Virology Lectures 2020 #24: HIV and AIDS

good afternoon, welcome back, today we have a talk about HIV and AIDS. This is the only lecture in this course dedicated to a virus because it is a really important virus that continues to cause a pandemic many years after it started and much of the story is mine. What I'm going to tell you today comes from this great book, the origins of AIDS by Jacques Pépin and I highly recommend it to get an idea of ​​how this started and I want to quote the book to give you an overview at the beginning of this tragedy. refer to the AIDS pandemic was facilitated or even caused by human interventions, colonization, urbanization and probably well-intentioned public health campaigns and, as we will see, this is the story of an emerging zoonotic virus infection that becomes a human virus, but the crossing is facilitated by ecological interventions and human public health campaigns This story begins in 1981 with the publication in MMWR, the CDC's weekly disease bulletin, of an observation made in Los Angeles, five young men who were treated for a pneumonia, two of them died and they all had cytomegalovirus infection in mucosal Candida infection they proceeded to give a case report of these patients and then at the end they said that Pneumocystis pneumonia in the US is almost exclusively limited to severely immunosuppressed patients.

All of the observations suggest the possibility of a cellular immune dysfunction related to a common exposure that predisposes people to opportunistic infectious infections such as Pneumocystis in candidiasis, so this was a report of few doctors who had these patients, very unusual young people who They got these opportunistic infections, so they got together and said, let's publish this and this was the beginning. This drew attention to what was happening. happening in many other cities at the same time in the US soon after that report clusters of Pneumocystis pneumonia and Kappa C sarcoma were found in other urban centers here is Kappa C sarcoma we will talk about that later and then The CDC established a case definition for this disease that did not yet have a name, but it was said that if you see Kaposi's sarcoma or opportunistic infections, let us know.

Something was happening here in 1982. The disease was called AIDS acquired immunodeficiency syndrome and at first it was called grid, which meant gay-related AU immunodeficiency, for a while it was thought. be exclusive to the gay community, which of course was completely wrong and influenced the early treatment of the disease. Nobody seemed to care. Very few seem to care. The president of the United States did not even mention the name of the disease for many years. until his friend Rock Hudson died from it and it was really a shame what happened, a lot of people died that didn't have to because the diagnostic antivirals were all slow and to start with it was finally discovered that it was transmitted at birth and heterosexually through blood products.

It's not called grid anymore the story of blood products is very interesting companies that sold blood collected blood and sold it denied that there was a virus in it and continued selling it and probably killed another million people before stopping it it's a horrible story the isolated virus in 1983 the lymph node of a patient with lymphatic adenopathy swollen lymph nodes and this was in Paris by the Montagnier and Berry group seemed to see they got the Nobel Prize in two in eighth for that and you will wonder why the lymph node, the virus in It actually goes there and replicates in the lymphoid cells, as you see, the swelling, of course, you know it happens because the dendritic cells have brought something foreign to the lymph node and the lymphocytes are proliferating.

Blood tests developed in 1984 and then electron microscopy and genome sequencing revealed that this is a member of a known group of retroviruses, so it is called human immunodeficiency virus and finally type one because the second was found. As you will see, here is an electron micrograph of the virus. You can see a very typical conical core. which we illustrate here on the left the typical retrovirus envelope spikes in the envelope for copies of RNA reverse transcriptase integrase and protease in the virus particle and this is a Lenti virus which was a known group of retroviruses so here is the retro viewer the family there is the Members of the lantee virus on the right are shown schematically with that conical nucleus and that contrasts with other retroviruses that have a spherical nucleus and more envelope spikes, so the subfamily here is called ortho retro Viren II and contains several generals Alpha Beta Delta Epsilon gamma and LAN There is the Lenti virus that has HIV 1 and 2, but these others we have mentioned some of these viruses in the course of our conversation about the ALV and RSV viruses, for example, we have mentioned the virus mouse and human T cell mammary tumor. lymphoma selection virus, a walleye dermal sarcoma virus, it's an epsilon and maloney murine leukemia virus, so this is an HIV lentivirus and now we have two evolutionarily distinct groups of human retroviruses, we have the lymphotropic virus htlv one, two, three and four, and htlv1 had It was discovered before HIV and some thought that HIV was another htlv, but they were wrong and we have the immunodeficiency virus as HIV 1 and 2 and as I said, these are lentiviruses, they are not neither new nor exclusive to humans, in fact, the equine infectious anemia virus causes a fatal disease. immunodeficiency virus from horses that was isolated in the early 20th century and there are also brine immunodeficiency viruses from cats, felines and bovines, and as soon as it was discovered to be a long-lived virus, studies on these other viruses provided no information on what HIV could be doing because I knew that these other so-called viruses caused immunosuppression or immunodeficiency in animals.

Here is a schematic again of the virus particle and below it the genomes of HIV 1 and 2 shown as proviruses, of course, integrated DNA with liters on each side, below are the proteins encoded in the genomes. we have the nopal gag in the envelope regions, as you know, and these are retroviruses with complex genomes because in addition to gag Pol and the envelope they have all these accessory proteins, some of which we have talked about viv tat Rev Neff, etc. they have several functions as an infection, so this contrasts with retroviruses with simple genomes that simply encode gag Pol and the envelope, so the virus is HIV and the disease is AIDS, and this should sound because we have Tsarskoe syndrome v2 and kovat 19a, who is incarnate.

In AIDS it is the joint appearance of a characteristic group or pattern of symptoms. Well, from the beginning they called it syndrome, I wasn't quite sure what was causing all this and the name stuck and there is no doubt that HIV causes AIDS. You will find in this world, along with other people who do not believe, for example, in vaccination, you will have lists of AIDS deniers who feel that HIV-1 has never been proven to cause AIDS. You can ignore them because they are wrong. There are many reasons to know that the virus causes AIDS, including the involuntary infection of people with HIV, contaminated blood given to people who had no other risk of infection, AIDS, there is no doubt, it is a loss. time to even talk more about it, let's take First let's take a look at the numbers just to give you an idea of ​​the scope of this pandemic that's actually been going on since the 1920s, as you'll see later, in the US, these we are.

In numbers, the virus has killed more than 600,000 people, which represents more deaths related to combat and all the wars we fought in the 20th century. Right now, more than a million people are living with HIV and one in seven people don't know it, so those who live with it usually receive triple therapy and these ones and sevens transmit it without realizing it, of course, In 2018, which are the most recent numbers we have, there were 30 almost 38,000 new infections in the US 69 percent of men who have sex with men 24 percent among heterosexuals Seven percent among users of intravenous drugs This is a lot of infections and this happens every year, so put Kovat Nineteen into perspective.

I know it's not a big disease and there are a lot of people are dying, but we still live with this and it's hard to prevent, it's hard to cure, as you will see new infections in 2018 divided by age groups, you can see that the older people Young people account for half of the infections and, in the right case, men. and women and different contacts, you know, we have men who have sex with men and then we have heterosexual contact between women and men, so we collected very detailed information about the transmission of this virus not only in the US but nationwide. global so let's look at global summary again as of 2018 there are about 38 million people living with HIV worldwide 1.7 million were newly infected in 2018 and 800,000 deaths there are 4,600 new HIV infections per day or 190 per hour every day in 2018 and it's been happening for years.

It's gone down a bit and at its peak it was a lot more and it's going down but not very quickly so it's a real problem and no one is talking about it. I was on a call the other night when people were talking about pandemics, they were talking about kovat 19. and influenza pandemics, no one mentioned the hiv/

aids

pandemic, well I sure did, here's another roundup of divided people, this one is the total of the numbers that I just gave you, we have adults, of course, most of the adults are infected and about half are women and half are men, but then the unfortunate one of the children down here 1.7 million children 160,000 new childhood infections in 2018 and a hundred thousand children are dying of AIDS, of course no one should die of AIDS because they can be treated, but that tells you that we are not getting medicine for everyone who needs it now why are children dying? do they infect?

In fact, they contract it at birth, from mothers who are infected, so children don't even have a choice as to whether they are infected or not. 38 million people live with HIV worldwide. And this is the breakdown into different WHO regions and you can see, by far, that Africa has the most infections, for a variety of reasons, one of which is that the pandemic started there and another is that the systems of health are not uniformly good and we can. There are not enough antiretrovirals there, followed by America Southeast Asia Europe Western Pacific in the Eastern Mediterranean some distributions of key populations sex workers 6% intravenous drug users 12% men who have sex with men 17 transgender women 1 and clients of sex workers and others 18 and then the rest is 46% the incidence of infection has decreased which is good since we discovered it so here in red newly infected people peaked in the 90s and have been steadily decreasing but still They are very high, as you can see in the numbers and then. deaths, which peaked shortly after the peak of cases, the time it takes years to die after being infected, which peaked in 2004 and which has also been declining, so this is all fine and as You know, we can control AIDS with triple medication. therapy mainly in countries with money and this is something that is changing very slowly, making medicines reach the people who need them and that is reflected in this graph.

Over time, antiretroviral coverage has reached 62%, which is good, this is the coverage of the people who need it. We have to get to 100% of course that is the goal so we can save lives because no one should die from this, but although we can save your life, there is no cure, we cannot remove the virus from an infected person once you are infected. you are stuck you have to take triple therapy all your life there is no vaccine so we cannot block the primary infection you have to continue taking your medications as we will see there are reservoirs in the hematopoietic progenitor cells even with the triple therapy drug Resistant viruses sometimes appear resistant all three are circulating and the drugs are expensive although the price is going down so okay, let's talk a little about the origins and then we will talk about the disease itself, so after the first alerts in the 1980s and the development from a blood test that looked for viral proteins in the blood of infected individuals carrying antibodies, many studies were done around the world, much like they are now being done with the v2 source code to find out who is infected and The The first studies in Africa were done in Zaire and Rwanda, so here Kinshasa, a year ago, Rwanda showed that it was very common for 90 percent of sex workers to be infected.

Ninety percent of sex workers in these countries were infected with HIV, so that said something right. away from these studies done in the 80s and 90s and then archival samples, serum samples from people from the early years of the 60s, 70s and before,showed that the virus was present in the 60s and 70s throughout Central Africa, but not in West or East Africa, there is one serum sample in particular. from a man in the Democratic Republic of the Congo and is called Zr 59 1959. This serum taken was a serum sample that was taken and tested positive in 1998 and another lymph node sample from a woman in the Democratic Republic of the Congo taken in 1960 was also positive for HIV, so these are the The first samples allowed us to establish a molecular clock to know when this virus originated, but it clearly already existed in the 50s and 60s.

These two viruses that I just mentioned To speak their genomes differ by approximately 12%, one year, twelve percent and so on. That gives you an idea of ​​how much circulation there was, so there is no doubt that HIV was present in Kinshasa, which at that time 5960 was called Leopoldville, capital of the Congo in these years and, as you will see even before, the virus was clearly originated. in Africa, but what was the source, so solving this problem required wildlife sampling. An extensive wildlife sampling that was carried out in this part of Africa. Central Africa, where these first positives were found, in particular chimpanzees were searched and sampled and in 1989 a virus related to the simian immunodeficiency virus was detected. isolated for the first time from a chimpanzee this had never been known before 1989 it is called SIV cpz for chimpanzee and Beatriz Hahn here this is my laboratory when the polio wall was in the independent laboratory she is a virologist at the University of Pennsylvania, so a little bit about her before her daughter took this course a couple of years ago, she and her team sampled chimpanzees, they collected over 7,000 chimpanzee fecal samples from 90 different field sites and all of these circles are different chimpanzee fields .

Places where chimpanzees live in communities and don't mix much, especially if there is a river between them, they don't swim, which is why she took samples. These chimpanzees are in the forest, but they are preserved, you are not allowed to hunt them. and so on, and she discovered that you can get a virus from feces, so she just shot genomes, of course, so that you can analyze it by PCR sequencing. You can also get it from urine, so they used to come out in the morning. Chimpanzees sleep in trees and in the morning, when they wake up, they urinate from the tree and these workers collected the urine, you can also contract viruses and they discovered that all these chimpanzees are infected, very specifically, only two species of chimpanzees harbor SIV cpz so here are the different species Petey then it is Pan troglodytes and then you have varus le ot troglodyte e schweinfurt Z and then Pepin is 'kisses the bonobos and its range is shown here in color troglodyte YZ here is an orange and schweinfurt e in blue only troglodyte facility and Schweinfurt hosted SIV cpz the virus closest to HIV, really amazing work and this link is to an interview I did with Beatrice in I don't know if it works, but I interviewed her if you have the book, there is also a book link so what is SIV?

SIV is a virus that is transmitted between chimpanzees through sexual relations from mother to child at birth and blood during aggression. Chimpanzees sometimes fight among themselves and probably transmit this virus. The estimated transmission probability is precoital. ACT is this number that is similar to that of humans, so it is transmitted in a very similar way to HIV and it turns out that SIV cpz is pathogenic in chimpanzees and leads to AIDS. At first when it was first discovered, people thought it was not pathogenic, but then they discovered Chimpanzees dead in the forests or in colonies turned out to have SIV, so it causes immunodeficiency in chimpanzees and sequencing of the isolates of chimpanzees and humans clearly showed that they had a common ancestor, so these are three phylogenetic trees from different regions of the genome.

Paul's gag and the Neph region of the envelope these are protein alignments so you can see here HIV right next to this SIV cpz another HIV is next to a gorilla SIV we'll talk about that in a moment here's another HIV next to a gorilla and that is valid for the three regions HIV and SIV cpz they have n Gor they have a common ancestor that's where this virus comes from so like SARS Co v2 is a bad virus HIV one at least one of these viruses HIV 1m is a chimpanzee virus became human, of course, so what happened, well, here's the story, these are monkeys on the left, these are chimpanzees, gorillas and humans, and these monkeys, these are monkeys from the old world, they live in Africa, of course, there are all kinds of species. green that's where the kidney cells of the green vervet monkey come from that are used to grow Tsarskoe v2 anyway these monkeys all have their own SIV very very important to listen to because many students get confused these monkeys these old world monkeys have each their own specific type of SIV, there are 40 different IVs and they match the monkey sykes SIV, the vervet SIV, etc.

What happened was these viruses were transferred to chimpanzees, probably a few hundred years ago, the chimpanzees are infected with SIV cpz, now the monkeys are fine with their SIVs they have been evolving with them for years, but they transferred them to more chimpanzees recently a few hundred years ago, so chimpanzees and all this is done by isolating viruses and sequencing them. Chimpanzees have a SIV cpz virus that is a recombinant of two s. Mona's IV and red cap mangabey, so Mona monkeys and red cap manga bees have their own IVs. What it was for the chimpanzees is a recombinant of these two, so probably the chimpanzee was probably infected with both viruses and became SIV. cpz is a recombinant of the two, so these red arrows mean SIV Mona and SIV redcap mangabey going to the chimpanzee.

You can ask how the chimpanzee got these viruses, while chimpanzees eat meat, they sometimes eat monkeys that could be one way or fight with them. they and then humans got a SIV cpz and that has led to HIV in the M and n groups and I'll tell you what a group is in a moment. There are also two other groups of HIV 1 p ni that came from gorillas that got it from gorillas SIV got it from chimpanzees, so SIV cpz not only reached humans but also gorillas and diversified in humans up to the pianos, so which actually four different crossings of - from chimpanzees - from gorillas to people and then we have another separate set of HIV crossings, which we'll talk about in a moment, is an infection noticed by a visual user that became a human virus.

When did this happen again? As I said, there are four separate crossings, of chimpanzees, of gorillas of the IV. SIV cpz and SIV gorillas m y o m y o probably the first three decades of the 20th century, more recently for N and people there are not many of these so there is not enough data to say between 1900 and 1930, so we will say 1920 as an average Well, that's when it went from a chimpanzee to humans, how did this happen? Well, one of the ideas is that it involves bushmeat hunters going out into the woods to hunt, where it's called the cut hunter hypothesis, this hunter gets a chimpanzee and is butchering it in the woods. he or she cuts himself or she cuts himself and some blood or fluids from the chimpanzee enter the wound and infect the hunter.

You can do a series of calculations that are in that book, the origin of AIDS, very interesting, which suggests that in 1921 I know that, given the number of people, the number of people hunting, and the number of chimpanzees, the number of people infected with SIV CPC was less than ten, but probably only one spread and multiplied and probably these chimpanzee crosses with humans, these infections between species have occurred many times. previously and probably many times as they probably still happen today because people hunt chimpanzees, it's getting harder to do so, so this one removed this particular call in 1921 that became HIV, why did it spread?

It's an interesting question and involves more humans. interventions so let's take a look briefly here is a graph of population growth in Africa from 1880 to 1970 and the capital of the Congo Leopoldville or Kinshasa was the capital of the Congo, the most dynamic city in the region with a large number of immigrants and merchants and people, then people who traveled or migrated from the countryside to the cities as the cities grew, so this cut hunter may have been cut, and in fact, and then traveled to a big city, he went to a brothel, picked up a person sexually. transmitted diseases and then there were STD clinics that she probably went to and there they injected her with something and we believe there was widespread use of unsterilized syringes that spread the infection to others, it was all so rampant that widespread sex some women had a thousand clients. per year in the brothels so that one of her clients could have given it to her and then she would have spread it widely so that someone would come from the countryside to one of these big cities and you can see the population around 1920 when the cut hunter, we believe infects, then city populations explode and this is substantially increasing the spread of this virus.

If this population had not exploded and remained small, it most likely would never have spread and that is probably why previous chimpanzee-to-human spillovers never spread another problem. Here it was that this involves European colonization of Africa, which we'll talk about in a moment, but the Congo that was once the Belgian Congo, of course, was not the Belgian Congo before, but you know, a lot of countries in F in Europe They decided they wanted a piece of Africa, just like the British took over what became the United States. Well, they said, "We want some countries too, so they came, claimed their own pieces of Africa and the Belgians claimed the Congo and in the sixties the native Congo Lions got tired of the Belgians and threw them out like a revolution." However, the Belgians were all the doctors, so when the Belgians left they had no doctors, so you know, they spoke French, they speak French in the Congo, so they reached out to Haiti to get some French-speaking doctors to replace them. to the Belgians, so you can probably guess what happened next, they got HIV and they went back to Haiti and brought it there and you'll see that genome sequencing supports that scenario, so we have European colonization of Africa starting in the late 19th century and this is a map. from Africa with all the European claimants and when they came in, what they wanted to do is make money, of course, there are many natural resources, so they want to build big cities, they take people from the rural areas.

You have known for many years that Africa is rural. country run by small communities with chiefs and all these small rural communities man moved to the cities in search of labor to build bridges and railways etc. for the Europeans large-scale prostitution, then the Europeans say, well, we need some medical care to take care of These individuals establish a colonial medicine that uses woefully dirty syringes and further transmits the viruses and we know that this could happen because at the beginning 20th century Egypt tried to get rid of schistosomiasis by injecting people with drugs, but they used contaminated drugs. needles that ended up spreading the hepatitis C virus to millions of people because I didn't autoclave, two syringes, all of this leads to large-scale amplification and, as you can see, all the factors that led to this, population growth , European colonization. colonial medicine, etc., perfect storm many years later, in this study, the genome sequences of many archival HIV samples were compared and that shows that the virus arrived from Africa to Haiti in 1969, so it had been leaking to me since the 20s in Africa and I went to Haiti. when those doctors returned to Haiti, it came from Haiti to New York in 1972 and then from New York it spread to California, it established there the epicenter that initiated the first MMWR report that we talked about about New Jersey, Pennsylvania, Georgia and there all kinds from parts of this phylogenetic tree that supports that as you can see the Haitian strain is ancestral to all the American strains, everything in the US diversified from the Haitian strain and one more thing I want to talk about here By the way, it's called Congo. to Haiti to the US You may have heard of patient zero, this was a Canadian flight attendant, Gaetan Dugas.

That's okay, since his story is very well known and he was a very promiscuous flight attendant and you know that in the early days of the AIDS epidemic he was thought to be patient zero. who started it is not true, you can see that it is buried here in the phylogenetic tree of Georgia, it did not start anything, it was just a virus of its own, it is just a part of this phylogenetic tree, that is how the virus got here, so we too I have HIV which is a separate virus first isolated in Guinea Bissau here and on the west coast.

It has between 30 and 40 percent identity in the genome sequence with HIV.It is mainly restricted to West Africa. It is less virulent than HIV 1 and, in fact, most infections are not. It does not progress with age as you will see it is less transmissible there is no transmission from mother to baby and this is a cross of the mangabey in fact it is eight separate crosses of eight separate factions people keep these monkeys as pets and they are infected with SIV. SMM, humans become infected and it diversifies into HIV, which then spreads from humans to humans, so we have eight distinct lineages of HIV, each from a separate zoonotic spillover, but now these are human viruses, they are no longer viruses zoonotic.

HIV is a diversity, so here we have HIV one that is widely diversified and HIV 2 that is less diversified, so HIV is diversified in the four groups according to sequence alignments and group M represents 99% of all HIV infections. M means main group or for the outlier it is less than a percentage, it is limited to Cameroon, Gabon and the neighboring countries for the group and there have only been thirteen cases in Cameroon and group P, only two cases in Cameroon, okay, each of these four, sorry, each of these for MN O and P again are an independent transmission event of SIV to humans, whether from chimpanzees or gorillas, the main one here, 99 percent of chimpanzees, SIV cpz , so those are the groups that you'll often hear about and, again, because the virus has been in so many people for so long, it diversifies. in different populations the group M diversifies further into subtypes, these subtypes have about 20% nucleotide differences, so let's say the group M viruses brought in are diversifying in Africa, you will see it diversifying into many different subtypes because it has been there the longest, but if then a person goes to another country with a c' and c seeds there then c is the dominant subtype in that country there also what we call circulating recombinant forms or CRF there are 48 of them so far and this happens in high-risk people such as brothel workers, they get multiple infections and recombinants come out that are selected because I have a replicative advantage, there is no clear difference between these subtypes and the propensity to cause AIDS, those infected with arrest die faster , predict that shedding and the female genital tract is greater and perhaps greater transmission from female to male this spreads widely in Africa now this diversification is useful for tracking the movement of the virus the virus evolves in a direction to numerous subtypes and is recombinant so it does not go backwards but forwards so you can reconstruct the sequence of progress in a region or country by batch by looking at the local distribution ofsubtypes, you could see which subtype appeared in the 1990s.

We developed nucleotide sequencing of a large number of samples and we were actually able to sequence many isolates, which we do now routinely, of course, for SARS Govi ​​2 and many other viruses, but we didn't do it back then. and this has made it possible to trace the spread of the virus globally and in Central Africa there is an extreme diversity of all these subtypes, which means that it is clearly the origin because the original M group then diversifies to all the subtypes in Africa where as You see, you've spent less time in other countries and have had less time to diversify.

In some cases subtypes are associated with specific transitional locations and modes of transmission and this is what we call the founder effect, so one subtype will predominate in a particular group, for example subtype B is found in 96 % of white homosexuals in South Africa, has been imported from the US, so most likely one person came from the US with subtype B and passed it on to another homosexual and then everyone transmitted to each other. themselves that is why subtype B predominates there, that is what we call the founder effect. Subtype C is 81 percent of black heterosexuals and this is also used in criminal cases where people are accused of transmitting HIV to others.

He is a person accused of infecting more than a thousand women. He knew he was infected and he did it on purpose because he is evil and we could condemn him for the founder effect. We were able to see which P subtype he transmitted and clearly show that it was him. Here is a map of the worldwide distribution of subtypes that I think is instructive. You can see in the pie chart the distribution of the subtypes by color here across the others or in colors and you can see that in central Africa it has the greatest diversity and the most different colors because that is where it originated in a diversified way in different populations within Central.

It's mostly seen in Africa than South Africa so someone went to South Africa and brought it there and that's mostly been seen in the US, mostly someone came to us from Africa and brought it there and it's mostly B and these are the percentages of global HIV and the different subtypes and some of them are also very limited let's talk about transmission how this virus is transmitted sex intravenous drug use and at birth there are 2 to 5 it is not transmitted by respiratory, food or vector you can't sneeze on someone and give it to them with feces they don't transmit it vector routes insects don't get it mosquitoes don't get it and here are the different transmissions in different areas, they are different depending on the region Western and Central Europe North America in their majority 57% men who have sex with men sex workers 26 intravenous drug users 7 and then the rest, while in Eastern Europe and Central Asia it is mainly intravenous drug use and then sex workers and then MSM MSM and let's not forget that from mother to child at the time of birth is about 5% infectivity can be reduced very easily they dry out in a day remove it sand wrap fires heating 56 30 minutes 10 percent bleach 70 percent alcohol but do not drink bleach to get rid of HIV or do not drink 70 percent alcohol in large enough quantities, the ph dreams, so it is a very fragile virus, it does not matter because it is transmitted sexually or through intravenous drug use, avoid the environment, the virus never It's out there, it's true, it goes from person to person, so it didn't have to do it and it does it in chimpanzees and monkeys, so it never had to evolve to support these things.

There is a risk of transmission here. I want to tell you about what he talks about about the lab experiment that someone asked about, so this. it is a mode of transmission and risk of infection for 10,000 exposures, so receptive anal sex 130 infections per 10,000 insertive anal sex this is for the person who inserts 11, so he has receptive penile-vaginal sex 8 and inserts 4, so the receptive is the most transmitted right, okay? now parenteral transfusion of infected blood almost one hundred percent if you get blood from an infected person 100 percent from needle sharing sixty-three punctures this is what happens in a laboratory so it's pretty low, it's probably because you get a low inoculum , but if you are treated with AZT post-exposure prophylaxis, you reduce it to one.

This is old data, so we don't use AZT anymore, but just to illustrate, you can touch, so when you get stuck with a needle in a lab that's potentially contaminated with HIV, you get a drug, you get double therapy. or triple and prevents infection, so yes, needle sticks in a lab are pretty low. Because? I think it's probably because there's not much virus there, but look here to see if they give you a transfusion. get a pint man you're getting a ton of virus and then we have mother to baby, if you don't treat the mother in 2200 out of every 10,000 births and with AZT you treat the mother with AZT just before birth you can reduce it. it may be even further now, where does this come from?

The percentage of cells and the concentration of viruses have been estimated, most viruses are found in peripheral blood, monocytes, blood plasma and cerebrospinal fluid, but also in semen and female genitalia. secretions that cause sexual transmission, the virus crosses the genital and rectal mucosal surfaces, which are different anatomically and immunologically, and that affects transmission and dissemination. Interesting in both male and female hormones, they seem to facilitate transmission by stimulating cell-to-cell contact, those would be prostaglandins or erosion of the vaginal lining that occurs from progestins and although these numbers show that the insertive partner is at low risk, transmission of infection occurs through cells in the lining of the penile canal, presumably from infected cells in the cervix or tube gastrointestinal.

The mucous membranes and, finally, uncircumcised males are at twice the risk of infection and studies have suggested that the foreskin may have high concentrations of immune cells which, of course, are susceptible to infection receptors and Co receptors. this virus. The primary coreceptor is the beta key. making ccr5, so the main receptor that all these HIV use is a cd4 shown in red here on cd4 positive cells and macrophages and then there is the coreceptor ccr5 x' ccr5 is a beta chemokine receptor and we call them The viruses that require CCI five are five tropic viruses and then we have x4 tropic viruses where the co-receptor is the alpha chemokine receptor cxcr4 so ccr5 is the main one and like I said there are five tropic HIV and people who have a deletion in Ccr five of course are resistant to R five viruses in some patients, so in fact the patient usually appears late in the disease some viruses that they can use to enter the cells, they are called tropic x4, we do not understand why the virus changes. at that late time, infection and that change to macrophages, these are the tropic M.

Virus: the number of cd4 molecules in macrophages is very low compared to T cells, so these viruses do not affect the Vanko phage very efficiently, but during the course of the infection, as the infection progresses, viruses evolved that can bind. to macrophages with low levels of cd4 and these viruses generally emerge in the central nervous system of patients in advanced stages of the disease, so those are two different types of receptors and co-receptors, as we mentioned before, there are people who lack ccr5 and They have a mutation. called delta 32 in the gene that encodes ccr5, is in between 4 and 16 percent of people of European ancestry and a couple of stem cell transplants have been performed that have cured German and London AIDS patients of HIV, so you can destroy the bone marrow with irradiation and replace it with a donor from another person who lacks the ccr5 gene and that will cure the infection as long as those individuals have our five tropical viruses and currently people are thinking about altering the ccr5 in the stem cell transplant to be able to take out your own stem cells and disrupt ccr5 with CRISPR cast 9 and put them back well, let's talk about the course of infection, a primary transmission of HIV infection and this image is shown by virus particles, but they could be virus particles or infected cells that we don't know about.

I know what's more important because experiments are really hard to do, if you think about it, a cell infected with viruses is always producing virus particles, so if you give them cells, you don't know if the cells produce viruses, in fact, if you are using In an animal model, much of what we know about infection comes from infecting macaques with SIV and these are usually inoculated vaginally and these studies have shown that free viruses can certainly initiate infection and that in these vaginal inoculations the cd4 t-activated and resting cells are the target of the infection and that's why we think that, well, these viruses or virus-infected cells are crossing the mucosal barrier, you know how the vaginal mucosal barrier is damaged, For example, during sexual relations, abrasions of the epithelial layer occur to which the virus binds. to the dendritic cells to a protein called DC sine does not infect the dendritic cells, but the dc then go to the lymph node and carry the virus to the lymph node where there are many cd4 positive T cells to infect, of course, and the activation of the cells T cause even more cd4 expression and more infection, so the incoming virus enters the submucosal tissues captured by the DCs and the lymph node.

Alternatively, there are T cells in these regions, viruses can infect the T cells, activate them and go into the lymph. nodes and then, of course, outside the lymph node, the virus can spread systemically. We also know that in addition to abrasions of the mucosal layer during sexual intercourse can allow infection or direct the mucosa during sexual intercourse, other pathogens that produce lesions can facilitate transmission because those pathogens can also induce not only lesions where the virus can pass, but also activated T cells that are the target ofthe infection. Now an HIV infection is divided into three phases, we have an acute phase, so in this graph we see at the top the copies of HIV RNA per thousand of plasma and then we are looking in the next graph cd4 positive T cells and antiviral CD8 positive CD positive T cells a total T cell and an anti HIV T cell response then at the bottom the three phases, the acute phase the chronic phase and the terminal stage or symptomatic phase are shown as boxes and the symptoms and what's happening and each of them has a lot of information here, but let me try to walk you through some of them, look at the time course here, so this acute phase.

The phase is 10 to 12 weeks and we have many years of chronic illness and then a couple of years of symptomatic illness where full-blown AIDS develops. So what happens in the first few days after infection, you get huge amounts of virus particles. by activated lymphocytes and lymph nodes and they swell the lymph nodes swell lymphatic adenopathy sometimes you have flu-like symptoms here you can also have diarrhea after three or four months the virus is reduced you have small births of virus particles that appear from time to time and the degree of viremia this is called set point viremia, how much it is, it is a direct predator of how quickly the disease will progress and sometimes if it is lower, the disease will regress more slowly, if it is higher, it will progress faster and then we have the end.

The stage in which AIDS develops is characterized by a large number of viruses that rapidly decrease CD4 counts to less than 200 cells per thousand and that causes a deterioration of the immune system which, of course, makes one not only able to eliminate the infection but also other pathogens and, in fact, most. AIDS patients die to operate from opportunistic infections with microorganisms that do not pose a threat to us, such as Pneumocystis and CME, as long as we have healthy immune systems, that is because the main target of this virus is the T cell positive cd4, both in which of course, is essential to orchestrate the adaptive response.

Both active and resting cd4-positive T cells can be infected in macaque models for vaginal transmission. The submucosa must be in fact, the T cells must be infected for dissemination to occur, so the submucosal tissues become infected within a few days the virus spreads through the lymph, remember, it goes to the lymph nodes, it spreads through the lymph to various gut-associated lymphoid tissues, which I'll show you in a minute, in humans, the gut-associated lymphoid tissue has 40% of its lymphocytes and there are a lot of cd4 positive ccr5 positive T cells there and that's a site important early stage of HIV reproduction and that causes a destruction of 30 to 60 percent of CD4-positive T cells and then, of course, that results in a large amount of virus being shed within the first ten to twenty days , that initial spike of viremia is reduced as susceptible T cells are depleted, a cell-mediated immune response is generated, you get an increase in cytotoxic T cells and then neutralizing antibodies.

If you get an inflammatory response, you will get more cd4 T cells as a consequence and those cd4 T cells return to normal levels here, so there is a drop and then they return to normal levels; However, as CD4 returns, more sites are created for the virus to replicate. and they become infected and produce many viruses, as you will see, but in particular the memory cd4 cells become infected, they are long-lived and they are part of an important latency reserve, so these cd4 T cells are replenished early and the infection, but ultimately that fails. there is too much virus reproduction and they decline at a steady rate over the years, as you can see here, and this is a long asymptomatic period, there are usually no symptoms, but you can have sporadic symptoms, as shown here, and this continues For years, the cd8 count. remain slightly elevated, but virus reproduction continues primarily in lymphoid tissues where a pool of viruses is produced, eventually destroys follicular dendritic cells, and typically only one in three to four hundred infected cells in the lymph nodes release viral particles. at this stage, the spread is suppressed by antiviral CTLs, antibody responses are Development and viral genetic diversity of course increase during this period because the virus multiplies and then eventually AIDS symptoms develop.

Very high amounts of viral particles, as you can see here, are huge, very low CD4 cells. This happens a lot in lymph nodes where the cells are destroyed by virus reproduction and you eventually get less than 200 cd4 cells per thousand your lymphoid tissue architecture is almost completely destroyed and you have very few T cells and virus population left at this point. is becoming relatively homogeneous and the envelope changes and this is associated with rapid reproduction kinetics, expanded tropism, the death of Moore's T cells and the ability to form sensations, and these viruses here are less sensitive to neutralizing antibodies , so here in the symptomatic phase, you obviously see a lot more symptoms, including cancers. opportunistic infections and the cellular level the things that I have described or written to you here, so the effect on the intestine is very substantial, the virus can enter the intestine, but even if it does not, the virus can reach the associated intestine. lymphoid tissues correct collections of lymphocytes such as Peyer's patches and the virus can replicate in the lymphocytes there, as shown here by these virus particles in the CD4-producing T cells, this causes disruption of the gastrointestinal epithelium quite early after infection, so this loss of integrity leads to translocation of the gut microbiome like lipopolysaccharide, so the intestinal lumen here is full of bacteria, it's full of lipopolysaccharide, this enters the circulation and LPS is not good, it alters metabolism, it alters digestive functions so this is what we call leaky, we think it also leads to the activation of T cells which of course causes the virus to replicate even more and here is a picture of what happens with lymphoid tissue associated with the intestine.

These are endoscopic photographs of an HIV negative colon. These are the collections of lymphoid cells throughout the intestine. They are good things and I look good, but there are a lot of T cells here and here is that HIV positive person, after a few weeks, they are all gone, the virus has killed all these T cells, the intestine is now leaky. There are no semolina-selling lymphoids in the terminal ileum and the structure of any lymphoid tissue is completely altered. All the sites on Olympus have disappeared. Now there are three different types of infections and those that we characterize have typical progressions in which there is acute clinical latency. of years and then AIDS and we have rapid progress errors where everything accelerates, the progression to AIDS is very rapid, maybe one or two years and, as I said, that correlates with higher virus set points, its Lower set point than the typical progressor we have. it doesn't progress, so we know about these non-progressors because we've studied cohorts of HIV-infected adults and even without antiviral therapy, ten percent of people get AIDS within two or three years over a ten-year period, about 80% of untreated infected adults have evidence of disease progression half of them develop AIDS less than 5% of patients do not have AIDS for many years with high peripheral CD4 cell counts are called long-term do not progress very , very few high cd4 viruses ever develop AIDS so what is happening?

Here these people are called elite controllers, they have been studied extensively. We would like to know what is different about them because maybe we can learn it and use it to help people, so elite controllers are people who have normal cd4 counts and undetectable viral loads. ten years in the absence of any viral therapy, one in 300 people, in approximately 20% of these individuals, the phenotype is attributed to protective MHC alleles. Particular alleles are expressed that are overrepresented, so remember that the MHC displays the peptide and in some ways they are good at displaying peptides and being resistant to the changes in the peptides that occur, the virus replicates, so these are very protective, but that does not explain everything, sometimes changes in chemokine receptors make the difference.

I don't really understand in all cases how it works but it is not associated with the ten viruses that you tied the virus is not evolving to become less virulent now during the viremia set point in the absence of drugs the reproduction rate of the virus has than match the shedding rate and the mathematical models that have been applied Clinical results can provide estimates of how much HIV appears and disappears in the blood and other compartments and the results are frankly surprising: the minimum estimated rate of virus release into the blood It is on the order of 10 to 10 virus particles per day of release. of virus particles from cells to blood 10 to 10 per day, that is, one cycle per infected cell per day and this continuous replication is the engine that drives pathogenesis and generates high mutation rates because, on average , all possible changes at each position in the genome occur several times a day and an HIV-infected person, in the absence of drug treatment, each position in the genome has changed several times a day, is surprising and, as you will see, the diversity genetics in a single patient is more than the world. wide diversity of influenza viruses during a pandemic.

I have a great image of that to show you in a few moments that the diversity of HIV in a country is amazing. I will show you that now also more than 90% of the particles in the blood come from Activated CD4 positive lymphocytes have half-lives of only one day, one point one, one to seven percent come from longer-lived cells and other compartments. with half-lives that can reach 145 days, so even if drug treatment can block virus production, it would take three to five years before these longer-lived compartments would be free of cells with the potential to produce viruses and that's probably an underestimate, so we can't eradicate the virus using drugs because these cells live too long, spontaneously, these newly infected cells start to make viruses and they die, but not long enough, that's the point, so What are the latent reservoirs?

We cannot take tissue samples from human patients. It is not practical, so most studies have focused on peripheral blood samples and there we know the latent viruses. The reservoir is central memory CD4-positive T cells. These are important, of course, in protection, which is why they are the reservoir of HIV. The insidious thing is that they are mainly found in the lymph nodes and lymphoid organs and although they are freely exchanged, these cells are exchanged between the blood and the lymphoid. In tissues, only a small fraction of central memory T cells circulate at any time, so you know that most of them hide in lymphoid organs and there, lately, the infected central T cells of these central memories often They are called resting T cells and are refractory. to the infection, then we think that the infection is established first in the activated T cells, so the T cells are activated by presenting the antigen correctly and these cells become activated and overproduce cd4 and become infected and then they start to become in some of them.

The memory T cells then harbor the virus and are silenced and these memory T cells are refractory to infection, so the ones that produce virus and die are the vated T cells when they become memory. The T cells, these pro viruses, are silenced and periodically reactivated and we know that a good fraction of these memory T cells have defective pro viruses, so they never produce viruses and we can say from a study of them that his clone arrived there. A single integration event and then this single cell becomes many clonal expansions in memory, many memory T cells, so most of them are defective due to April Beck and other hypermutations, so these are the populations which we cannot get rid of through antiretroviral therapy because they reactivate infrequently and last too long these types of latently infected cells have been followed in patients for up to 11 years they can last up to 11 years probably longer we also see cancers in patients with HIV we have An increased incidence of malignant neoplasms in some form occurs in approximately 40% of untreated infected people and themechanism is very different from that of other retroviruses that we talked about earlier in this course.

HIV kills the target cell, so it does not promote immortalization and proliferation as aquagenesis does with other retroviruses and malignancies appear to arise from regulation of the host's immune system. We do not have adequate immune surveillance, so we cannot get rid of other viruses, including aquagenic viruses, and high levels of cytokines are produced that are associated with HIV infection. Inflammation leads to high level of cytokine production and it can promote the generation of blood vessels in geogenesis can promote infection with other viruses that can cause cancers such as the epsilon bar virus hhv-8 and human papillomaviruses these cancers that develop are usually more aggressive than in uninfected people.

In people, they can develop in various tissues and organs, but certain types, such as Kaposi's sarcoma and B-cell lymphoma, are prevalent in HIV-infected patients. Kaposi's sarcoma, which was the characteristic early cancer in these patients, was described by a Hungarian doctor in 1872 and is a multifocal cancer. The lesions have many types of cells. It was typically found before HIV/AIDS in older men in the Mediterranean region. and Eastern Europe in these areas it is usually a non-aggressive or classic form that is limited to the skin; the classic form is rarely lethal and a more aggressive form is also found in sub-Saharan Africa, where there are more immunocompromised people, so that in people infected with HIV, Kaposi's sarcoma is an aggressive form in which it affects both the mucocutaneous areas, where the mucosa passes into the skin, and the visceral areas, the internal organs, so you can look at this individual and see lesions on the skin, but inside it is also full of tumors and that is what kills you.

Before treatment, this disease occurred in approximately 20% of HIV-infected men and 2% of HIV-infected women; in fact, women had occurred in transfusion recipients and hemophiliacs infected with blood products in the United States, it turns out. that Kaposi's sarcoma is actually caused by a second virus, human herpesvirus 8, that is causing the tumor, so HIV is immunosuppressive and then hhv-8 comes in and causes the tumor to take over. kappa was first described in HIV patients in 1981, but the virus was not discovered until human herpesvirus 8 was not discovered until many years later, infection of macrophages and CD4 cells leads to the production of cytokines .

These cytokines can cause proliferation. from other cells like B cells, endothelial cells, epithelial cells, and that alone can lead to malignancy, you know, as cells proliferate uncontrollably, they accumulate mutations that lead to cancers, but in some cases viruses that infect these patients because they are immunocompromised can also cause these cancers as well, so the last part I want to talk about prevention and cure. Can we make a vaccine? We know that during infection we develop antiviral immunity. It appears to control viral load over a period of time, both antibody and cell-mediated immunity, but why? the virus persists, how does it overcome immune control?

We know it works to some extent because superinfection occurs less frequently than initial infection, so the ability to become superinfected in high-risk populations doesn't get as many infections as you do. I think there must be some role for immunity and one of the problems, however, is that there is a leak of neutralizing antibodies. The virus mutates in the course of infection over many years and you produce antibodies against the initial infecting virus at the time those antibodies. arises, the virus has changed to another envelope that does not react with those antibodies, so antibodies are produced for that orange envelope and then the virus changes, it changes during the infection, that is why the antibodies do not control the infection, however, many trials of vaccines have done it.

What has been done is a very famous one called RV 144, which consisted of a primary reinforcement strategy. They had gag Pol and envelope proteins in a canarypox vector and another vector carrying the gp120 protein. This was done with 16,000 adult volunteers in Thailand, which is a high-risk area for HIV infection. There were six first injections and six booster injections, but what a logistical nightmare they have to keep track of all these people and, unfortunately, Immunization reduced the rate of HIV infection by 31% compared to placebo in one out of three analyses. here the numbers in the vaccine group 51 people got AIDS in the control group 74 the difference of 23 people out of 16,000 so this is the only one that has shown any effect and this is really marginal compared to all the other trials and others that are ongoing at this time. everyone had failed has failed, it just doesn't work and I'm not sure we're ever going to get it to work, part of the reason is the amazing diversity, so this is the envelope and influenza H, one diversity per phylogenetic tree. the diversity of 1996 on the influence of hemagglutinin h3 all of 1996 this little one here is sitting there these are two scales the top one so we have expanded this here as well so you can see it 96 different h3 sequences these are rows in a year here a single individual in a single person all the diversity is more than the diversity of the flu in a single year and then on the right we have all the diversity of HIV in the Democratic Republic of the Congo in a year of 993 people.

I mean, that's the problem, look at this diversity and then this is based on 96 H h3 sequences, nine sequences from a single individual, 193 sequences from the Democratic Republic of the Congo and that's the problem. diverse and it's unlikely that any Once we get over that aspect that seems encouraging when addressed is that of broadly neutralizing antibodies, so here is again our representative course of acute infection, then we have that long chronic period where the virus replicates at certain levels. for many years and during that time the virus is escaping from neutralism to neutralizing antibodies as I showed you before, but during this time these antibodies drive the selection of the antibody escape mutants, of course, but the somatic mutations in the germ lines of antibodies generate new antibodies with a greater neutralization breath. and in some individuals and on rare occasions they give rise to broadly neutralizing antibodies and we have been able to clone single cell B cells from these patients and clone the antibodies and study them, so now we have a collection of patients with broadly neutralizing antibodies.

NAB B antibodies that will inhibit more than 90% of viruses in a panel of divergent HIV strains and these broadly neutralizing antibodies target three distinct regions of the envelope. Here is a structure of the gp120 envelope in gray and then these colored molecules are antibodies. first these blue ones are directed against these v1 v2 these are highly variable loops at the top of the trimer the yellow abs rays are directed against the cd4 binding site and the red molecules these are antibodies directed at what is called the proximal region of the trimer membrane proximal region of the trimer membrane, so three different binding sites have been inserted for these and, as I think I mentioned before, the coding sequences for these broadly neutralizing antibodies have been inserted into virus vectors associated with the DNA virus, so here is an unattached ad virus that has been designed to be GI heavy. and light chains that have been given to mice, these mice will produce these antibodies throughout their lives, the viruses remain expressed in them, they produce grams of antibodies per milliliter, and when challenged repeatedly, these are humanized mice that have been reconstituted with a human immune system and can be infected with HIV, otherwise mice or be resistant to HIV, it is necessary to give them a human immune system.

These mice are challenged every week for 21 weeks with HIV and these are copies of HIV per thousand and plasma and these are challenged every week and the mice that receive the vector all become infected and the mice that receive the vector that carries this antibody broadly neutralizing, they are all protected and here is a summary that the mice that receive the vector become infected less and less, they are all infected after 18 challenges on the vector, the antibody expresses my dinner and this is not phase one, now a single AB beam is unlikely to be effective because the virus can mutate to escape a single AB beam, however if you put a couple in it might help since then so I'm sure those tests will come into play and eventually , a few words about how to deal with persistence and latency, as I have said, eradicating ancient traces is challenging because of this long-lived reservoir, people have tried to eliminate the reservoir by giving many drugs, including broadly neutralizing antibodies, they have failed.

Expression of the pro viral gene in memory cd4 cells can be silenced by epigenetic suppression or depletion of essential host transcriptional regulators and by using this we attempt to control these late reservoirs and one treatment strategy is called shock. and kill, you induce the expression of the Pro virus by activating these transcriptional regulators that would otherwise keep the Pro virus silent and then the virus begins to replicate. You treat them with antiviral medications to kill and inactivate the virus and you can administer neutralizing antibodies and these are. in clinical trials, but some of the first treatments treat patients with IL-2, which would induce T cell proliferation and replication, or epigenetic drugs that reduce histone silencing to activate transcription, They haven't worked, so yeah.

We haven't impacted the size of the latent reservoir, the other strategy is called blocking and blocking, you try to irreversibly inhibit transcription, but that hasn't shown any promise either. More recently, people have tried gene editing with methamphetamine to try to eliminate the provirus. It's essentially, but it's yet to be determined if you can do that for all cells, so we're left with the reality that you can certainly prevent infection, but many people choose not to, once they're infected, we can give them a therapy. triple and you You can live your whole life on drugs, but we still can't reverse it.

However, people are working hard to try to do this. This is called a cure, which would mean eliminating the proviruses and all openly infected cells and if many people feel. that can be done, we will see that it will require a lot more work, but I think this lecture gives you an idea of ​​the magnitude of this problem and just to finish an amazing story that began in 1921, patient zero acquired SIV from a chimpanzee has since become HIV-positive and today we have had 75 million infections in thirty-two million deaths. It's just a remarkable story next time we talk about unusual infectious agents that don't fit into our typical view of what viruses really are. are