Some vaccine accepting participants, whom we classified as n et al. . This meBy contrast, vaccine hesitant participants took different and varying journeys. This is reminiscent of the work of Wiley et al., which found that vaccine hesitant and refusing parents had various vaccination trajectories for their children’s vaccinations, with study participants’ vaccination journeys involving continual risk assessment over time . ContrarIt was striking that mandates operated as an external force on half of the vaccine hesitant participants and that these individuals chose to get vaccinated despite not altering their perceptions about COVID-19 or the vaccines. Rather, the costs of not vaccinating were too high for them to bear. The anger expressed by Charlie, in particular, indicates that mandates may pose costs later, generating psychological “reactance” and orienting people away from voluntary vaccination programs . This maCautious Acceptors and the Wait Awhile participant thought about their vaccination decisions by couching them within a ‘fragility framing’ [non-medical risks of non-vaccination. For example, vaccine mandates as a policy lever introduced social threats for vaccine hesitant participants, as these threats touched upon their ability to travel to see loved ones and on participants’ livelihoods.The purposive sampling of non-elderly adults (aged 18–60 years old) with comorbidities provides important insight into a priority group for COVID-19 vaccination services. Contrary to what may have commonly been assumed in a purely rational risk-assessment biomedical approach, this ‘invisible’ risk-group did not categorically accept COVID-19 vaccination, despite increased objective risk to severe COVID-19 health consequences. There were individuals in our sample who did not immediately vaccinate in order to mitigate their risk of COVID-19 illness. Some ‘felt the fear but did it anyway’, some waited awhile, some were coerced into vaccination by mandates, and some refused. Vaccine hesitant individuals had other risks in mind and expressed concerns about vaccine safety, efficacy, and necessity. Some framing’ . In otheThis study has some limitations. Its qualitative design precludes us generalizing findings to the wider population of WA and to other contexts with different epidemiological and political realities. Our recruitment methods for interviews resulted in participants with high English proficiency and living in metropolitan Perth. However, within our sample, we aimed to interview a variety of ages, genders, and people with different conditions and to speak to people who were hesitant or refusing as well as those who had been fully vaccinated. Furthermore, we specifically focused on an ‘invisible’ group of people with comorbidities who were not also elderly; this group is often under-served by both comorbid vaccination programs and by researchers. Additional limitations include that people who agreed to participate in the research may have held stronger vaccination views (either in favour or opposed) compared with those who did not sign up. Furthermore, we had few participants who were outright vaccine refusers, due to Western Australia’s high vaccination rate of over 95% limiting the pool from which we could recruit. Relying on self-identification of comorbidities and not insisting that people disclose them to us, we did not medically verify that all participants fit into the comorbidity COVID-19 vaccination group in Australia.Vaccination social science research will need to stay abreast of developments such as uptake of future dosages of existing or new COVID-19 vaccines, and it will be important to focus, as we have, on non-elderly adults with comorbidities because they will once again be priority groups for protection. Future research could more formally mobilize the EPPM in its entirety to understand people’s responses to vaccination threats and risks, going beyond our use of it as a coding framework and heuristic.threat, severity, susceptibility, response efficacy, self efficacy) and vaccine belief models . Adults with comorbidities in Western Australia have a unique perspective in how they were thinking about the risk of COVID-19 disease and vaccinations because there was a very low threat of contracting COVID-19 at the beginning of the pandemic. By tracing these adults’ vaccination or non-vaccination journeys, we saw how their consideration of health threats were highly contextual and therefore changed over time. Furthermore, their vaccination decisions were influenced by not only disease threat; policy factors, such as border closures, vaccination requirements for travel, and mandates linked to employment were important deciding factors for some.This research provides an important perspective from adults with comorbidities and their thoughts and feelings about COVID-19 disease and vaccination. The Extended Parallel Process Model was a useful heuristic for analysis in the context of West Australia in which, unlike many other settings, COVID-19 border policies allowed for mass vaccination in anticipation of widespread coronavirus infection. As an analytic frame, we combined the EPPM with vaccine belief models, which allowed us to produce and analyze a repertoire of factors influencing how adults with comorbidities evaluated risks around COVID-19 disease and made subsequent vaccination decisions. This included valuable concepts from the EPPM (


The COVID-19 pandemic not only had detrimental effects on physical health but also had adverse effects on college students’ mental health. This paper begins to fill a gap in knowledge related to the contextual factors that impacted college students’ mental health during COVID. Using in-depth interviews with a diverse sample of 33 college students at a Midwestern university, during Spring 2021, we highlight the pandemic’s role in shaping college students’ mental health and their outlook of the future. Thematic analysis revealed student reports of mental health decline during the pandemic attributed to campus closures and social distancing policies implemented by the institution to reduce the spread of COVID-19. Students shared that the pandemic created uncertainties about their future opportunities for education, career fulfillment, and employment. However, the interviews also suggested a general sense of adaptation to the pandemic’s impact which was students achieved via a combination of active and passive coping strategies. Expanding institution-based mental health services to include a variety of modalities and off-line toolkits for students can help students cope with mental health challenges, whether in ‘normal times’ or during national crises. Future research should focus on identifying strategies for promoting mental wellness among college students and exploring post-pandemic mental health wellbeing. Since March 2020, the COVID-19 pandemic has impacted all aspects of life and society globally . In the Even before the onset of the pandemic, college students experienced high levels of depression, anxiety, and stress ,11,12,13While college and university closures or move to online learning was a necessary COVID-19 prevention strategy, there were significant unintended impacts on the academic and social lives of college students . The traResearchers have focused a lot of attention on the COVID-19 pandemic’s effects on mental health, but less is known about how these effects have shaped college students’ experiences or students’ outlook on the future. Much of the published work to date is quantitative, highlighting the prevalence of mental health symptoms. This paper seeks to expand the literature on college students’ mental health during the pandemic using qualitative interview data to highlight students’ experiences of declining mental health, shifting perspectives on the future, and coping. Our study of a diverse sample of 33 college students at a Midwestern University (MWU) offers depth and insight into the perceived reasons for depression and anxiety. Even though most US college campuses have drastically reduced or entirely removed COVID-19 restrictions, it is important to understand how students’ mental health was impacted by the COVID-19 pandemic, in efforts to provide ongoing support and to better prepare for future pandemics.Our qualitative data originate from students at Midwestern University (MWU) who participated in a survey conducted in the Fall of 2020 as part of a study titled, “Seropositivity and Risk for SARS-CoV-2 and COVID-19” (N = 1446 undergraduate and graduate students). At the end of the survey, students were asked if they were willing to be contacted for follow-up interviews; the majority (77%) consented and thus served as the sampling pool for this study. We purposefully sampled students to ensure that the qualitative sample was diverse in terms of gender, race, and sexual orientation; students were recruited from the sampling pool via email. The final sample included 10 students randomly selected irrespective of personal characteristics (sampled from N = 1155); 13 non-white students (sampled from N = 117); and 10 self-identified LGBTQ+ students (sampled from N = 151) as shown in At the participants’ request, interviews were conducted by phone or Zoom and lasted around 30 min. Interview questions focused on a variety of elements of students’ life throughout COVID-19, including academics, relationships with friends and family, illness, and mental health see . These qUsing thematic analysis, the first three authors reviewed the transcribed data independently to generate a list of themes around mental health experiences. The authors subsequently met to discuss, compare and consolidate ideas—developing major themes to comprise a codebook . Using tThe pandemic affected our participants’ lives in ways that shaped their perspectives on mental health issues. Changes in what was previously normal with family, education, and social routines dampened emotions and resulted in three major categories related to mental health: (1) experiences of mental health decline, (2) changing perspectives and ruminations about the future, and (3) adapting to the pandemic’s impact. The students identified occurrences of anxiety, depression, and stress during the pandemic as they made adjustments to their everyday routines. For some, struggles with mental health were new, while for others, the pandemic exacerbated pre-existing mental health conditions. Concerns about COVID-19 infection and its potential short- and long-term health consequences were widely discussed. Beyond their own social world, participants expressed concerns about the pandemic’s possible implications on social and political strife and how these might affect society as a whole. Through this lens, they discussed worries about future career, economic, and higher education opportunities. In response to dealing with these personal and social impacts, participants reported a variety of response mechanisms that they employed to deal with the pandemic worries while being intentional about maintaining optimal mental health despite the challenging context.The COVID-19 pandemic presented a new set of challenges and stressors for college students. Campus closures and return to family homes meant that social activities were few or absent for most students. Still, students had to keep up with school demands virtually, a feat that required extensive efforts to manage and accommodate academic work in non-academic environments. At the same time, public health recommendations for reducing social interaction to reduce transmission led to students feeling isolated and limited in their college experience. Our participants universally discussed mental health declines and identified specific incidents of stress, anxiety, loneliness, and depression citing the pandemic as having had a significant impact on their mental health.Students experienced attending to the new social and academic landscape as stressful. Thriving during the pandemic presented unique challenges making academics and everyday activities a constant source of stress. Jeff, a White, LGBTQ student, bemoaned these issues.Um, I definitely would say that this year has tested my mental health. If I had to compare it to all my other years of college, it would be the worst year. I know there are resources out there available to me, but I feel like everyone just kind of plays it off like, ‘Oh, it’s the pandemic’ so I’m just trying to push through and graduate. I have 5 weeks now of this semester but a big toll on my mental health has been because of my work. And, because my work has been completely altered by COVID. I used to love my job, going there almost every single day and now it’s just stressful. The turnover because of COVID has increased so it’s more job responsibilities on myself.Even activities that Jeff loved or experienced as joyful prior to the pandemic led to stress and discontent.Anxiety was raised in relation to everyday life activities, family, and academic work. Natasha who identifies as a White, LGBTQ student shared, “[the pandemic] taught me that I am susceptible to anxiety. I never really felt anxiety like that, kind of like a pervasive anxiety, from COVID. And I’ve had lots of drama and trauma in my life, but it was a different kind of worry and anxiety that wasn’t healthy.” Experiences of anxiety were reported in relation to potential exposure to COVID-19 as the interviewers were occurring at a time when there were many reports of severe illness and death resulting from COVID-19 infection and regular reports of cases on campus.A number of our participants expressed a strong desire to stay healthy during the pandemic and dreaded the thought of possible infection resulting from exposure to COVID-19. Kelley, a White LGBTQ student, highlighted this sentiment. She said she was aware of her, “mental health, [I have] a lot more anxiety. But [my] physical health is mostly the same. Yeah, definitely increased anxiety from not wanting to get sick. Or if I did get sick, worrying that it was COVID. So that was the biggest mental health thing.” Anxiety for these students influenced how they went about their ‘normal’ life activities. COVID-related anxiety was pervasive and felt uncharacteristic for many of the students who experienced this anxiety.Social isolation was a key factor in deteriorating mood impacting feelings of loneliness and depression; our participants struggled to maintain optimal mental health in the absence of the social and community experiences associated with higher education. Students connected loneliness to mental health decline. Benjamin a non-White male student said, “At times, I would say that it [my mental health] declined just because I’ve felt lonely.” Jasmine, a White female, LGBTQ student, shared similar experiences, and as the pandemic progressed, her mental health decline intensified. She stated, “it’s now been kind of bumpy because I’m getting to the point where I’m more burnt out on the pandemic, and just sick and tired of spending so much time by myself in my apartment.” This sense of social isolation and loneliness may have facilitated lowered transmission, but the cost was the mental well-being of students like Jasmine and Benjamin. Noah, a non-White male student, shared his experiences, remarking, “And [the pandemic has] led to me like, just like staying in my room, and staying in my room like one place that’s made me sometimes like, in a depressed mood. Um, definitely more prone to depressing episodes.” Suggesting that isolation was not just experienced as episodes of loneliness, but also of feeling depressed.While some students were able to manage depressive episodes with physical exercise or other positive coping strategies, the proximity to COVID infection and deaths, and well as the multiple waves of the pandemic meant that many students cycled into and out of depressed states and some managed their feelings with less ideal coping strategies. Jasmine a White, LGBTQ student noted that.In general, and this is something I have personally noticed, is, a lot of people’s, like, substance abuse—well, substance use, I should say, use, not abuse—use has gone up significantly throughout all of this. And I personally can attest, I’m smoking a lot more weed than I should be, probably, and drinking and stuff, because it’s—you know, you’re burnt out, and you’re exhausted. And I’m seeing that trend a lot with, just, people in general. And especially with college students, because you already have that culture where a lot of that is accepted.For some students managing pandemic challenges led to new experiences of burnout and mental health decline. For a number of our respondents with preexisting mental health conditions, however, the pandemic aggravated their existing symptoms or conditions.For some, their mental health condition worsened to the point where they felt the need to seek additional professional help. Kalia a White, LGBTQ student emphasized her experience with mental health during the pandemic and she recognizes the role of the pandemic in her remarks “[My] mental health definitely went down. I actually got a therapist a few months ago. I don’t think it was onset from COVID-related things, but COVID is another layer of problematic things, you know?” She did not ascribe COVID as the cause of her mental health condition but did feel it contributed to her need for a therapist’s help.One respondent experienced a relapse of a mental health condition she had been successfully managing. Rebecca, a White female student, shared her experiences with the pandemic’s impact on her depression, “God, it’s [COVID] changed everything. I mean, you listed quite a long list there. Where should I start? My mental health has taken a big hit. I was diagnosed with depression probably three or four years ago when I was on vacation. I’m actually going to get back into therapy.” Rebecca’s comments highlight how the COVID-19 pandemic had aggravated pre-existing mental health problems.Social seclusion and distancing that were common in the first year of the pandemic proved particularly difficult for individuals with pre-existing mental health challenges. For Lloyd, a White, LGBTQ student loneliness during the pandemic was a precursor to depression episodes. While he had been dealing with depression prior to the pandemic, his symptoms worsened increasing his medication needs.Yeah, I would say in that kind of isolation, I have been more depressed. I started seeing a therapist again recently, which I had done prior. And I’m also on SSRIs, so selective serotonin reuptake inhibitors, so I have been put on them in increasingly higher dosages since COVID and I have only started on them in COVID, so last fall is when I started that medication, so a definite decline in mental health following COVID, not that I had great mental health before, but some of my predilections towards anxiety and depression increased during COVID.As evidenced above, the pandemic took its toll on college students whether they had pre-existing conditions or not, students experience a variety of negative mental health consequences related to fear, isolation, and missing out on a ‘normal’ college experience.For many students, the pandemic experience involved more than just mental health symptoms; it also affected how they viewed the world. Respondents noted that the COVID-19 pandemic had uncovered vast differences in personal, religious, and political beliefs leading to worries about their own futures in terms of ways the pandemic could impact their academic goals, career path, and employment opportunities. While some of our participants did not identify these concerns as mental health issues and hence did not discuss them in relation to stress, anxiety, loneliness, or depression, all narratives that mentioned these issues offered insights into the emotional landscapes experienced as the pandemic progressed.Participants expressed worries about the implications of the COVID-19 outbreak on societal norms and values. Due to conflicting beliefs and perceptions around COVID-19, public emotional flares had not been uncommon. These experiences contributed to emotional dampening and were a source of concern during the pandemic. Martin, a non-White male student, considers the pandemic’s impact on societal values his “biggest worry” and explains how he feels about the situation.I think my biggest worry is how we’re going to get back to what is normal. I personally feel like people have overreacted, and then there are people who have underreacted to it. So, I think that my biggest issue is that, as a society, we aren’t able to find a common ground or whatever on how to get back to what’s normal.Jimmy, another non-White male student, explained similar concerns about the strains on normality and interpersonal relations in public spaces.I think more of not COVID itself but you know you see in a society where people are like extreme on wearing PPE and social distancing. Even here in the clinic, we have had patients get very aggressive. People out there trying to be a little too cautious and therefore they are getting aggressive. You see it at the stores and people call the cops on people. I have not personally seen that. That is my only concern. Eventually one day we have a lot of people out there upset because they are not doing what someone else expects them to do. That wasn’t a big deal before. No one ever yelled at you if you had a runny nose and you weren’t wearing a mask.Students expressed concern about other tears in the social fabric. Rebecca, a White female student, shared fears for altered family and job situations and she shared her thoughts with the following remarks, “I worry about people who have lost their jobs, people who are struggling to feed their families, people who are on the brink of getting evicted, losing their homes. There are so many things.”The uncertainties and concerns went beyond what had already occurred to worries about changes in future opportunities for education, career fulfillment, and employment. Our participants believed that the economic downturn associated with the COVID-19 outbreak could have dire consequences on future aspirations which made students feel more stressed during the pandemic.Janelle, a non-White female student, shared her thoughts about the abrupt disruption in opportunities for students to gather necessary experiences as they prepare for various career trajectories.But yeah, I guess the biggest worry is worrying about these consequences whether it’s within this college or within the country, the world, whatever, in the future because a lot of students, especially in STEM fields who want to get into labs, people want to try to get experience before they go to med school or whatever they’re doing are stopped because they can’t get into labs. So, I really worry about the future in terms of career goals and stuff like that.Even though the transition to online learning was a success, students pursuing academic fields that require in-person training missed out on key experiences. Shawn, a non-White, non-binary student went further by citing their experiences as they felt that the COVID-19 disruptions could delay his academic goals.I’m worried that with COVID, I haven’t [had a chance to do] as much research as I would have previously which might affect my graduate school application. I might—in the past couple of weeks, I’ve been thinking what if I take another year after graduation to do more research instead of going straight to graduate school. But my career goals are still the same. I want to grad school, and I want to do research.In addition to fears about careers and furthering their education, participants expressed a general feeling of uncertainty about the future. Not knowing what to expect was particularly uncomfortable. Grace, White female student, articulated this discomfort in this way.I feel like in general, just how it’s going to impact our country and world. Also, jobs I feel like it’s going to impact because I know so many people have already lost their jobs. So, just how it’s going to change that and just change our dynamic in the world, in general, is a big fear of mine.For our participants, uncertainty, and apprehension about the future intertwined with their experience of the COVID-19 pandemic. While uncertainty about the future may be common at this stage of the life course, in Spring 2021 this uncertainty was connected with negative emotions  that were also linked with negative mental health outcomes . While tSome of our conversations with participants revealed a sense of adaptation rather than helplessness. Despite the challenges to goal achievement posed by social isolation, individuals enacted practices to address the emotional slump associated with the pandemic. Coping strategies included actively taking control of their lives or more passively engaging in optimism; most students used a combination of active and passive strategies.The pandemic increased the visibility and awareness of mental health issues making students feel that it was more acceptable to discuss mental health and do something about it. Students took agency to manage their mental health in a number of forms: professional care including therapy, courses, and medication, as well as building community online and in-person.According to some participants, the decision to seek mental health care was motivated by how the pandemic itself had contributed to mental health declines. Some students noted this was their first time seeking formal mental health care. Ana, a non-White female student, shared her experiences with the following remarks.In terms of anxiety though, I’d say that COVID has made me more willing to seek out help because it’s more normalized, I guess? So, I did take an [anti-] anxiety course through the counseling center, back when I was rooming with the girl who didn’t care about COVID, and that was one of my biggest sources of anxiety. I do have a generalized anxiety disorder, and my workload is a huge contributor, but COVID is also a big part of it. Just struggling to fit in and make friends on campus when I care a lot. So I took that course and then this semester I actually reached out to a psychiatrist and got medicated for anxiety for the first time and that’s been beneficial to me as well.While Kalia believed that the pandemic exacerbated rather than was the source of her mental health decline, the additional ‘layer’ led her to seek help, “Yeah. Mental health definitely went down. I actually got a therapist a few months ago. I don’t think it was onset from COVID-related things, but COVID is another layer of problematic things, you know?”Kelley outlined her coping process in this way, “I did take strides to help myself. I went to group therapy and didn’t let myself just sit at the computer all day long. I at least got up and I did something else in the apartment. I think it kind of helped me there not get into a depression.” As mental health therapy services were offered virtually, participants also took advantage of this opportunity. For Janelle, virtual therapy visits were not something she had done before the pandemic but were an integral part of her path to taking back control of her mental health,”… I see a therapist virtually, and I started seeing her in June of 2020. I haven’t stepped foot in the office ever. I’ve only known her for this computer screen. That was something that was interesting because I’m not used to seeing therapists on the computer screens, it’s usually in person.” The availability of both in-person and virtual services was vital for college students. Even though some had not used such services before, each of these students took action to seek care to address what they saw as declining mental health related to the pandemic.Forming, maintaining, and leaning on social communities was another common coping strategy among our participants. These virtual or in-person communities provided needed social interaction and social support.In some instances, these communities were achieved virtually via cooperative activities such as video gaming. Lucas, a non-White male student, disclosed his ADHD made social isolation particularly challenging; he found, however, that online video gaming provided him with needed social interaction, but also not having to just sit still.Hell, yeah. I’d say it’s difficult, to say the least because I’m registered through the disability center. I have moderate to severe ADHD. I feel like it’s a need for me to go out and move. It’s really hard for me to sit down. So, I’ve just found different things like—I don’t know. One of the necessities I made when we first came up here with my brothers was everybody had some type of Playstation so we could talk to each other through the headset. We could play with each other. It was some type of indirect social interaction. I’d make sure I talked to my brothers, I talked to my older sisters, all through kind of that. And it was just a way to keep my hands busy because I really can’t go outside and get my own body energy out of there.Alex, a non-White male student, reported similar practices, “Another thing is how much more we use virtual sources, for example, now whenever my friends can’t really hang out, like my friend group, we’ll go on Discord, and we’ll all be playing video games together, but separately.”Other participants opted for in-person social communities including friends with whom they share similar health and behavioral attributes. Students formed social “bubbles” where they interacted with a small designated group of friends. While social “bubbling” was not a perfect COVID-19 prevention practice, was a good risk mitigation strategy that reduced the chance of transmission while allowing for social interaction with a select group to reduce the adverse consequences of loneliness among members. Social “bubbling” also provided some form of accountability towards observing infection prevention practices since members would not want to risk exposing others through negligence. Janelle described her bubble in this way.It’s just me and like two or three friends. And it’s us together in general. And so, we were bubbling before bubbling was cool and everything. And so, we still keep ourselves safe. And we’re all scientists so we believe and listen to what’s going on. We’re not going to bars and we’re not doing anything like that… My friends are the ones that are keeping me sane. Us, each other, we’re kind of there for each other and keep each other grounded and not have cabin fever or whatever.Noah described a similar situation, “But uhh, in the beginning, like, the pandemic was like, really scary, and like I wasn’t seeing any of my friends, but I had like this small bubble, and all of my friends have just been hanging out inside that small bubble of like, like, 4 to 7 people. So like, a decent amount, but those are the only people that I’m not social distancing with.” This active risk mitigation strategy allowed students to have social interaction to address mental health needs while limiting COVID exposure.As the pandemic progressed, students felt it was increasingly doubtful that things will be returning to “normal” soon. And yet, a sense of optimism and hope was a major source of comfort for many of our participants. Optimism and hope were spurred by news of COVID-19 vaccine approval and availability, but also by a desire to stay positive in a difficult situation. Alex expressed his thoughts on this “I think America is hopefully close to the end of the tunnel here. I’m seeing the light at the end of the tunnel, but I don’t know if that’s accurate or not”.COVID-19 vaccines represented a major source of hope and optimism about the pandemic’s end for a certain group of students. Since vaccines prevent infection and reduce transmission of infectious diseases, it was not surprising that college students viewed vaccine availability as a major breakthrough in the pandemic. Courtney explained her perspective, “But, I think, overall, there’s still a lot of hope. Especially with the vaccine coming out and that kind of thing. I think—especially with my friends. We’re just counting down the days and just hoping that soon, it’ll all just slowly start going back to normal I think.” Kalia was lucky to have been among the first groups of individuals eligible for the vaccines, “But, I got the first vaccine, and that has definitely brought down some anxiety about it.” For her, receipt of her first vaccine dose played a crucial role in reducing anxiety about possible COVID-19 exposure.When asked about thoughts on the future and whether they felt worried, rather than focusing on the challenges, some students felt COVID-19 was providing them with lessons and preparing them for the future. Noah shared his belief that the COVID-19 pandemic was preparing the world to combat potentially more fatal health challenges later, “Um, not really. I’m actually pretty optimistic about the future because I think that while COVID-19 was bad, it was honestly like, one of the best-case scenarios for global pandemics. And I think that this would, this will shock people enough to be prepared for a worse epidemic in the future.” He went on to highlight the ways pandemic health and workplace practices have ingrained important lessons.I think that masks will be more common when people are sick for anything. I am looking forward to that. And I think that there will be less pressure for people to come to work when they have like the flu or something, I think people would be more conscientious about illnesses and contagion. So my outlook on the future is very optimistic, and that might be naive, but I can hope.Even though little was known about the effectiveness of the vaccine at the time of our study, optimism among our participants allowed students to feel hopeful about better conditions in the future, which may have protected them against some of the negative mental health effects of the pandemic.The COVID-19 pandemic affected college students’ lives in many ways. Our participants reported experiences of mental health decline during the peak of the pandemic when COVID-19 prevention policies led to campus closure. Additionally, the pandemic experiences of our participants had an impact on their perspectives of the future, creating uncertainties about societal norms and values as well as future opportunities for education, career fulfillment, and employment. Lastly, participant conversations indicate a general sense of adaptation to the pandemic’s impact which was achieved via a combination of active and passive coping strategies.Identified experiences of anxiety, depression, and stress were discussed in relation to changes in daily routines during the pandemic. For some, mental health decline was a first-time experience and for others, it was an exacerbation of pre-existing mental health challenges. By uncovering connections between the COVID-19 pandemic and mental health outcomes, our findings build upon existing research showing that college students experienced high levels of depression, anxiety, and stress during the COVID-19 pandemic ,21. Lee College students also reported that pandemic-induced concerns for the broader society impacted the ways they were thinking about the future. Students discussed concerns about the job market, social distancing, and the political divisions resulting from conflicting beliefs about the COVID-19 infection. Our participants were therefore concerned that life may not return to what we know as “normal”. As students, they had additional concerns about opportunities for quality educational experiences, career advancement, and employment. This is similar to findings from existing literature among college students in the USA which suggest that concerns about academics, one’s health, job, employment, and uncertainties about the future were frequently reported among college students and were strongly linked with declining mental health ,29,30.Coping strategies were an essential part of our participants’ adaptation to changes in lifestyle during the pandemic. Some participants maintained a sense of optimism and reportedly invested time in maintaining close-knit social groups virtually and sometimes in-person while others sought professional help in the form of counseling and therapy. Like our study findings, college students have demonstrated more optimism about the future in spite of high-stress levels experiences. This was evident in Chierichetti & Backer’s 2021) study from Fall 2020 involving students at the San Jose State University, where more than half of the 400 study participants reported being positive about their long-term goals and prospects, which helped them deal with pandemic challenges better [ study frContrary to existing discourse suggesting that college students are more likely to ignore or be reluctant to identify and accept mental health challenges ,32, our Thus, our findings describe college students’ experiences during the pandemic and highlight important lessons from those experiences. We also recognize that the COVID-19 pandemic contributed to a decline in mental health, even among students who had no prior history of such problems. For college students with pre-existing mental health conditions, the COVID-19 pandemic presented “an extra layer of problems”.Mental health challenges reported in this study were based on participant self-report rather than clinical evaluation, but we believe that self-reporting was ideal to elicit discussions around mental health experiences and actions of college students during the pandemic. Additionally, the sampling for our study was intended to highlight the experiences of a diverse set of college students but did not aim to be representative; thus, while we met saturation in our findings, and the themes represent findings across groups, caution must be used in generalizing these results to the student body at our own or other academic institutions. Our findings, however, suggest that college students at large predominantly white public universities may have had similar experiences during the COVID-19 pandemic.The study findings show that college students were vulnerable to mental health issues during the pandemic as they feared potential exposure and illness from the COVID-19 virus and were limited in their social interactions. As predicted by the social stress theory , our parFuture research should be directed toward identifying ways of reaching college student populations for mental wellness. More research is also needed to explore trends in college student mental wellness before, during, and after the COVID-19 pandemic. College students reporting an incidence of mental health decline during the pandemic should be followed up to see whether these issues remain after the pandemic and how coping and adaptation practices evolve over time. For future outbreaks, policymakers should prioritize implementing physical and mental health interventions simultaneously, especially among college student populations. Academic institutions should prioritize setting infrastructures that would provide students with adequate mental health support for future disease outbreaks or crises. While beyond the scope of this paper, the data from this project also suggest the opportunity to explore how crises impact the building of life strategies in new circumstances especially in relation to mental health and wellness. Additionally, the findings of our paper point to the need to assess these themes presented among other vulnerable populations such as older individuals, people living with underlying conditions, and immigrants, as they are increasingly susceptible to physical and mental health issues during crises ,34,35,36


Since Kraepelin and Bleuler, schizotypy was understood as a mild expression of psychosis, a latent form with the same trajectory but different severity. They pointed characteristics such as being eccentric, unreasonable, supersticious or hipersensitive, interpersonal aversiveness (often related to suspiciousness and expectation of rejection), ambivalence, anhedonia,… and psychosis-like features that don’t usually lead to help-seeking.To do a case reviewWe report a case of a 17 years old boy with a childhood trauma history who started psychiatric consultations a year and a half ago because his “usual” (as his mother referred) strange behaviour got worse, which was perceived by hisENT specialist. During the appointments, the patient showed suspiciousness, odd speech, inappropriate affect, tendency to social withdrawal, obsessive ruminations with sexual content and occasional perceptual experiences .Psychosis and schizotypy are linked historically and phenomenologically, which is evidenced by their placement in non-affective psychosis in the ICD-10 and DSM-5, and it is known that the direct observation (by clinicians or family members) during the childhood and adolescence are key for a correct diagnosis. In fact, this construct reflects a phenotypic expression of vulnerability to schizophrenia, and during childhood or adolescence it may be understood as an early mental risk state.In contrast to models of psychosis that mainly rely on positive features and assume a progression of them, the positive traits of schizotypy seem to be beneficial and related to a “benign or happy schizotypy” according to the articles we reviewed.No significant relationships.


Dear Editor,One of the themes that has arisen frequently in recent ENT conferences is soft palate sclerotherapy for the treatment of snoring and sleep disordered breathing (SDB); this method is a promising option for outpatient therapy, given its ease and low cost. Although this theme is discussed routinely, its naming lacks standardization. Our proposition is to suggest a new term in Portuguese for this form of treatment: “Injeção Roncoplástica” (Rhonchoplastic Injection).In medical practice, the term sclerotherapy is well established in naming the esthetic treatment of varices and telangiectasis; it may be used to describe numerous and distinct types of treatment, such as in the approach to thyroid cysts, hydroceles, cystic hygroma, hemangiomas, venous malformations, esophageal varicose veins, hemorrhoids, and others.Even when this theme is discussed in papers and otorhinolaryngological conferences, there is no standard name for the use of sclerosing agents in the treatment of snoring, which might lead to confusion. The same theme has been described as: sclerotherapy for the treatment of snoring, injection of sclerosing substances for the treatment of snoring, soft palate treatment with sclerosing substances, interstitial therapy for snoring, etc.Although Straus 1943) was the first to use sclerotherapy for the treatment of snoring, Brietzke and Mair were truly responsible for the main studies of this treament.943 was t6There are very few studies on this theme in Brazil. In 2002, Lopes et al. injected Ethamolin® (monoethanolamine oleate) in the base of the tongue of pigs and then analyzed histologically the injection sites. They found that collagen had become compacted and thickened and that fibrosis had formed much more significantly compared to controls.The term sclerotherapy is well established and widely disseminated for naming many different medical therapies, especially sclerosis of varicose veins and telangiectasis. Thus, our proposition is to use the term “Injeção Roncoplástica” (Rhonchoplastic Injection) in Portuguese specifically to designate the injection of sclerosing substances into the soft palate for the treatment of snoring and SDB. We believe that this term is more adequate, since it is distinct and self-explanatory, and closer to the English term “Injection Snoreplasty”.


The rise of metagenomics offers a leap forward for understanding the genetic diversity of microorganisms in many different complex environments by providing a platform that can identify potentially unlimited numbers of known and novel microorganisms. As such, it is impossible to imagine new major initiatives without metagenomics. Nevertheless, it represents a relatively new discipline with various levels of complexity and demands on bioinformatics. The underlying principles and methods used in metagenomics are often seen as common knowledge and often not detailed or fragmented. Therefore, we reviewed these to guide microbiologists in taking the first steps into metagenomics. We specifically focus on a workflow aimed at reconstructing individual genomes, that is, metagenome‐assembled genomes, integrating DNA sequencing, assembly, binning, identification and annotation. Metagenomics greatly facilitates the identification and characterization of known and novel microorganisms. The plethora of available bioinformatics tools with various levels of complexity rely on (shared) fundamental principles and methods, which are often not detailed or scattered. Here, we review these principles and methods with a focus on reconstructing individual genomes from metagenomics data by integrating DNA sequencing, assembly, binning, identification and annotation. Thanks to the ability to bypass the labor‐intensive isolation and cultivation steps, this approach could theoretically be used to detect and characterize a much wider range of prokaryotes. However, metagenomics is a broad term that encompasses different types of analyses, with various levels of complexity. Furthermore, the underlying principles and techniques are often seen as common knowledge and either not detailed or fragmented. Therefore, we reviewed these to guide microbiologists in taking the first steps into metagenomics. We specifically focus on a workflow aimed at reconstructing individual genomes in a sample, integrating DNA sequencing, assembly, binning, identification and annotation Figure .2A few steps precede the actual DNA sequencing, that is, sample collection and storage, and DNA extraction and purification. Although out of the scope, it is important to highlight the importance of these steps  sequencers, including the MiSeq, HiSeq, NovaSeq and NextSeq series of sequencers, which produce short reads 100−300 bases) with low error rates (<1%). Although variants of the technique are used, including single‐end and mate‐pair sequencing, paired‐end sequencing in which reads represent the ends of DNA fragments with a size specified by the library preparation step is most common in metagenomics applications , exist but have mostly been replaced by those mentioned above. This is likely due to their issues with identifying homopolymeric repeats and lower throughput  sequencers, including the RS, RS II, Sequel and Sequel II sequencers, use adapters to circularize DNA fragments, which are then placed inside wells where a polymerase copies the fragment using labeled nucleotides, producing a detectable fluorescent signal when they are bound to their complement by the polymerase. As each well should only contain one fragment and each nucleotide is labeled with a different fluorescent molecule, the polymerization process produces a continuous signal that represents the fragment being sequenced. Because the fragments are circularized, short fragments may be read multiple times before the polymerization process terminates, whereas long fragments may sometimes fail to be sequenced fully Figure . As a reIn one approach, DNA is fragmented into shorter sequences of a length varying between 1,000 and 15,000 bases. Because these fragments are relatively short, the process described above can read the same sequence multiple times, with each pass of the polymerase producing a “subread” Figure . This prIn the other approach, fragmentation results in lengths of around 50 kb. This produces a much lower accuracy (an error rate of 10%−15%) when compared to CCS, but the reads are also longer and can cover larger portions of the target genome. Since the number of reads produced in a run is limited by the sequencer, this effectively also increases throughput.2.3The Oxford Nanopore Technologies (ONT) sequencers, like the PacBio sequencers, operate in real time and are capable of producing the longest reads out of the three technologies. These instruments reconstruct DNA sequences based on current fluctuations elicited by DNA molecules when they pass through nanopores embedded in a membrane genome analysis is assembly, in which reads are assembled into longer, contiguous sequences (contigs). Ideally, contigs should correspond to individual replicons, but this is rarely the case. It is also important to mention that in metagenomics the sequenced DNA fragments originate from different cells and include potential differences. As such, genomes assembled from metagenomes (MAGs) produced with current technology cannot be obtained directly after an assembly step, and are derived from the pan‐genome of taxonomically related groups within the target environment rather than individual genomes.There are currently two dominant approaches to performing assembly. The first, and older, approach is called overlap, layout, consensus (OLC), whereas the newer approach is de Bruijn graph‐based (DBG)  as the basis for building a graph, thereby avoiding explicit alignment. This graph can then be traversed to uncover the original sequence. Although it removed the need to explicitly align sequences, the DBG approach is more sensitive to sequencing errors and has trouble resolving repetitive regions. However, neither of these drawbacks is particularly relevant for Illumina short reads, which have high accuracy, and whose length is also insufficient to resolve long repeats.DBG functions in a different manner, as it was proposed to bypass the overlapping step, which rendered OLC unusable for the kind of data produced by second‐generation sequencers such as those in the Illumina family of sequencers. Rather than building a graph based on overlaps, DBG uses overlapping oligonucleotides of fixed size  is becoming more common, and available computational resources are increasing, OLC assemblers are once again gaining importance thanks to their ability to resolve repeats. However, because of this recent paradigm change, the state‐of‐the‐art in assembly software is evolving rapidly. New more performant tools that can handle multiple types of reads, either separately or together as “hybrid” assemblers, are being published frequently.3.1“Overlap−layout−consensus” (OLC) assemblers, which are conceptually more straightforward than the DBG assemblers, are separated into three steps Figure , each wiIn the first—overlapping—step, matching fragments are identified. There are ways to determine whether two reads have the potential to contain alignments rapidly, including for example whether or not they contain identical subsequences Pop, . This cak‐mer length, and can therefore be more flexible and accurate, especially for long reads, because they use the full length of the supplied reads rather than splittng them further. The main disadvantage of OLC assemblers is their speed. Although heuristic methods have been developed, which can drastically reduce the computational costs of alignment (see below), these remain slower than the DBG approach.Unlike DBG assemblers, OLC assemblers are not constrained by a fixed In the early 2000s, a number of OLC assemblers were developed, which have for the most part become irrelevant due to lacking the optimizations necessary to make these assemblers usable in a modern context. Notable among these was the Celera assembler  is assigned a numeric value that solely depends on its content. By doing this, searching for relatively large elements in a database becomes considerably faster. This is necessary for connecting the subgraphs generated from each read to each other, which is done by checking whether a given node has already been recorded in the hash table for the whole graph. Hash tables can also be used to reduce memory requirements if handled cleverly. Another, more drastic approach to reducing memory requirements is a Bloom filter. A Bloom filter is similar to a hash table in that it relies on hashes, but unlike hash tables, Bloom filters can only be used to indicate whether an element might be present or is absent. A Bloom filter stores its data in a predefined set of bits. When adding elements to a Bloom filter, multiple hashes of that element are produced, which correspond to the indices of the bits of the Bloom filter that should be set. Checking whether an element has been added to the filter, consists of checking whether all the associated bits have been set. Because each element sets multiple bits, it is possible for all the bits associated with an element that have not been added to the filter to have been set by accident. However, this issue can be minimized through proper parametrization and the resulting structure can still be very compact.Two techniques that handle DBGs stand out in particular: hash tables , then assembling these long reads. The second approach consists of creating a preliminary assembly graph using only the short reads, then using long reads as a guide to traverse said graph, which is the strategy used by most assemblers, including HybridSPAdes  standard was introduced to ensure quality , it is necessary to find a signal that is similar within closely related DNA sequences, but dissimilar to less‐related genomes. In bacterial genomes, such a signal is found in oligonucleotide frequencies, with each species having a specific set of over‐ and underrepresented oligonucleotides. This has already been observed three decades ago  whose total number is 107 according to Ankenbrand and Keller  genes, and others, such as d Keller . MaxBin d Keller  is an exAnother intuitive method to separate genomes within an assembly is to rely on coverage, which is computed by counting the total number of bases from the reads that can be aligned to the final assembly. Assuming that the relative abundances of each species within a metagenome are different from each other, the relative abundance of reads should follow a similar trend. This principle was first used in AbundanceBin Wu & Ye,  and lateComposition, universally conserved genes and coverage can be derived from any assembly without additional external information. However, a plethora of statistical and machine‐learning approaches can be used to augment and exploit these data. As an example, BMC3C uses automatic gene detection that enables codon usage analysis  . In the case of metagenomes, identification may also be performed on individual contigs or reads. This process, called classification, can be performed in combination with or as an alternative to binning, depending on the extent to which the target environment has been characterized.5.1Identification is in most cases rather straightforward—as it consists of aligning the contigs to known reference genomes to find the best match. Despite significantly improved alignment algorithms through the use of indexing and heuristics, this step remains computationally expensive if a rigorous approach involving local alignment is used  steps in the described metagenomics workflow rely on alignment, that is, the process of finding similar subsequences within sets of sequences and identifying the differences. Therefore, for the sake of completeness, alignment concepts were included in this overview.Conceptually, alignment can be seen as a number of string matching operations, which can be exact or approximate. Exact string matching is useful for locating short sequences and its results can be used as a starting point for approximate string matching of larger strings. Exact string matching is generally not relevant for longer sequences, either due to the presence of sequencing or assembly errors or to a biological divergence between the query and reference sequences. However, even with these changes, homologous sequences can still be found using inexact string matching. For this case, there are essentially two ways of aligning sequences to one another: either to identify all the changes that need to occur to convert one sequence into another  or to find the best matching regions of the two sequences .The distinction between global and local alignment is particularly relevant in genomes, as both types of alignment are used, but in different contexts. However, on the whole‐genome sequence scale, alignment must also handle transpositions, where a long sequence is located in one place in one genome and in another place in the other, and inversions, where sequences are replaced by their reversed complementary sequence. For this task, it is necessary to first identify orthologous sequences, a process that is severely complicated by the fact that there are usually differences between these sequences and that the abundance of these differences varies from pair to pair.6.1m, such as an oligonucleotide, within a larger set of characters of length n, such as a genome. The “naïve” approach to finding similar strings is simply to check every possible position within the larger set of characters, then verify if the subsequent characters match the query. However, this approach is extremely inefficient and more efficient approaches have been developed, culminating in suffix trees stored as suffix arrays.String matching is the process of finding a given set of ordered characters (a string) of length O(m) (Big O notation), rather than the O(m × n) of the naïve method. Construction and required memory are both O(n2)  time, they can also be constructed in O(n) time and occupy O(n) memory  Figure , which r Skiena, . By usinO(n) time to be built. While this is useful for performing multiple searches on the same genome, when searching for a single sequence within a larger sequence only once, an alternative approach exists that requires less than O(n) time in a usual case and O(n/m) in the best case, called the Boyer−Moore algorithm. In this approach, the query string is first used to construct a table that contains the relative location of the next identical character for each possible character. Once this array is built, it becomes possible to skip portions of the text whose ending does not match that of the query, since a mismatch can be used to infer the closest possible position of a potential match, and avoid comparing the query against all intermediate positions. Because this algorithm indexes the query rather than the larger sequence, suffix trees are generally more practical.However, the suffix array approach still requires Unlike the ideal case of searching exact matches, for which objective and fast methods have been presented above, alignment of genetic sequences typically involves mismatches. This can be because of inherent mismatches in sequences that occur when searching for known genes in novel organisms, or when attempting to find overlaps between reads of sequencing data that contain errors. In either case, approximate string matching algorithms become necessary.6.2O) computational time and space  are expected to be. This means that for sequences that are expected to be similar, distance can be computed at a low computational cost.Identifying differences between two sequences is a relatively straightforward process that usually relies on edit distances, the most well‐known of which is the Levenshtein distance, which assigns an error cost for each insertion, deletion and substitution between two strings of text, and reports the sum of produced mismatches between two strings as the distance between them. Under specific conditions, these edit distances can be calculated in Ukkonen, , where sBecause global alignment can be viewed as an optimization problem, the result of such an operation is intrinsically linked to the evaluation criteria that are sought to be optimized by the algorithm. Because of this, it is important to remember the context in which such alignments are performed. In the present work, two such contexts are particularly relevant. The first relevant context is assembly, since long‐read sequencers tend to produce more insertions and/or deletions than their short‐read counterparts  in the worst case, the computational cost of finding an optimal solution to an MSA problem is factorial in the number of sequences. This means that the only realistic options are to rely on heuristics with no guarantees of producing an optimal solution. MSA is necessary for establishing the consensus sequences, be it for establishing the “true” sequence of the genome underlying a set of sequencing reads, or to find the common ancestor of a set of orthologous genes. For global alignment, MUSCLE  can be computed within a reasonable time frame of E Edgar, , ClustalE Edgar, , and theE Edgar,  are all 6.3Unlike global alignment, where the focus lies in uncovering the “least expensive” set of changes necessary to convert one sequence to another, local alignment focuses on locating the position of matching (sub)sequences. The most common local alignment approach is the seed and extend approach, which operates by identifying short matching subsequences within the sequences to be compared and then attempts to extend them until a significant enough number of inconsistencies is detected or one of the two sequences ends. The way these shorter sequences are identified varies from program to program.Some programs, such as the first incarnation of BLAST  implemented in Bowtie , although the latter is not strictly unique to metagenomics.Unlike alignment of assembled sequences against a reference, nonspecialized tools have an insufficient performance to perform read alignment. BWA and Bowtie2 have long been established as standard tools for aligning reads against a known reference or an assembly, but are intended for short highly accurate reads produced by Illumina and older short‐read technologies. With the advent of long error‐prone reads, newer approaches such as Minimap2 had to be developed to perform the same operation on long reads. Moreover, for metagenomics specifically, these tools are not sufficient to extract meaningful information on their own, nor are they intended to align reads against large databases. Because of this, when aligning reads against a reference database, the tools mentioned in Section Gleb Goussarov: Conceptualization (lead); writing—original draft (lead); writing—review and editing ; Mohamed Mysara: Conceptualization (supporting); writing—review and editing (supporting); Peter Vandamme: Conceptualization (supporting); writing—review and editing (supporting); Rob Van Houdt: Conceptualization (supporting); writing—original draft (supporting); writing—review and editing .None declared.None required.